US20130337442A1 - Genetic loci associated with soybean cyst nematode resistance and methods of use - Google Patents

Genetic loci associated with soybean cyst nematode resistance and methods of use Download PDF

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US20130337442A1
US20130337442A1 US13/780,390 US201313780390A US2013337442A1 US 20130337442 A1 US20130337442 A1 US 20130337442A1 US 201313780390 A US201313780390 A US 201313780390A US 2013337442 A1 US2013337442 A1 US 2013337442A1
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marker
linkage group
seq
soybean
barc
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Joshua M. Shendelman
John B. Woodward
Meizhu Yang
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Pioneer Hi Bred International Inc
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Pioneer Hi Bred International Inc
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Priority to US13/780,390 priority Critical patent/US20130337442A1/en
Priority to PCT/US2013/045552 priority patent/WO2013188612A1/en
Priority to CA2876869A priority patent/CA2876869A1/en
Priority to BR112014031410A priority patent/BR112014031410A2/en
Priority to ARP130102119 priority patent/AR091460A1/en
Publication of US20130337442A1 publication Critical patent/US20130337442A1/en
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
    • C12N15/8285—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for nematode resistance
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/13—Plant traits
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • This invention relates to methods of identifying and/or selecting soybean plants or germplasm that display improved resistance to Soybean Cyst Nematode.
  • sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 429573seqlist.txt, a creation date of Feb. 18, 2013 and a size of 39 KB.
  • ASCII American Standard Code for Information Interchange
  • sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.
  • Soybeans Glycine max L. Merr.
  • Soybean oil is one of the most widely used edible oils, and soybeans are used worldwide both in animal feed and in human food production. Additionally, soybean utilization is expanding to industrial, manufacturing, and pharmaceutical applications.
  • Soybean Cyst Nematode is a parasitic pest which has threatened soybean production in the U.S. for more than fifty years. Soybean cyst nematode resistance is an economically important trait as infection can substantially reduce yields. Molecular characterization of soybean cyst nematode resistance would have important implications for soybean cultivar improvement.
  • the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.
  • soybean markers have been used to selectively improve soybean crops through the use of marker assisted selection. Any detectable polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest.
  • a number of soybean markers have been mapped and linkage groups created, as described in Cregan, P. B., et al., “An Integrated Genetic Linkage Map of the Soybean Genome” (1999) Crop Science 39:1464-90, and more recently in Choi, et al., “A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis” (2007) Genetics 176:685-96. Many soybean markers are publicly available at the USDA affiliated soybase website (www.soybase.org).
  • QTL quantitative trait loci
  • the genetic distance is also typically related to the physical distance between the marker and the QTL; however, certain biological phenomenon (including recombinational “hot spots”) can affect the relationship between physical distance and genetic distance.
  • certain biological phenomenon including recombinational “hot spots”
  • the usefulness of a molecular marker is determined by the genetic and physical distance between the marker and the selectable trait of interest.
  • multiple closely linked markers such as Single Nucleotide Polymorphism (SNP) markers
  • SNP Single Nucleotide Polymorphism
  • a haplotype for that region of the plant genome can be determined.
  • a marker profile for that trait can be determined.
  • haplotype and marker profile information can be useful in identifying and selecting plants with certain desired traits.
  • kits comprising one pair of oligonucleotide primers may have two or more pairs of oligonucleotide primers.
  • the term “comprising” is intended to include examples encompassed by the terms “consisting essentially of” and “consisting of:” Similarly, the term “consisting essentially of” is intended to include examples encompassed by the term “consisting of:”
  • Agronomics refers to the traits (and underlying genetic elements) of a given plant variety that contribute to yield over the course of a growing season.
  • Individual agronomic traits include emergence vigor, vegetative vigor, stress tolerance, disease resistance or tolerance, insect resistance or tolerance, herbicide resistance, branching, flowering, seed set, seed size, seed density, standability, threshability, and the like.
  • Allele means any of one or more alternative forms of a genetic sequence. In a diploid cell or organism, the two alleles of a given sequence typically occupy corresponding loci on a pair of homologous chromosomes. With regard to a SNP marker, allele refers to the specific nucleotide base present at that SNP locus in that individual plant.
  • amplifying in the context of nucleic acid amplification is any process whereby additional copies of a selected nucleic acid (or a transcribed form thereof) are produced.
  • An “amplicon” is an amplified nucleic acid, e.g., a nucleic acid that is produced by amplifying a template nucleic acid by any available amplification.
  • An “ancestral line” is a parent line used as a source of genes, e.g., for the development of elite lines.
  • An “ancestral population” is a group of ancestors that have contributed the bulk of the genetic variation that was used to develop elite lines.
  • Backcrossing is a process in which a breeder crosses a progeny variety back to one of the parental genotypes one or more times.
  • chromosome segment designates a contiguous linear span of genomic DNA that resides in planta on a single chromosome.
  • Chrosome interval refers to a chromosome segment defined by specific flanking marker loci.
  • Crop and “variety” are used synonymously and mean a group of plants within a species (e.g., Glycine max ) that share certain genetic traits that separate them from other possible varieties within that species. Soybean cultivars are inbred lines produced after several generations of self-pollinations. Individuals within a soybean cultivar are homogeneous, nearly genetically identical, with most loci in the homozygous state.
  • An “elite line” is an agronomically superior line that has resulted from many cycles of breeding and selection for superior agronomic performance. Numerous elite lines are available and known to those of skill in the art of soybean breeding.
  • An “elite population” is an assortment of elite individuals or lines that can be used to represent the state of the art in terms of agronomically superior genotypes of a given crop species, such as soybean.
  • an “exotic soybean strain” or an “exotic soybean germplasm” is a strain or germplasm derived from a soybean not belonging to an available elite soybean line or strain of germplasm.
  • an exotic germplasm is not closely related by descent to the elite germplasm with which it is crossed. Most commonly, the exotic germplasm is not derived from any known elite line of soybean, but rather is selected to introduce novel genetic elements (typically novel alleles) into a breeding program.
  • a “genetic map” is a description of genetic association or linkage relationships among loci on one or more chromosomes (or linkage groups) within a given species, generally depicted in a diagrammatic or tabular form.
  • Gene is a description of the allelic state at one or more loci.
  • Germplasm means the genetic material that comprises the physical foundation of the hereditary qualities of an organism. As used herein, germplasm includes seeds and living tissue from which new plants may be grown; or, another plant part, such as leaf, stem, pollen, or cells, that may be cultured into a whole plant. Germplasm resources provide sources of genetic traits used by plant breeders to improve commercial cultivars.
  • An individual is “homozygous” if the individual has only one type of allele at a given locus (e.g., a diploid individual has a copy of the same allele at a locus for each of two homologous chromosomes).
  • An individual is “heterozygous” if more than one allele type is present at a given locus (e.g., a diploid individual with one copy each of two different alleles).
  • the term “homogeneity” indicates that members of a group have the same genotype at one or more specific loci. In contrast, the term “heterogeneity” is used to indicate that individuals within the group differ in genotype at one or more specific loci.
  • “Introgression” means the entry or introduction of a gene, QTL, haplotype, marker profile, trait, or trait locus from the genome of one plant into the genome of another plant.
  • label or “detectable label” refer to a molecule capable of detection.
  • a detectable label can also include a combination of a reporter and a quencher, such as are employed in FRET probes or TaqManTM probes.
  • reporter refers to a substance or a portion thereof which is capable of exhibiting a detectable signal, which signal can be suppressed by a quencher.
  • the detectable signal of the reporter is, e.g., fluorescence in the detectable range.
  • quencher refers to a substance or portion thereof which is capable of suppressing, reducing, inhibiting, etc., the detectable signal produced by the reporter.
  • quenching and “fluorescence energy transfer” refer to the process whereby, when a reporter and a quencher are in close proximity, and the reporter is excited by an energy source, a substantial portion of the energy of the excited state non-radiatively transfers to the quencher where it either dissipates non-radiatively or is emitted at a different emission wavelength than that of the reporter.
  • a “line” or “strain” is a group of individuals of identical parentage that are generally inbred to some degree and that are generally homozygous and homogeneous at most loci (isogenic or near isogenic).
  • a “subline” refers to an inbred subset of descendants that are genetically distinct from other similarly inbred subsets descended from the same progenitor. Traditionally, a subline has been derived by inbreeding the seed from an individual soybean plant selected at the F3 to F5 generation until the residual segregating loci are “fixed” or homozygous across most or all loci.
  • soybean varieties are typically produced by aggregating (“bulking”) the self-pollinated progeny of a single F3 to F5 plant from a controlled cross between 2 genetically different parents. While the variety typically appears uniform, the self-pollinating variety derived from the selected plant eventually (e.g., F8) becomes a mixture of homozygous plants that can vary in genotype at any locus that was heterozygous in the originally selected F3 to F5 plant.
  • Marker-based sublines that differ from each other based on qualitative polymorphism at the DNA level at one or more specific marker loci are derived by genotyping a sample of seed derived from individual self-pollinated progeny derived from a selected F3-F5 plant.
  • the seed sample can be genotyped directly as seed, or as plant tissue grown from such a seed sample.
  • seed sharing a common genotype at the specified locus (or loci) are bulked providing a subline that is genetically homogenous at identified loci important for a trait of interest (e.g., yield, tolerance, etc.).
  • Linkage refers to the tendency for alleles to segregate together more often than expected by chance if their transmission was independent. Typically, linkage refers to alleles on the same chromosome. Genetic recombination occurs with an assumed random frequency over the entire genome. Genetic maps are constructed by measuring the frequency of recombination between pairs of traits or markers, the lower the frequency of recombination, and the greater the degree of linkage.
  • Linkage disequilibrium is a non-random association of alleles at two or more loci and can occur between unlinked markers. It is based on allele frequencies within a population and is influenced by but not dependent on linkage.
  • Linkage group refers to traits or markers that generally co-segregate.
  • a linkage group generally corresponds to a chromosomal region containing genetic material that encodes the traits or markers.
  • “Locus” is a defined segment of DNA.
  • a “map location” or “map position” is an assigned location on a genetic map relative to linked genetic markers where a specified marker can be found within a given species. Map positions are generally provided in centimorgans (cM)), unless otherwise indicated, genetic positions provided are based on the Glycine max consensus map v 4.0 as provided by Hyten et al. (2010) Crop Sci 50:960-968.
  • a “physical position” or “physical location” or “physical map location” is the position, typically in nucleotides bases, of a particular nucleotide, such as a SNP nucleotide, on a chromosome. Unless otherwise indicated, the physical position within the soybean genome provided is based on the Glyma 1.0 genome sequence described in Schmutz et al. (2010) Nature 463:178-183, available from the Phytozome website (phytozome-dot-net/soybean).
  • Mapping is the process of defining the association and relationships of loci through the use of genetic markers, populations segregating for the markers, and standard genetic principles of recombination frequency.
  • Marker or “molecular marker” or “marker locus” is a term used to denote a nucleic acid or amino acid sequence that is sufficiently unique to characterize a specific locus on the genome. Any detectable polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest.
  • Marker assisted selection refers to the process of selecting a desired trait or traits in a plant or plants by detecting one or more nucleic acids from the plant, where the nucleic acid is linked to the desired trait, and then selecting the plant or germplasm possessing those one or more nucleic acids.
  • Haplotype refers to a combination of particular alleles present within a particular plant's genome at two or more linked marker loci, for instance at two or more loci on a particular linkage group. For instance, in one example, two specific marker loci on LG-O are used to define a haplotype for a particular plant. In still further examples, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more linked marker loci are used to define a haplotype for a particular plant.
  • a “marker profile” means a combination of particular alleles present within a particular plant's genome at two or more marker loci which are not linked, for instance two or more loci on two or more different linkage groups or two or more chromosomes.
  • a particular combination of marker loci or a particular combination of haplotypes define the marker profile of a particular plant.
  • plant includes reference to an immature or mature whole plant, including a plant from which seed or grain or anthers have been removed. Seed or embryo that will produce the plant is also considered to be the plant.
  • Plant parts means any portion or piece of a plant, including leaves, stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen, ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks, tissues, tissue cultures, cells and the like.
  • Polymorphism means a change or difference between two related nucleic acids.
  • a “nucleotide polymorphism” refers to a nucleotide that is different in one sequence when compared to a related sequence when the two nucleic acids are aligned for maximal correspondence.
  • Polynucleotide “polynucleotide sequence,” “nucleic acid,” “nucleic acid molecule,” “nucleic acid sequence,” “nucleic acid fragment,” and “oligonucleotide” are used interchangeably herein to indicate a polymer of nucleotides that is single- or multi-stranded, that optionally contains synthetic, non-natural, or altered RNA or DNA nucleotide bases.
  • a DNA polynucleotide may be comprised of one or more strands of cDNA, genomic DNA, synthetic DNA, or mixtures thereof.
  • Primer refers to an oligonucleotide which is capable of acting as a point of initiation of nucleic acid synthesis or replication along a complementary strand when placed under conditions in which synthesis of a complementary strand is catalyzed by a polymerase.
  • primers are about 10 to 30 nucleotides in length, but longer or shorter sequences can be employed.
  • Primers may be provided in double-stranded form, though the single-stranded form is more typically used.
  • a primer can further contain a detectable label, for example a 5′ end label.
  • Probe refers to an oligonucleotide that is complementary (though not necessarily fully complementary) to a polynucleotide of interest and forms a duplexed structure by hybridization with at least one strand of the polynucleotide of interest.
  • probes are oligonucleotides from 10 to 50 nucleotides in length, but longer or shorter sequences can be employed.
  • a probe can further contain a detectable label.
  • Quantitative trait loci or “QTL” refer to the genetic elements controlling a quantitative trait.
  • Recombination frequency is the frequency of a crossing over event (recombination) between two genetic loci. Recombination frequency can be observed by following the segregation of markers and/or traits during meiosis.
  • Resistance and “improved resistance” are used interchangeably herein and refer to any type of increase in resistance or resistance to, or any type of decrease in susceptibility.
  • a “resistant plant” or “resistant plant variety” need not possess absolute or complete resistance. Instead, a “resistant plant,” “resistant plant variety,” or a plant or plant variety with “improved resistance” will have a level of resistance or tolerance which is higher than that of a comparable susceptible plant or variety.
  • Self-crossing or “self-pollination” or “selfing” is a process through which a breeder crosses a plant with itself; for example, a second generation hybrid F2 with itself to yield progeny designated F2:3.
  • SNP single nucleotide polymorphism
  • yield refers to the productivity per unit area of a particular plant product of commercial value. For example, yield of soybean is commonly measured in bushels of seed per acre or metric tons of seed per hectare per season. Yield is affected by both genetic and environmental factors.
  • an “isolated” or “purified” polynucleotide or polypeptide, or biologically active portion thereof is substantially or essentially free from components that normally accompany or interact with the polynucleotide or polypeptide as found in its naturally occurring environment.
  • an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived.
  • the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived.
  • a polypeptide that is substantially free of cellular material includes preparations of polypeptides having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein, culture media or other chemical components.
  • Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter “Sambrook”).
  • Methods are provided for identifying and/or selecting a soybean plant or soybean germplasm that displays improved resistance to soybean cyst nematode.
  • the method comprises detecting in the soybean plant or germplasm, or a part thereof, at least one marker locus associated with resistance to soybean cyst nematode.
  • marker loci associated with soybean cyst nematode resistance that have been identified and mapped to genomic loci on linkage group G. These findings have important implications for soybean production, as identifying markers that can be used for selection of soybean cyst nematode resistance will greatly expedite the development of soybean cyst nematode resistance into elite cultivars.
  • Marker loci, haplotypes and marker profiles associated with resistance to soybean cyst nematode are provided. Further provided are genomic loci that are associated with soybean resistance to soybean cyst nematode.
  • soybean plants or germplasm are identified that have at least one favorable allele, marker locus, haplotype or marker profile that positively correlates with resistance or improved resistance to soybean cyst nematode.
  • it is useful for exclusionary purposes during breeding to identify alleles, marker loci, haplotypes, or marker profiles that negatively correlate with resistance for example, to eliminate such plants or germplasm from subsequent rounds of breeding.
  • marker loci useful for identifying a first soybean plant or first soybean germplasm that displays improved resistance to soybean cyst nematode comprises a marker locus comprising one or more of (a) the at least one marker locus comprises 508271-1-Q2 or a marker closely linked thereto on linkage group G; (b) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (f) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) the at least one marker locus comprises S06820-1-Q
  • Non-limiting examples of marker loci located within, linked to, or closely linked to these genomic loci are provided in Table 1A.
  • multiple marker loci that collectively make up the soybean cyst nematode resistance haplotype of interest are investigated.
  • 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the various marker loci provided herein can comprise a soybean cyst nematode resistance haplotype.
  • the haplotype comprises: two or more marker locus comprising (a) at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G; (b) at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (0 at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group 0; (h) at least one marker locus comprises S06821-1-Q2
  • the method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or in the genome of the first soybean germplasm at least one haplotype that is associated with the resistance, wherein the at least one haplotype comprises at least two of the various marker loci provided herein. For example, one is more likely to get PI88788 Rhg1 if A, T is selected at S08271-1 and P7659-2 respectively. S07158-1 and S07159-1 are used in combination with S08051-1 to distinguish PI437654 and Peking haplotype.
  • two or more marker loci or haplotypes can collectively make up a marker profile.
  • the marker profile can comprise any two or more marker loci comprising: (a) at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G; (b) at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (f) at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on on link
  • the marker profile can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more marker loci or haplotypes associated with resistance to soybean cyst nematode provided herein.
  • a method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or in the genome of the first soybean germplasm at least one marker profile that is associated with the resistance, wherein the at least one marker profile comprises at least two of the various marker loci provided herein.
  • soybean markers In addition to the markers discussed herein, information regarding useful soybean markers can be found, for example, on the USDA's Soybase website, available at www.soybase.org.
  • identification of favorable marker alleles may be germplasm-specific. The determination of which marker alleles correlate with resistance (or susceptibility) is determined for the particular germplasm under study.
  • methods for identifying the favorable alleles are routine and well known in the art, and furthermore, that the identification and use of such favorable alleles is well within the scope of the invention.
  • the method of identifying comprises detecting at least one marker locus associated with resistance to soybean cyst nematode.
  • the term “associated with” in connection with a relationship between a marker locus and a phenotype refers to a statistically significant dependence of marker frequency with respect to a quantitative scale or qualitative gradation of the phenotype.
  • an allele of a marker is associated with a trait of interest when the allele of the marker locus and the trait phenotypes are found together in the progeny of an organism more often than if the marker genotypes and trait phenotypes segregated separately.
  • Any combination of the marker loci provided herein can be used in the methods to identify a soybean plant or soybean germplasm that displays improved resistance to soybean cyst nematode. Any one marker locus or any combination of the markers set forth in Table 1, or any closely linked marker can be used to aid in identifying and selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.
  • a method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or first soybean germplasm at least one marker locus that is associated with resistance.
  • the at least one marker locus comprises (a) at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G; (b) at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (f) at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G; (h) at least one marker locus comprises S06821-1-Q2 or a marker
  • two or more marker loci are detected in the method.
  • the germplasm is a soybean variety.
  • the method further comprises crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm.
  • the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
  • the first soybean plant or first soybean germplasm comprises a soybean variety. Any soybean line known to the art or disclosed herein may be used. Non-limiting examples of soybean varieties and their associated soybean cyst nematode resistance alleles encompassed by the methods are provided herein.
  • the detection method comprises amplifying at least one marker locus and detecting the resulting amplified marker amplicon.
  • amplifying comprises (a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm such that the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and (b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon.
  • the primer or primer pair can comprise a variant or fragment of one or more of the genomic loci provided herein.
  • the method involves amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 1-171 or variants or fragments thereof.
  • the primer or primer pair can comprise a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof.
  • the primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOS: SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168
  • the primer pair comprises SEQ ID NOS: 81 and 82; SEQ ID NOS: 87 and 88; SEQ ID NOS: 89 and 90; SEQ ID NOS: 91 and 92; SEQ ID NOS: 93 and 94; SEQ ID NOS:95 and 96; SEQ ID NOS: 97 and 98; SEQ ID NOS: 99 and 100; SEQ ID NOS: 101 and 102, SEQ ID NOS: 121 and 122; SEQ ID NO: 121 and 123; SEQ ID NO:124 and 125; SEQ ID NO: 126 and 127; SEQ ID NO: 128 and 129; SEQ ID NO: 130 and 131, SEQ ID NOS: 136 and 137; SEQ ID NOS: 140 and 141; SEQ ID NOS: 144 and 145; SEQ ID NOS: 148 and 149; SEQ ID NOS: 152 and 153; SEQ ID NOS: 156 and 157; SEQ ID NOS:
  • the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified.
  • the labeled nucleic acid probe can comprise a sequence comprising a variant or fragment of one or more of the genomic loci provided herein.
  • the labeled nucleic acid probe can comprise a sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof.
  • the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOS: 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, 135 or variants or fragments thereof.
  • Non-limiting examples of primers, probes, genomic loci and amplicons that can be used in the methods and compositions provided herein are summarized in Tables 3, 4, 5 and 6, respectively.
  • Genomic Loci Comprising the Various Marker Loci Provided Herein.
  • SEQ ID Marker NO Name (Res/Sus) Reference Sequence [Res/Sus] SEQ ID NO S08271-1- A/T CTGAAATGCAACGCAAATTCGAGTTTAGTAGAAACTTATCATCCAAAAT 103, 104 Q2 TAAAATTGAAAACTTTAATACAAATGCACATTTTGGAGCCATTCATGTS respectively (P10355B- ATCTCTTGGTCTGAGTCTTATCATTCTGTGGATTGAATTCATGGTTTCTC 1) TTATVACATTGTTGCCAAGTAATACTACTATATAAATTCAGATTTGGGTT TC[A/T]GATAACCGTGGTCGTTARTACTATATATATAATACCTTGCAGG AGCTTGCGCGATACTTGAAACAGGAGCAGGGACAGTGGAAAATAAAG GAGCCATAGCRCCATCTGCTTGCTTATGTAATGTAACCCAATCTGTCTAT ATTTY
  • the method of detecting comprises DNA sequencing of at least one of the marker loci provided herein.
  • sequencing refers to sequencing methods for determining the order of nucleotides in a molecule of DNA. Any DNA sequencing method known in the art can be used in the methods provided herein. Non-limiting examples of DNA sequencing methods useful in the methods provided herein include Next Generation Sequencing (NGS) technologies, for example, as described in Egan, A. N, et al. (2012) American Journal of Botany 99(2):175-185; genotyping by sequencing (GBS) methods, for example, as described in Elshire, R. J., et al.
  • NGS Next Generation Sequencing
  • fragment is intended a portion of the polynucleotide.
  • a fragment or portion can comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, 100, 150, 200, 250, 300, 350, 400 contiguous nucleotides of SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101
  • sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; or any equivalent program thereof.
  • equivalent program is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • Traits or markers are considered to be linked if they co-segregate.
  • a 1/100 probability of recombination per generation is defined as a map distance of 1.0 centiMorgan (1.0 cM).
  • Genetic elements or genes located on a single chromosome segment are physically linked. Two loci can be located in close proximity such that recombination between homologous chromosome pairs does not occur between the two loci during meiosis with high frequency, e.g., such that linked loci co-segregate at least about 90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more of the time.
  • Genetic elements located within a chromosome segment are also genetically linked, typically within a genetic recombination distance of less than or equal to 50 centimorgans (cM), e.g., about 49, 40, 30, 20, 10, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25 cM or less. That is, two genetic elements within a single chromosome segment undergo recombination during meiosis with each other at a frequency of less than or equal to about 50%, e.g., about 49%, 40%, 30%, 20%, 10%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less.
  • cM centimorgans
  • Closely linked markers display a cross over frequency with a given marker of about 10% or less (the given marker is within about 10 cM of a closely linked marker).
  • a closely linked marker is within 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM or 1 cM of any given marker disclosed herein.
  • a marker associated with one of the markers disclosed herein can be within 75 Kb, 60 Kb, 50 Kb, 40 Kb, 30 Kb, 20K, 10 Kb, 5 Kb or less of the disclosed marker. Put another way, closely linked loci co-segregate at least about 90% of the time.
  • Genetic linkage as evaluated by recombination frequency is impacted by the chromatin structure of the region comprising the loci.
  • the region is assumed to have a euchromatin structure during initial evaluations.
  • some regions such are regions closer to centrosomes, have a heterochromatin structure.
  • the predicted physical distance between genetic map positions is based on the assumption that the region is Vietnamese, however if the region comprises heterochromatin the markers may be physically closer together.
  • closely linked markers can be separated, for example, by about 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb; 1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100 Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 2 Kb, about 1 Kb, about 500 nucleotides, about 250 nucleotides, or less.
  • Mb megabase
  • Kb 500 kilobases
  • “coupling” phase linkage indicates the state where the “favorable” allele at the resistance locus is physically associated on the same chromosome strand as the “favorable” allele of the respective linked marker locus.
  • both favorable alleles are inherited together by progeny that inherit that chromosome strand.
  • the “favorable” allele at the locus of interest e.g., a QTL for resistance
  • the two “favorable” alleles are not inherited together (i.e., the two loci are “out of phase” with each other).
  • Markers are used to define a specific locus on the soybean genome. Each marker is therefore an indicator of a specific segment of DNA, having a unique nucleotide sequence. Map positions provide a measure of the relative positions of particular markers with respect to one another. When a trait is stated to be linked to a given marker it will be understood that the actual DNA segment whose sequence affects the trait generally co-segregates with the marker. More precise and definite localization of a trait can be obtained if markers are identified on both sides of the trait.
  • Favorable genotypes associated with at least trait of interest may be identified by one or more methodologies.
  • one or more markers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs, SNPs, indels, padlock probes, molecular inversion probes, microarrays, sequencing, and the like.
  • a target nucleic acid is amplified prior to hybridization with a probe. In other cases, the target nucleic acid is not amplified prior to hybridization, such as methods using molecular inversion probes (see, for example Hardenbol et al. (2003) Nat Biotech 21:673-678).
  • the genotype related to a specific trait is monitored, while in other examples, a genome-wide evaluation including but not limited to one or more of marker panels, library screens, association studies, microarrays, gene chips, expression studies, or sequencing such as whole-genome resequencing and genotyping-by-sequencing (GBS) may be used.
  • a genome-wide evaluation including but not limited to one or more of marker panels, library screens, association studies, microarrays, gene chips, expression studies, or sequencing such as whole-genome resequencing and genotyping-by-sequencing (GBS) may be used.
  • GGS genotyping-by-sequencing
  • no target-specific probe is needed, for example by using sequencing technologies, including but not limited to next-generation sequencing methods (see, for example, Metzker (2010) Nat Rev Genet. 11:31-46; and, Egan et al.
  • Each of these may be coupled with one or more enrichment strategies for organellar or nuclear genomes in order to reduce the complexity of the genome under investigation via PCR, hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoS ONE 6:e19379), and expression methods.
  • no reference genome sequence is needed in order to complete the analysis.
  • MAS marker assisted selection
  • soybean plants or germplasm can be selected for markers or marker alleles that positively correlate with soybean cyst nematode resistance, without actually raising soybean and measuring for resistance (or, contrawise, soybean plants can be selected against if they possess markers that negatively correlate with resistance).
  • MAS is a powerful tool to select for desired phenotypes and for introgressing desired traits into cultivars of soybean (e.g., introgressing desired traits into elite lines).
  • MAS is easily adapted to high throughput molecular analysis methods that can quickly screen large numbers of plant or germplasm genetic material for the markers of interest and is much more cost effective than raising and observing plants for visible traits.
  • the molecular markers or marker loci are detected using a suitable amplification-based detection method.
  • nucleic acid primers are typically hybridized to the conserved regions flanking the polymorphic marker region.
  • nucleic acid probes that bind to the amplified region are also employed.
  • synthetic methods for making oligonucleotides, including primers and probes are well known in the art.
  • oligonucleotides can be synthesized chemically according to the solid phase phosphoramidite triester method described by Beaucage and Caruthers (1981) Tetrahedron Letts 22:1859-1862, e.g., using a commercially available automated synthesizer, e.g., as described in Needham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168.
  • Oligonucleotides, including modified oligonucleotides can also be ordered from a variety of commercial sources known to persons of skill in the art.
  • primers and probes to be used can be designed using any suitable method. It is not intended that the invention be limited to any particular primer, primer pair or probe.
  • primers can be designed using any suitable software program, such as LASERGENE® or Primer3.
  • primers be limited to generating an amplicon of any particular size.
  • the primers used to amplify the marker loci and alleles herein are not limited to amplifying the entire region of the relevant locus.
  • marker amplification produces an amplicon at least 20 nucleotides in length, or alternatively, at least 50 nucleotides in length, or alternatively, at least 100 nucleotides in length, or alternatively, at least 200 nucleotides in length.
  • Non-limiting examples of polynucleotide primers useful for detecting the marker loci provided herein are provided in Table 3 and include, for example, SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114
  • PCR, RT-PCR, and LCR are in particularly broad use as amplification and amplification-detection methods for amplifying nucleic acids of interest (e.g., those comprising marker loci), facilitating detection of the markers.
  • nucleic acids of interest e.g., those comprising marker loci
  • Details regarding the use of these and other amplification methods are well known in the art and can be found in any of a variety of standard texts. Details for these techniques can also be found in numerous journal and patent references, such as Mullis, et al. (1987) U.S. Pat. No. 4,683,202; Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47; Kwoh, et al. (1989) Proc. Natl. Acad. Sci.
  • nucleic acid amplification techniques can be applied to amplify and/or detect nucleic acids of interest, such as nucleic acids comprising marker loci.
  • Amplification primers for amplifying useful marker loci and suitable probes to detect useful marker loci or to genotype SNP alleles are provided.
  • exemplary primers and probes are provided in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144,
  • Non-limiting examples of amplicon sequences comprising the marker loci provided herein are provided in Table 6.
  • primers to either side of the given primers can be used in place of the given primers, so long as the primers can amplify a region that includes the allele to be detected, as can primers and probes directed to other SNP marker loci.
  • the precise probe to be used for detection can vary, e.g., any probe that can identify the region of a marker amplicon to be detected can be substituted for those examples provided herein.
  • the configuration of the amplification primers and detection probes can, of course, vary. Thus, the compositions and methods are not limited to the primers and probes specifically recited herein.
  • probes will possess a detectable label. Any suitable label can be used with a probe.
  • Detectable labels suitable for use with nucleic acid probes include, for example, any composition detectable by spectroscopic, radioisotopic, photochemical, biochemical, immunochemical, electrical, optical, or chemical means.
  • Useful labels include biotin for staining with labeled streptavidin conjugate, magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetric labels.
  • Other labels include ligands, which bind to antibodies labeled with fluorophores, chemiluminescent agents, and enzymes.
  • a probe can also constitute radiolabelled PCR primers that are used to generate a radiolabelled amplicon.
  • Labeling strategies for labeling nucleic acids and corresponding detection strategies can be found, e.g., in Haugland (1996) Handbook of Fluorescent Probes and Research Chemicals Sixth Edition by Molecular Probes, Inc. (Eugene Oreg.); or Haugland (2001) Handbook of Fluorescent Probes and Research Chemicals Eighth Edition by Molecular Probes, Inc. (Eugene Oreg.).
  • Detectable labels may also include reporter-quencher pairs, such as are employed in Molecular Beacon and TaqManTM probes.
  • the reporter may be a fluorescent organic dye modified with a suitable linking group for attachment to the oligonucleotide, such as to the terminal 3′ carbon or terminal 5′ carbon.
  • the quencher may also be an organic dye, which may or may not be fluorescent, depending on the embodiment. Generally, whether the quencher is fluorescent or simply releases the transferred energy from the reporter by non-radiative decay, the absorption band of the quencher should at least substantially overlap the fluorescent emission band of the reporter to optimize the quenching.
  • Non-fluorescent quenchers or dark quenchers typically function by absorbing energy from excited reporters, but do not release the energy radiatively.
  • reporter-quencher pairs for particular probes may be undertaken in accordance with known techniques. Fluorescent and dark quenchers and their relevant optical properties from which exemplary reporter-quencher pairs may be selected are listed and described, for example, in Berlman, Handbook of Fluorescence Spectra of Aromatic Molecules, 2nd ed., Academic Press, New York, 1971, the content of which is incorporated herein by reference.
  • modifying reporters and quenchers for covalent attachment via common reactive groups that can be added to an oligonucleotide in the present invention may be found, for example, in Haugland, Handbook of Fluorescent Probes and Research Chemicals , Molecular Probes of Eugene, Oreg., 1992, the content of which is incorporated herein by reference.
  • reporter-quencher pairs are selected from xanthene dyes including fluoresceins and rhodamine dyes. Many suitable forms of these compounds are available commercially with substituents on the phenyl groups, which can be used as the site for bonding or as the bonding functionality for attachment to an oligonucleotide. Another useful group of fluorescent compounds for use as reporters are the naphthylamines, having an amino group in the alpha or beta position.
  • naphthylamino compounds include 1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-touidinyl-6-naphthalene sulfonate.
  • Other dyes include 3-phenyl-7-isocyanatocoumarin; acridines such as 9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide; benzoxadiazoles; stilbenes; pyrenes and the like.
  • the reporters and quenchers are selected from fluorescein and rhodamine dyes.
  • Suitable examples of reporters may be selected from dyes such as SYBR green, 5-carboxyfluorescein (5-FAMTM available from Applied Biosystems of Foster City, Calif.), 6-carboxyfluorescein (6-FAM), tetrachloro-6-carboxyfluorescein (TET), 2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein, hexachloro-6-carboxyfluorescein (HEX), 6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TETTM available from Applied Biosystems), carboxy-X-rhodamine (ROX), 6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOETM available from Applied Biosystems), VICTM dye products available from Molecular Probes, Inc., NEDTM dye products available from Applied Biosystems, and the like.
  • dyes such as SYBR green
  • Suitable examples of quenchers may be selected from 6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoic acid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0TM, BHQ-1TM, BHQ-2TM, and BHQ-3TM, each of which are available from Biosearch Technologies, Inc. of Novato, Calif., QSY-7TM, QSY-9TM, QSY-21TM and QSY-35TM, each of which are available from Molecular Probes, Inc., and the like.
  • DABYL 4-(4-dimethylaminophenylazo) benzoic acid
  • TAMRA tetramethylrhodamine
  • a molecular beacon is an oligonucleotide which, under appropriate hybridization conditions, self-hybridizes to form a stem and loop structure.
  • the MB has a label and a quencher at the termini of the oligonucleotide; thus, under conditions that permit intra-molecular hybridization, the label is typically quenched (or at least altered in its fluorescence) by the quencher.
  • the MB label is unquenched. Details regarding standard methods of making and using MBs are well established in the literature and MBs are available from a number of commercial reagent sources. See also, e.g., Leone, et al., (1995) Molecular beacon probes combined with amplification by NASBA enable homogenous real-time detection of RNA, Nucleic Acids Res.
  • TaqManTM assay Another real-time detection method is the 5′-exonuclease detection method, also called the TaqManTM assay, as set forth in U.S. Pat. Nos. 5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is hereby incorporated by reference in its entirety.
  • a modified probe typically 10-25 nucleic acids in length, is employed during PCR which binds intermediate to or between the two members of the amplification primer pair.
  • the modified probe possesses a reporter and a quencher and is designed to generate a detectable signal to indicate that it has hybridized with the target nucleic acid sequence during PCR.
  • the quencher stops the reporter from emitting a detectable signal.
  • the polymerase extends the primer during amplification, the intrinsic 5′ to 3′ nuclease activity of the polymerase degrades the probe, separating the reporter from the quencher, and enabling the detectable signal to be emitted.
  • the amount of detectable signal generated during the amplification cycle is proportional to the amount of product generated in each cycle.
  • the efficiency of quenching is a strong function of the proximity of the reporter and the quencher, i.e., as the two molecules get closer, the quenching efficiency increases.
  • the reporter and the quencher are preferably attached to the probe within a few nucleotides of one another, usually within 30 nucleotides of one another, more preferably with a separation of from about 6 to 16 nucleotides. Typically, this separation is achieved by attaching one member of a reporter-quencher pair to the 5′ end of the probe and the other member to a nucleotide about 6 to 16 nucleotides away, in some cases at the 3′ end of the probe.
  • Separate detection probes can also be omitted in amplification/detection methods, e.g., by performing a real time amplification reaction that detects product formation by modification of the relevant amplification primer upon incorporation into a product, incorporation of labeled nucleotides into an amplicon, or by monitoring changes in molecular rotation properties of amplicons as compared to unamplified precursors (e.g., by fluorescence polarization).
  • amplification is not a requirement for marker detection—for example, one can directly detect unamplified genomic DNA simply by performing a Southern blot on a sample of genomic DNA.
  • Procedures for performing Southern blotting, amplification e.g., (PCR, LCR, or the like), and many other nucleic acid detection methods are well established and are taught, e.g., in Sambrook, et al., Molecular Cloning—A Laboratory Manual (3d ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); Current Protocols in Molecular Biology , F. M.
  • ASH allele specific hybridization
  • ASH technology is based on the stable annealing of a short, single-stranded, oligonucleotide probe to a completely complementary single-stranded target nucleic acid. Detection is via an isotopic or non-isotopic label attached to the probe.
  • two or more different ASH probes are designed to have identical DNA sequences except at the polymorphic nucleotides. Each probe will have exact homology with one allele sequence so that the range of probes can distinguish all the known alternative allele sequences.
  • Each probe is hybridized to the target DNA. With appropriate probe design and hybridization conditions, a single-base mismatch between the probe and target DNA will prevent hybridization.
  • Real-time amplification assays including MB or TaqManTM based assays, are especially useful for detecting SNP alleles.
  • probes are typically designed to bind to the amplicon region that includes the SNP locus, with one allele-specific probe being designed for each possible SNP allele. For instance, if there are two known SNP alleles for a particular SNP locus, “A” or “C,” then one probe is designed with an “A” at the SNP position, while a separate probe is designed with a “C” at the SNP position. While the probes are typically identical to one another other than at the SNP position, they need not be.
  • the two allele-specific probes could be shifted upstream or downstream relative to one another by one or more bases.
  • the probes are not otherwise identical, they should be designed such that they bind with approximately equal efficiencies, which can be accomplished by designing under a strict set of parameters that restrict the chemical properties of the probes.
  • a different detectable label for instance a different reporter-quencher pair, is typically employed on each different allele-specific probe to permit differential detection of each probe.
  • each allele-specific probe for a certain SNP locus is 11-20 nucleotides in length, dual-labeled with a florescence quencher at the 3′ end and either the 6-FAM (6-carboxyfluorescein) or VIC (4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′ end.
  • a real-time PCR reaction can be performed using primers that amplify the region including the SNP locus, for instance the sequences listed in Table 5, the reaction being performed in the presence of all allele-specific probes for the given SNP locus.
  • detecting signal for each detectable label employed and determining which detectable label(s) demonstrated an increased signal a determination can be made of which allele-specific probe(s) bound to the amplicon and, thus, which SNP allele(s) the amplicon possessed.
  • 6-FAM- and VIC-labeled probes the distinct emission wavelengths of 6-FAM (518 nm) and VIC (554 nm) can be captured.
  • a sample that is homozygous for one allele will have fluorescence from only the respective 6-FAM or VIC fluorophore, while a sample that is heterozygous at the analyzed locus will have both 6-FAM and VIC fluorescence.
  • KASPar® and Illumina® Detection Systems are additional examples of commercially-available marker detection systems.
  • KASPar® is a homogeneous fluorescent genotyping system which utilizes allele specific hybridization and a unique form of allele specific PCR (primer extension) in order to identify genetic markers (e.g. a particular SNP locus associated with soybean cyst nematode resistance).
  • Illumina® detection systems utilize similar technology in a fixed platform format. The fixed platform utilizes a physical plate that can be created with up to 384 markers. The Illumina® system is created with a single set of markers that cannot be changed and utilizes dyes to indicate marker detection.
  • Introgression of soybean cyst nematode resistance into non-resistant or less-resistant soybean germplasm is provided. Any method for introgressing one or more marker loci into soybean plants known to one of skill in the art can be used. Typically, a first soybean germplasm that contains soybean cyst nematode resistance derived from a particular marker locus, haplotype or marker profile and a second soybean germplasm that lacks such resistance derived from the marker locus, haplotype or marker profile are provided. The first soybean germplasm may be crossed with the second soybean germplasm to provide progeny soybean germplasm.
  • progeny germplasm are screened to determine the presence of soybean cyst nematode resistance derived from the marker locus, haplotype or marker profile, and progeny that tests positive for the presence of resistance derived from the marker locus, haplotype or marker profile are selected as being soybean germplasm into which the marker locus, haplotype or marker profile has been introgressed. Methods for performing such screening are well known in the art and any suitable method can be used.
  • MAS One application of MAS is to use the resistance markers, haplotypes or marker profiles to increase the efficiency of an introgression or backcrossing effort aimed at introducing a resistance trait into a desired (typically high yielding) background.
  • marker assisted backcrossing of specific markers from a donor source e.g., to an elite genetic background
  • markers and methods can be utilized to guide marker assisted selection or breeding of soybean varieties with the desired complement (set) of allelic forms of chromosome segments associated with superior agronomic performance (resistance, along with any other available markers for yield, disease tolerance, etc.).
  • Any of the disclosed marker loci, marker alleles, haplotypes, or marker profiles can be introduced into a soybean line via introgression, by traditional breeding (or introduced via transformation, or both) to yield a soybean plant with superior agronomic performance.
  • the number of alleles associated with resistance that can be introduced or be present in a soybean plant ranges from 1 to the number of alleles disclosed herein, each integer of which is incorporated herein as if explicitly recited.
  • any of the marker loci provided herein can be introduced into a soybean line having one or more of the soybean cyst nematode resistance loci rhg1, rhg2, rhg3 or rhg5.
  • any one or more of the marker loci provided herein can be stacked with the rhg1 locus.
  • any one or more of the marker loci provided herein can be stacked with the rhg2 locus.
  • any one or more of the marker loci provided herein can be stacked with the rhg1 and rhg2 loci.
  • This also provides a method of making a progeny soybean plant and these progeny soybean plants, per se.
  • the method comprises crossing a first parent soybean plant with a second soybean plant and growing the female soybean plant under plant growth conditions to yield soybean plant progeny. Methods of crossing and growing soybean plants are well within the ability of those of ordinary skill in the art.
  • Such soybean plant progeny can be assayed for alleles associated with resistance and, thereby, the desired progeny selected.
  • Such progeny plants or seed can be sold commercially for soybean production, used for food, processed to obtain a desired constituent of the soybean, or further utilized in subsequent rounds of breeding.
  • At least one of the first or second soybean plants is a soybean plant in that it comprises at least one of the marker loci or marker profiles, such that the progeny are capable of inheriting the marker locus or marker profile.
  • a method is applied to at least one related soybean plant such as from progenitor or descendant lines in the subject soybean plants pedigree such that inheritance of the desired resistance can be traced.
  • the number of generations separating the soybean plants being subject to the methods provided herein will generally be from 1 to 20, commonly 1 to 5, and typically 1, 2, or 3 generations of separation, and quite often a direct descendant or parent of the soybean plant will be subject to the method (i.e., 1 generation of separation).
  • MAS provides an indication of which genomic regions and which favorable alleles from the original ancestors have been selected for and conserved over time, facilitating efforts to incorporate favorable variation from exotic germplasm sources (parents that are unrelated to the elite gene pool) in the hopes of finding favorable alleles that do not currently exist in the elite gene pool.
  • markers, haplotypes, primers, probes, and marker profiles can be used for MAS in crosses involving elite ⁇ exotic soybean lines by subjecting the segregating progeny to MAS to maintain major yield alleles, along with the resistance marker alleles herein.
  • transgenic approaches can also be used to create transgenic plants with the desired traits.
  • exogenous nucleic acids that encode a desired marker loci, marker profile or haplotype are introduced into target plants or germplasm.
  • a nucleic acid that codes for a resistance trait is cloned, e.g., via positional cloning, and introduced into a target plant or germplasm.
  • plant breeders can recognize resistant soybean plants in the field, and can select the resistant individuals or populations for breeding purposes or for propagation.
  • the plant breeder recognizes “resistant” and “non-resistant” or “susceptible” soybean plants.
  • plant resistance is a phenotypic spectrum consisting of extremes in resistance and susceptibility, as well as a continuum of intermediate resistance phenotypes. Evaluation of these intermediate phenotypes using reproducible assays are of value to scientists who seek to identify genetic loci that impart resistance, to conduct marker assisted selection for resistant populations, and to use introgression techniques to breed a resistance trait into an elite soybean line, for example.
  • improved resistance is intended that the plants show a decrease in the disease symptoms that are the outcome of plant exposure to soybean cyst nematode. That is, the damage caused by soybean cyst nematode is prevented, or alternatively, the disease symptoms caused by soybean cyst nematode is minimized or lessened.
  • improved resistance to soybean cyst nematode can result in reduction of the disease symptoms by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater.
  • the methods provided herein can be utilized to protect plants from soybean cyst nematode.
  • soybean cyst nematode resistance can be determined by visual observations after plant exposure to a particular race of soybean cyst nematode, such as race 1, 2, 3, 5 or 14. Scores range from 1 to 9 and indicate visual observations of resistance as compared to other genotypes in the test. A score of 1 indicates soybean cyst nematode are able to infect the plant and cause yield loss, while a score of 9 indicates soybean cyst nematode resistance. Preliminary scores are reported as double digits, for example, ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.
  • Non-limiting examples of soybean cyst nematode resistance phenotypic screening are described in detail below.
  • E2 Eggs or second stage juveniles (J2) are used to inoculate host plants to increase their population. Soybean cyst nematode infestation requires a minimum 35 days before the cysts reach maturity and can be used to inoculate soybean experiments. Cyst eggs/J2 inoculant is harvested through a series of washings, grindings, and screenings. Screens are used progressing from larger to smaller sizes, ending with a #500 (25 ⁇ m) screen.
  • Soybean plants are grown in cones.
  • Cones are long containers approximately 12 inches long and 1.5 inches in diameter at the top (e.g., Ray Leach Cone-TainersTM).
  • the cone is designed to easily remove the root mass.
  • an inoculum channel is made in the cone containing the experimental line by poking a 4 inch hole with a 10 ml pipette tip.
  • One ml of inoculum is dispensed into the channel.
  • the plants are watered manually for the duration of the test, with watering being moderately light during the first 3-5 days until J2 infects the roots.
  • Plants are scored approximately 28-35 days following inoculation when cyst reproduction on susceptible checks is sufficiently high. Plants are removed from their cones and the soil is removed from the roots by gently dipping the roots into a bucket of water. The plants are screened to identify native resistance to one or more of the five races of soybean cyst nematode inoculated using a combination of three methods (1) visual 9-6-1 score; (2) visual full count; and/or (3) microscope count score depending on the stage of the line when screened. In general, lines earlier in the development cycle (R1-R2) are screened by the visual 9-6-1 method, and lines that have progressed to later development phases (R3-R5) are screened by the visual full count and/or microscope count method(s).
  • One typical phenotyping method is a visual evaluation of the roots. Susceptible checks are first evaluated for the development of cysts on the root system. These counts are recorded and averaged across the experiment to determine the susceptible (SUS) check average. Roots from the test plants are then scored based on a comparison with the average of the susceptible checks as follows:
  • FI female index
  • Cysts counts for soybean cyst nematode assays for checks and experimental line are determined by washing cysts from roots and counting the number of cysts under the microscope.
  • roots from the susceptible check controls are examined for yellow cysts to assess whether to begin the process of evaluating the test.
  • Experimental lines are compared with known standard checks. Once adequate levels of cysts are detected on the check varieties, plants from the test lines are removed from cones one at a time. Soil is removed from roots by gently dipping the roots into a bucket of water. The root tissue is placed on a 850 micron (#20) pore sieve stacked over a 250 micron (#60) pore sieve and sprayed with a jet of water to dislodge cysts from the roots. Collected cysts are rinsed from the #60 sieve into a clean labeled cup using no more than 30 mls of additional water.
  • each sample is counted using a gridded counting dish under a stereo microscope. The number of cysts counted are recorded for each sample. Cyst counts on the test plants are converted to the 1-9 scoring scale based on the female index (FI) described above.
  • soybean cyst nematode checks can be planted and used to monitor cyst development:
  • kit refers to a set of reagents for the purpose of performing the various methods of detecting or identifying herein, more particularly, the identification and/or the detection of a soybean plant or germplasm having improved resistance to soybean cyst nematode.
  • a kit for detecting or selecting at least one soybean plant or soybean germplasm with improved resistance to soybean cyst nematode comprises (a) primers or probes for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein at least one of the primers and probes in the kit are capable of detecting a marker locus comprising one or more of S08271-1-Q2, P7659A-2, S08051-1-Q1, S07158-1-Q1, S07159-1-Q1, S06818-3-Q2, S06820-1-Q3, S06821-1-Q2, S16001-001-Q001 or a marker closely linked thereto on linkage group G; and, (b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
  • a typical kit or system can include a set of marker probes or primers configured to detect at least one favorable allele of one or more marker loci associated with resistance to soybean cyst nematode, for instance a favorable marker locus, haplotype or marker profile.
  • These probes or primers can be configured, for example, to detect the marker loci noted in the tables and examples herein, e.g., using any available allele detection format, such as solid or liquid phase array based detection, microfluidic-based sample detection, etc.
  • the systems and kits can further include packaging materials for packaging the probes, primers, or instructions, controls such as control amplification reactions that include probes, primers or template nucleic acids for amplifications, molecular size markers, or the like.
  • a typical system can also include a detector that is configured to detect one or more signal outputs from the set of marker probes or primers, or amplicon thereof, thereby identifying the presence or absence of the allele.
  • a detector that is configured to detect one or more signal outputs from the set of marker probes or primers, or amplicon thereof, thereby identifying the presence or absence of the allele.
  • signal detection apparatus including photo multiplier tubes, spectrophotometers, CCD arrays, scanning detectors, phototubes and photodiodes, microscope stations, galvo-scans, microfluidic nucleic acid amplification detection appliances and the like.
  • the precise configuration of the detector will depend, in part, on the type of label used to detect the marker allele, as well as the instrumentation that is most conveniently obtained for the user.
  • Detectors that detect fluorescence, phosphorescence, radioactivity, pH, charge, absorbance, luminescence, temperature, magnetism or the like can be used.
  • Typical detector examples include light (e.g., fluorescence) detectors or radioactivity detectors.
  • detection of a light emission (e.g., a fluorescence emission) or other probe label is indicative of the presence or absence of a marker allele.
  • Fluorescent detection is generally used for detection of amplified nucleic acids (however, upstream and/or downstream operations can also be performed on amplicons, which can involve other detection methods).
  • the detector detects one or more label (e.g., light) emission from a probe label, which is indicative of the presence or absence of a marker allele.
  • the detector(s) optionally monitors one or a plurality of signals from an amplification reaction. For example, the detector can monitor optical signals which correspond to “real time” amplification assay results.
  • System or kit instructions that describe how to use the system or kit or that correlate the presence or absence of the favorable allele with the predicted resistance are also provided.
  • the instructions can include at least one look-up table that includes a correlation between the presence or absence of the favorable alleles, haplotypes, or marker profiles and the predicted resistance.
  • the precise form of the instructions can vary depending on the components of the system, e.g., they can be present as system software in one or more integrated unit of the system (e.g., a microprocessor, computer or computer readable medium), or can be present in one or more units (e.g., computers or computer readable media) operably coupled to the detector.
  • the system instructions include at least one look-up table that includes a correlation between the presence or absence of the favorable alleles and predicted resistance.
  • the instructions also typically include instructions providing a user interface with the system, e.g., to permit a user to view results of a sample analysis and to input parameters into the system.
  • the isolated polynucleotide comprises a polynucleotide capable of detecting a marker locus of the soybean genome comprising a marker locus comprising one or more of S08271-1-Q2, P7659A-2, S08051-1-Q1, S07158-1-Q1, S07159-1-Q1, S06818-3-Q2, S06820-1-Q3, S06821-1-Q2, S16001-001-Q001 or a marker closely linked thereto on linkage group G.
  • the isolated polynucleotide comprises: (a) a polynucleotide comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
  • the isolated nucleic acids are capable of hybridizing under stringent conditions to nucleic acids of a soybean cultivar resistant to soybean cyst nematode, for instance to particular SNPs that comprise a marker locus, haplotype or marker profile.
  • a substantially identical or complementary sequence is a polynucleotide that will specifically hybridize to the complement of the nucleic acid molecule to which it is being compared under high stringency conditions.
  • a polynucleotide is said to be the “complement” of another polynucleotide if they exhibit complementarity.
  • molecules are said to exhibit “complete complementarity” when every nucleotide of one of the polynucleotide molecules is complementary to a nucleotide of the other.
  • Two molecules are said to be “minimally complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional “low-stringency” conditions.
  • the molecules are said to be “complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional “high-stringency” conditions.
  • Appropriate stringency conditions which promote DNA hybridization for example, 6 ⁇ sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2 ⁇ SSC at 50° C., are known to those skilled in the art or can be found in Current Protocols in Molecular Biology , John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • stringent conditions for hybridization and detection will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C.
  • Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide.
  • Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5 ⁇ to 1 ⁇ SSC at 55 to 60° C.
  • Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1 ⁇ SSC at 60 to 65° C.
  • wash buffers may comprise about 0.1% to about 1% SDS.
  • Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
  • a method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode comprising detecting in the genome of said first soybean plant or in the genome of said first soybean germplasm at least one marker locus that is associated with the resistance, wherein:
  • the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
  • the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR — 18 — 0093 on linkage group G;
  • the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
  • the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR — 18 — 0093 on linkage group G;
  • the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR — 18 — 0093 on linkage group G; or
  • the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225;
  • the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
  • the detecting comprises amplifying at least one of said marker loci and detecting the resulting amplified marker amplicon. 10. The method of embodiment 9, wherein the amplifying comprises:
  • amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm, wherein the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template;
  • said primer or primer pair comprises a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171. 13.
  • said primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or
  • the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified.
  • said labeled nucleic acid probe comprises a nucleic acid sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof.
  • the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, or 135. 18. The method of any one of embodiments 1-19, wherein the detecting comprises DNA sequencing of at least one of said marker loci. 19. An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising
  • the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises 507158-1-Q1 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
  • the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
  • the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR — 18 — 0093 on linkage group G;
  • the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
  • the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR — 18 — 0093 on linkage group G;
  • the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR — 18 — 0093 on linkage group G; or
  • the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225;
  • a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144,
  • a kit for detecting or selecting at least one soybean plant or soybean germplasm with improved resistance to soybean cyst nematode comprising:
  • a primer or a probe for detecting one or more marker loci associated with resistance to soybean cyst nematode wherein the primer or probe are capable of detecting a marker locus, wherein:
  • Rhg1 Soybean Sequence and SNP Marker Assays Associated with Soybean Cyst Nematode Resistance, Rhg1
  • Rhg1 locus Soybean Cyst Nematode Resistance
  • Linkage Group G markers for the Rhg1 locus (Soybean Cyst Nematode Resistance) on Linkage Group G have been produced, as well as, markers genetically linked to these markers. Markers from this region are relevant in breeding populations and will facilitate selection of soybean plants with resistance to SCN at the Rhg1 locus tracing back to PI437654, Peking, and/or PI88788, as well as stacks with other marker assisted traits, including yield genes.
  • Markers were developed to characterize, identify, and/or select resistant or susceptible alleles at the Rhg1 locus on linkage group G (ch 18). Markers were screened against various known resistant and susceptible parents.
  • Marker S08271-1-Q2 was developed to identify alleles associated with SCN phenotype, this marker detects an A/T polymorphism at position 1749394 on ch 18, which is likely derived from PI88788. During development, this marker was validated against SCN resistant line BSR101, and susceptible line P1437654. The marker was further validated and confirmed against a panel of 31 varieties which included proprietary experimental lines, proprietary commercial lines, and public lines.
  • S08271-1-Q2 was chosen for high throughput analysis needs, but other versions can be used to detect the polymorphism. There is a 5 bp deletion in the region, the S08271 forward primer is inside of this indel, and avoids any assay difficulties that may arise from this deletion.
  • markers were validated against the panel of SCN resistant or susceptible varieties described above.
  • the markers are capable of detecting SCN loci likely derived from one or more of PI88788, Peking, PI437654, as well markers from other sources. These markers may have further been optimized for robust and consistent performance in high throughput assay conditions.
  • markers can be used in other assays or with other assay conditions. Some markers were assayed under additional conditions. For example, S06818-3-Q2, S06820-Q3, and S06821-1-Q2 were tested under the following conditions.
  • the parameters used for the TaqMan assay are as follows:
  • Rhg1 locus from Peking associated with resistance to soybean cyst nematode was fine-mapped to a region between 1548716-1881755 bp on Gm18 (Lg G).
  • Lg G soybean cyst nematode
  • Phenotypic data for selected case group lines was based on lab screening and pedigree information. DNA was prepped using standard Illumina TruSeq chemistry. Selected resistant and susceptible soybean lines formed the case group and were sequenced to ⁇ 0.5-40 ⁇ genome coverage on an Illumina HiSeq2000. SNPs were called using a proprietary software to automate the process, missing data was imputed using a separate proprietary software. Haploview was used to conduct a case-control association analysis on a set of 12,449 SNPs identified in the region from 688871-2675880 bp on Gm18. The case group comprised 41 public and proprietary soybean lines susceptible to SCN and the control group comprised 7 public and proprietary lines with resistance derived from Peking. Following Haploview filtering using the settings noted below, 12,093 SNPs remained in the analysis.
  • the case-control analysis identified several SNPs in linkage disequilibrium with Rhg1 (Peking) phenotypic scores.
  • the case-control association analysis using 12,093 SNPs reveals a peak of allele to phenotype association between 1548716-1881755 bp on Gm18 (Lg G), suggesting that Rhg1 from Peking is in this region, as evaluated using a plot of chi square values.
  • 158 SNPs have a perfect association between 41 susceptible (case) and 7 resistant (control) lines (Table 13). These markers are ideal for TaqMan assay design, or for evaluation by other methods, including sequencing, hybridization, or other technologies. Numerous additional SNPs analyzed here that are linked to region but are not in perfect LD with trait could be very informative markers when used in select germplasm.
  • Rhg1 locus from P188788 associated with resistance to soybean cyst nematode was fine-mapped to a region between 1477584-1933546 bp on Gm18 (Lg G).
  • Lg G soybean cyst nematode
  • Phenotypic data for selected case group lines was based on lab screening and pedigree information. DNA was prepped using standard Illumina TruSeq chemistry. Selected resistant and susceptible soybean lines formed the case group and were sequenced to ⁇ 0.5-40 ⁇ genome coverage on an Illumina HiSeq2000. SNPs were called using a proprietary software to automate the process, missing data was imputed using a separate proprietary software. Haploview was used to conduct a case-control association analysis on a set of 13,147 SNPs identified in the region from 688871-2675880 bp on Gm18. The case group comprised 41 public and proprietary soybean lines susceptible to SCN and the control group comprised 78 proprietary lines with resistance derived from P188788. Following Haploview filtering using the settings noted below, 10,872 SNPs remained in the analysis.
  • the case-control analysis identified several SNPs in linkage disequilibrium with Rhg1 (Peking) phenotypic scores.
  • the case-control association analysis using 10,872 SNPs reveals a peak of allele to phenotype association between 1477584-1933546 bp on Gm18 (Lg G), suggesting that Rhg1 from P188788 is in this region, as evaluated using a plot of chi square values.
  • 158 SNPs have a perfect association between 41 susceptible (case) and 78 resistant (control) lines (Table A). These markers are ideal for TaqMan assay design, or for evaluation by other methods, including sequencing, hybridization, or other technologies. Numerous additional SNPs analyzed here that are linked to region but are not in perfect LD with trait could be very informative markers when used in select germplasm.

Abstract

Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.

Description

    CROSS-REFERENCES TO RELATED APPLICATIONS
  • This application claims priority to U.S. Provisional Patent Application Ser. No. 61/740,526, filed on Dec. 21, 2012, U.S. Provisional Patent Application Ser. No. 61/660,387, filed on Jun. 15, 2012, and U.S. Provisional Patent Application Ser. No. 61/671,937, filed Jul. 16, 2012, each of which is hereby incorporated herein in its entirety by reference.
    • FIELD OF THE INVENTION
  • This invention relates to methods of identifying and/or selecting soybean plants or germplasm that display improved resistance to Soybean Cyst Nematode.
    • REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB
  • The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 429573seqlist.txt, a creation date of Feb. 18, 2013 and a size of 39 KB. The sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.
    • BACKGROUND
  • Soybeans (Glycine max L. Merr.) are a major cash crop and investment commodity in North America and elsewhere. Soybean oil is one of the most widely used edible oils, and soybeans are used worldwide both in animal feed and in human food production. Additionally, soybean utilization is expanding to industrial, manufacturing, and pharmaceutical applications.
  • Soybean Cyst Nematode (SCN) is a parasitic pest which has threatened soybean production in the U.S. for more than fifty years. Soybean cyst nematode resistance is an economically important trait as infection can substantially reduce yields. Molecular characterization of soybean cyst nematode resistance would have important implications for soybean cultivar improvement.
  • There remains a need for soybean plants with improved resistance to soybean cyst nematode and methods for identifying and selecting such plants.
    • SUMMARY
  • Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.
    • DETAILED DESCRIPTION
  • Molecular markers have been used to selectively improve soybean crops through the use of marker assisted selection. Any detectable polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest. A number of soybean markers have been mapped and linkage groups created, as described in Cregan, P. B., et al., “An Integrated Genetic Linkage Map of the Soybean Genome” (1999) Crop Science 39:1464-90, and more recently in Choi, et al., “A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis” (2007) Genetics 176:685-96. Many soybean markers are publicly available at the USDA affiliated soybase website (www.soybase.org).
  • Most plant traits of agronomic importance are polygenic, otherwise known as quantitative, traits. A quantitative trait is controlled by several genes located at various locations, or loci, in the plant's genome. The multiple genes have a cumulative effect which contributes to the continuous range of phenotypes observed in many plant traits. These genes are referred to as quantitative trait loci (QTL). Recombination frequency measures the extent to which a molecular marker is linked with a QTL. Lower recombination frequencies, typically measured in centiMorgans (cM), indicate greater linkage between the QTL and the molecular marker. The extent to which two features are linked is often referred to as the genetic distance. The genetic distance is also typically related to the physical distance between the marker and the QTL; however, certain biological phenomenon (including recombinational “hot spots”) can affect the relationship between physical distance and genetic distance. Generally, the usefulness of a molecular marker is determined by the genetic and physical distance between the marker and the selectable trait of interest.
  • In some cases, multiple closely linked markers, such as Single Nucleotide Polymorphism (SNP) markers, can be found to exist in a certain region of a plant genome encompassing one or more QTL. In such cases, by determining the allele present at each of those marker loci, a haplotype for that region of the plant genome can be determined. Further, by determining alleles or haplotypes present at multiple regions of the plant genome related to the same phenotypic trait, a marker profile for that trait can be determined. Such haplotype and marker profile information can be useful in identifying and selecting plants with certain desired traits.
  • Before describing the present invention in detail, it is to be understood that this invention is not limited to particular embodiments, which can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.
  • Certain definitions used in the specification and claims are provided below. In order to provide a clear and consistent understanding of the specification and claims, including the scope to be given such terms, the following definitions are provided:
  • As used in this specification and the appended claims, terms in the singular and the singular forms “a,” “an,” and “the,” for example, include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “plant,” “the plant,” or “a plant” also includes a plurality of plants; also, depending on the context, use of the term “plant” can also include genetically similar or identical progeny of that plant; use of the term “a nucleic acid” optionally includes, as a practical matter, many copies of that nucleic acid molecule; similarly, the term “probe” optionally (and typically) encompasses many similar or identical probe molecules.
  • Additionally, as used herein, “comprising” is to be interpreted as specifying the presence of the stated features, integers, steps, or components as referred to, but does not preclude the presence or addition of one or more features, integers, steps, or components, or groups thereof. Thus, for example, a kit comprising one pair of oligonucleotide primers may have two or more pairs of oligonucleotide primers. Additionally, the term “comprising” is intended to include examples encompassed by the terms “consisting essentially of” and “consisting of:” Similarly, the term “consisting essentially of” is intended to include examples encompassed by the term “consisting of:”
  • “Agronomics,” “agronomic traits,” and “agronomic performance” refer to the traits (and underlying genetic elements) of a given plant variety that contribute to yield over the course of a growing season. Individual agronomic traits include emergence vigor, vegetative vigor, stress tolerance, disease resistance or tolerance, insect resistance or tolerance, herbicide resistance, branching, flowering, seed set, seed size, seed density, standability, threshability, and the like.
  • “Allele” means any of one or more alternative forms of a genetic sequence. In a diploid cell or organism, the two alleles of a given sequence typically occupy corresponding loci on a pair of homologous chromosomes. With regard to a SNP marker, allele refers to the specific nucleotide base present at that SNP locus in that individual plant.
  • The term “amplifying” in the context of nucleic acid amplification is any process whereby additional copies of a selected nucleic acid (or a transcribed form thereof) are produced. An “amplicon” is an amplified nucleic acid, e.g., a nucleic acid that is produced by amplifying a template nucleic acid by any available amplification.
  • An “ancestral line” is a parent line used as a source of genes, e.g., for the development of elite lines.
  • An “ancestral population” is a group of ancestors that have contributed the bulk of the genetic variation that was used to develop elite lines.
  • “Backcrossing” is a process in which a breeder crosses a progeny variety back to one of the parental genotypes one or more times.
  • The term “chromosome segment” designates a contiguous linear span of genomic DNA that resides in planta on a single chromosome. “Chromosome interval” refers to a chromosome segment defined by specific flanking marker loci.
  • “Cultivar” and “variety” are used synonymously and mean a group of plants within a species (e.g., Glycine max) that share certain genetic traits that separate them from other possible varieties within that species. Soybean cultivars are inbred lines produced after several generations of self-pollinations. Individuals within a soybean cultivar are homogeneous, nearly genetically identical, with most loci in the homozygous state.
  • An “elite line” is an agronomically superior line that has resulted from many cycles of breeding and selection for superior agronomic performance. Numerous elite lines are available and known to those of skill in the art of soybean breeding.
  • An “elite population” is an assortment of elite individuals or lines that can be used to represent the state of the art in terms of agronomically superior genotypes of a given crop species, such as soybean.
  • An “exotic soybean strain” or an “exotic soybean germplasm” is a strain or germplasm derived from a soybean not belonging to an available elite soybean line or strain of germplasm. In the context of a cross between two soybean plants or strains of germplasm, an exotic germplasm is not closely related by descent to the elite germplasm with which it is crossed. Most commonly, the exotic germplasm is not derived from any known elite line of soybean, but rather is selected to introduce novel genetic elements (typically novel alleles) into a breeding program.
  • A “genetic map” is a description of genetic association or linkage relationships among loci on one or more chromosomes (or linkage groups) within a given species, generally depicted in a diagrammatic or tabular form.
  • “Genotype” is a description of the allelic state at one or more loci.
  • “Germplasm” means the genetic material that comprises the physical foundation of the hereditary qualities of an organism. As used herein, germplasm includes seeds and living tissue from which new plants may be grown; or, another plant part, such as leaf, stem, pollen, or cells, that may be cultured into a whole plant. Germplasm resources provide sources of genetic traits used by plant breeders to improve commercial cultivars.
  • An individual is “homozygous” if the individual has only one type of allele at a given locus (e.g., a diploid individual has a copy of the same allele at a locus for each of two homologous chromosomes). An individual is “heterozygous” if more than one allele type is present at a given locus (e.g., a diploid individual with one copy each of two different alleles). The term “homogeneity” indicates that members of a group have the same genotype at one or more specific loci. In contrast, the term “heterogeneity” is used to indicate that individuals within the group differ in genotype at one or more specific loci.
  • “Introgression” means the entry or introduction of a gene, QTL, haplotype, marker profile, trait, or trait locus from the genome of one plant into the genome of another plant.
  • The terms “label” or “detectable label” refer to a molecule capable of detection. A detectable label can also include a combination of a reporter and a quencher, such as are employed in FRET probes or TaqMan™ probes. The term “reporter” refers to a substance or a portion thereof which is capable of exhibiting a detectable signal, which signal can be suppressed by a quencher. The detectable signal of the reporter is, e.g., fluorescence in the detectable range. The term “quencher” refers to a substance or portion thereof which is capable of suppressing, reducing, inhibiting, etc., the detectable signal produced by the reporter. As used herein, the terms “quenching” and “fluorescence energy transfer” refer to the process whereby, when a reporter and a quencher are in close proximity, and the reporter is excited by an energy source, a substantial portion of the energy of the excited state non-radiatively transfers to the quencher where it either dissipates non-radiatively or is emitted at a different emission wavelength than that of the reporter.
  • A “line” or “strain” is a group of individuals of identical parentage that are generally inbred to some degree and that are generally homozygous and homogeneous at most loci (isogenic or near isogenic). A “subline” refers to an inbred subset of descendants that are genetically distinct from other similarly inbred subsets descended from the same progenitor. Traditionally, a subline has been derived by inbreeding the seed from an individual soybean plant selected at the F3 to F5 generation until the residual segregating loci are “fixed” or homozygous across most or all loci. Commercial soybean varieties (or lines) are typically produced by aggregating (“bulking”) the self-pollinated progeny of a single F3 to F5 plant from a controlled cross between 2 genetically different parents. While the variety typically appears uniform, the self-pollinating variety derived from the selected plant eventually (e.g., F8) becomes a mixture of homozygous plants that can vary in genotype at any locus that was heterozygous in the originally selected F3 to F5 plant. Marker-based sublines that differ from each other based on qualitative polymorphism at the DNA level at one or more specific marker loci are derived by genotyping a sample of seed derived from individual self-pollinated progeny derived from a selected F3-F5 plant. The seed sample can be genotyped directly as seed, or as plant tissue grown from such a seed sample. Optionally, seed sharing a common genotype at the specified locus (or loci) are bulked providing a subline that is genetically homogenous at identified loci important for a trait of interest (e.g., yield, tolerance, etc.).
  • “Linkage” refers to the tendency for alleles to segregate together more often than expected by chance if their transmission was independent. Typically, linkage refers to alleles on the same chromosome. Genetic recombination occurs with an assumed random frequency over the entire genome. Genetic maps are constructed by measuring the frequency of recombination between pairs of traits or markers, the lower the frequency of recombination, and the greater the degree of linkage.
  • “Linkage disequilibrium” is a non-random association of alleles at two or more loci and can occur between unlinked markers. It is based on allele frequencies within a population and is influenced by but not dependent on linkage.
  • “Linkage group” (LG) refers to traits or markers that generally co-segregate. A linkage group generally corresponds to a chromosomal region containing genetic material that encodes the traits or markers.
  • “Locus” is a defined segment of DNA.
  • A “map location” or “map position” is an assigned location on a genetic map relative to linked genetic markers where a specified marker can be found within a given species. Map positions are generally provided in centimorgans (cM)), unless otherwise indicated, genetic positions provided are based on the Glycine max consensus map v 4.0 as provided by Hyten et al. (2010) Crop Sci 50:960-968. A “physical position” or “physical location” or “physical map location” is the position, typically in nucleotides bases, of a particular nucleotide, such as a SNP nucleotide, on a chromosome. Unless otherwise indicated, the physical position within the soybean genome provided is based on the Glyma 1.0 genome sequence described in Schmutz et al. (2010) Nature 463:178-183, available from the Phytozome website (phytozome-dot-net/soybean).
  • “Mapping” is the process of defining the association and relationships of loci through the use of genetic markers, populations segregating for the markers, and standard genetic principles of recombination frequency.
  • “Marker” or “molecular marker” or “marker locus” is a term used to denote a nucleic acid or amino acid sequence that is sufficiently unique to characterize a specific locus on the genome. Any detectable polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest.
  • “Marker assisted selection” refers to the process of selecting a desired trait or traits in a plant or plants by detecting one or more nucleic acids from the plant, where the nucleic acid is linked to the desired trait, and then selecting the plant or germplasm possessing those one or more nucleic acids.
  • “Haplotype” refers to a combination of particular alleles present within a particular plant's genome at two or more linked marker loci, for instance at two or more loci on a particular linkage group. For instance, in one example, two specific marker loci on LG-O are used to define a haplotype for a particular plant. In still further examples, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more linked marker loci are used to define a haplotype for a particular plant.
  • As used herein, a “marker profile” means a combination of particular alleles present within a particular plant's genome at two or more marker loci which are not linked, for instance two or more loci on two or more different linkage groups or two or more chromosomes. For instance, in one example, a particular combination of marker loci or a particular combination of haplotypes define the marker profile of a particular plant.
  • The term “plant” includes reference to an immature or mature whole plant, including a plant from which seed or grain or anthers have been removed. Seed or embryo that will produce the plant is also considered to be the plant.
  • “Plant parts” means any portion or piece of a plant, including leaves, stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen, ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks, tissues, tissue cultures, cells and the like.
  • “Polymorphism” means a change or difference between two related nucleic acids. A “nucleotide polymorphism” refers to a nucleotide that is different in one sequence when compared to a related sequence when the two nucleic acids are aligned for maximal correspondence.
  • “Polynucleotide,” “polynucleotide sequence,” “nucleic acid,” “nucleic acid molecule,” “nucleic acid sequence,” “nucleic acid fragment,” and “oligonucleotide” are used interchangeably herein to indicate a polymer of nucleotides that is single- or multi-stranded, that optionally contains synthetic, non-natural, or altered RNA or DNA nucleotide bases. A DNA polynucleotide may be comprised of one or more strands of cDNA, genomic DNA, synthetic DNA, or mixtures thereof.
  • “Primer” refers to an oligonucleotide which is capable of acting as a point of initiation of nucleic acid synthesis or replication along a complementary strand when placed under conditions in which synthesis of a complementary strand is catalyzed by a polymerase. Typically, primers are about 10 to 30 nucleotides in length, but longer or shorter sequences can be employed. Primers may be provided in double-stranded form, though the single-stranded form is more typically used. A primer can further contain a detectable label, for example a 5′ end label.
  • “Probe” refers to an oligonucleotide that is complementary (though not necessarily fully complementary) to a polynucleotide of interest and forms a duplexed structure by hybridization with at least one strand of the polynucleotide of interest. Typically, probes are oligonucleotides from 10 to 50 nucleotides in length, but longer or shorter sequences can be employed. A probe can further contain a detectable label.
  • “Quantitative trait loci” or “QTL” refer to the genetic elements controlling a quantitative trait.
  • “Recombination frequency” is the frequency of a crossing over event (recombination) between two genetic loci. Recombination frequency can be observed by following the segregation of markers and/or traits during meiosis.
  • “Resistance and “improved resistance” are used interchangeably herein and refer to any type of increase in resistance or resistance to, or any type of decrease in susceptibility. A “resistant plant” or “resistant plant variety” need not possess absolute or complete resistance. Instead, a “resistant plant,” “resistant plant variety,” or a plant or plant variety with “improved resistance” will have a level of resistance or tolerance which is higher than that of a comparable susceptible plant or variety.
  • “Self-crossing” or “self-pollination” or “selfing” is a process through which a breeder crosses a plant with itself; for example, a second generation hybrid F2 with itself to yield progeny designated F2:3.
  • “SNP” or “single nucleotide polymorphism” means a sequence variation that occurs when a single nucleotide (A, T, C, or G) in the genome sequence is altered or variable. “SNP markers” exist when SNPs are mapped to sites on the soybean genome.
  • The term “yield” refers to the productivity per unit area of a particular plant product of commercial value. For example, yield of soybean is commonly measured in bushels of seed per acre or metric tons of seed per hectare per season. Yield is affected by both genetic and environmental factors.
  • As used herein, an “isolated” or “purified” polynucleotide or polypeptide, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or polypeptide as found in its naturally occurring environment. Typically, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived. A polypeptide that is substantially free of cellular material includes preparations of polypeptides having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein, culture media or other chemical components.
  • Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter “Sambrook”).
  • Methods are provided for identifying and/or selecting a soybean plant or soybean germplasm that displays improved resistance to soybean cyst nematode. The method comprises detecting in the soybean plant or germplasm, or a part thereof, at least one marker locus associated with resistance to soybean cyst nematode. Also provided are isolated polynucleotides and kits for use in identifying and/or detecting a soybean plant or soybean germplasm that displays improved resistance to soybean cyst nematode, and soybean plants, cells, and/or seeds comprising at least one marker locus conferring improved resistance to soybean cyst nematode.
  • Provided herein are marker loci associated with soybean cyst nematode resistance that have been identified and mapped to genomic loci on linkage group G. These findings have important implications for soybean production, as identifying markers that can be used for selection of soybean cyst nematode resistance will greatly expedite the development of soybean cyst nematode resistance into elite cultivars.
  • Marker loci, haplotypes and marker profiles associated with resistance to soybean cyst nematode are provided. Further provided are genomic loci that are associated with soybean resistance to soybean cyst nematode.
  • In certain embodiments, soybean plants or germplasm are identified that have at least one favorable allele, marker locus, haplotype or marker profile that positively correlates with resistance or improved resistance to soybean cyst nematode. However, in other embodiments, it is useful for exclusionary purposes during breeding to identify alleles, marker loci, haplotypes, or marker profiles that negatively correlate with resistance, for example, to eliminate such plants or germplasm from subsequent rounds of breeding.
  • In one embodiment, marker loci useful for identifying a first soybean plant or first soybean germplasm that displays improved resistance to soybean cyst nematode comprises a marker locus comprising one or more of (a) the at least one marker locus comprises 508271-1-Q2 or a marker closely linked thereto on linkage group G; (b) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (f) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G; (h) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G; (i) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G; (j) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G; (k) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (l) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (n) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or (o) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
  • Non-limiting examples of marker loci located within, linked to, or closely linked to these genomic loci are provided in Table 1A.
  • TABLE 1
    Marker Positions For Marker Loci Associated With Resistance to Soybean Cyst Nematode.
    Linkage GmConsensus % var
    Marker ID group Flanking public marker 4.0 (cM) Phys Map Allele (R/S) Analysis, Statistic Xplnd Source
    S08271-1-Q2 G ‘Satt309 (10.1); ‘BARC- 10.16 1749394 A/T Association Mapping, p- PI88788
    (P10355B-1) 012285-01798 (11.0) value
    0.0000000000012402, chi
    square 50.422
    P7659A-2 G ‘BARC-015371-01813 9.27 1580305 T/C
    (8.63);
    ‘BARCSOYSSR_18_0093
    (9.44)
    S08051-1-Q1 G ‘BARC-015371-01813 9.26 1579707 GT/TC Association Mapping, p- Peking,
    (P7659A-1) (8.63); and value 2.3816E−21, chi PI437654
    ‘BARCSOYSSR_18_0093 1579708 square 90
    (9.44)
    S07158-1-Q1 G ‘BARC-030055-06792 12.34 2098742 TG/GT PI437654,
    (P5219A-1) (12.15); ‘BARC-025777- and PI88788,
    05064 (12.92) 2098741 Peking
    S07159-1-Q1 G ‘BARC-030055-06792 12.33 2095977 T/A PI437654
    (P5219A-2) (12.15); ‘BARC-025777-
    05064 (12.92)
    S06818-3-Q2 G ‘BARC-015371-01813 9.23 1573060 C/G Association mapping, p-
    (8.63); value 1.2876E−37, chi
    ‘BARCSOYSSR_18_0093 square 164.32
    (9.44)
    S06820-1-Q3 G ‘BARC-015371-01813 9.22 1571774 G/A
    (8.63);
    ‘BARCSOYSSR_18_0093
    (9.44)
    S06821-1-Q2 G ‘BARC-015371-01813 9.19 1563924 T/G
    (8.63);
    ‘BARCSOYSSR_18_0093
    (9.44)
    S16001-001- G ‘BARC-015371-01813 9.38 1607524 C/A Association Mapping, p- PI88788
    Q001 (8.63); value 2.0885E−45, chi
    ‘BARCSOYSSR_18_0093 square 200
    (9.44)
    Gm18: 926125 G  926125 See table 13
    Gm18: 1138152 G 1138152 See table 13
    Gm18: 1517146 G 1517146 See table 13
    Gm18: 1518206 G 1518206 See table 13
    Gm18: 1520624 G 1520624 See table 13
    Gm18: 1520675 G 1520675 See table 13
    Gm18: 1520743 G 1520743 See table 13
    Gm18: 1524498 G 1524498 See table 13
    Gm18: 1548716 G 1548716 See table 13
    Gm18: 1550153 G 1550153 See table 13
    Gm18: 1550231 G 1550231 See table 13
    Gm18: 1552799 G 1552799 See table 13
    Gm18: 1554392 G 1554392 See table 13
    Gm18: 1554570 G 1554570 See table 13
    Gm18: 1554604 G 1554604 See table 13
    Gm18: 1554689 G 1554689 See table 13
    Gm18: 1555210 G 1555210 See table 13
    Gm18: 1560043 G 1560043 See table 13
    Gm18: 1560088 G 1560088 See table 13
    Gm18: 1560390 G 1560390 See table 13
    Gm18: 1560442 G 1560442 See table 13
    Gm18: 1560784 G 1560784 See table 13
    Gm18: 1561009 G 1561009 See table 13
    Gm18: 1561190 G 1561190 See table 13
    Gm18: 1561429 G 1561429 See table 13
    Gm18: 1561725 G 1561725 See table 13
    Gm18: 1562884 G 1562884 See table 13
    Gm18: 1563153 G 1563153 See table 13
    Gm18: 1564092 G 1564092 See table 13
    Gm18: 1565225 G 1565225 See table 13
    Gm18: 1565646 G 1565646 See table 13
    Gm18: 1566882 G 1566882 See table 13
    Gm18: 1567685 G 1567685 See table 13
    Gm18: 1567843 G 1567843 See table 13
    Gm18: 1568490 G 1568490 See table 13
    Gm18: 1568999 G 1568999 See table 13
    Gm18: 1569035 G 1569035 See table 13
    Gm18: 1569146 G 1569146 See table 13
    Gm18: 1570660 G 1570660 See table 13
    Gm18: 1572368 G 1572368 See table 13
    Gm18: 1577559 G 1577559 See table 13
    Gm18: 1578727 G 1578727 See table 13
    Gm18: 1579201 G 1579201 See table 13
    Gm18: 1579270 G 1579270 See table 13
    Gm18: 1579707 G 1579707 See table 13
    Gm18: 1579708 G 1579708 See table 13
    Gm18: 1581688 G 1581688 See table 13
    Gm18: 1583772 G 1583772 See table 13
    Gm18: 1584054 G 1584054 See table 13
    Gm18: 1584659 G 1584659 See table 13
    Gm18: 1589032 G 1589032 See table 13
    Gm18: 1595321 G 1595321 See table 13
    Gm18: 1598101 G 1598101 See table 13
    Gm18: 1599717 G 1599717 See table 13
    Gm18: 1599752 G 1599752 See table 13
    Gm18: 1599841 G 1599841 See table 13
    Gm18: 1600011 G 1600011 See table 13
    Gm18: 1600033 G 1600033 See table 13
    Gm18: 1600179 G 1600179 See table 13
    Gm18: 1601192 G 1601192 See table 13
    Gm18: 1601614 G 1601614 See table 13
    Gm18: 1602244 G 1602244 See table 13
    Gm18: 1603722 G 1603722 See table 13
    Gm18: 1604031 G 1604031 See table 13
    Gm18: 1605443 G 1605443 See table 13
    Gm18: 1606442 G 1606442 See table 13
    Gm18: 1606566 G 1606566 See table 13
    Gm18: 1606647 G 1606647 See table 13
    Gm18: 1609397 G 1609397 See table 13
    Gm18: 1610935 G 1610935 See table 13
    Gm18: 1612466 G 1612466 See table 13
    Gm18: 1612553 G 1612553 See table 13
    Gm18: 1614300 G 1614300 See table 13
    Gm18: 1614960 G 1614960 See table 13
    Gm18: 1618118 G 1618118 See table 13
    Gm18: 1626263 G 1626263 See table 13
    Gm18: 1626278 G 1626278 See table 13
    Gm18: 1627202 G 1627202 See table 13
    Gm18: 1627204 G 1627204 See table 13
    Gm18: 1629930 G 1629930 See table 13
    Gm18: 1634611 G 1634611 See table 13
    Gm18: 1643225 G 1643225 See table 13
    Gm18: 1653887 G 1653887 See table 13
    Gm18: 1654681 G 1654681 See table 13
    Gm18: 1654687 G 1654687 See table 13
    Gm18: 1657025 G 1657025 See table 13
    Gm18: 1680507 G 1680507 See table 13
    Gm18: 1700832 G 1700832 See table 13
    Gm18: 1700885 G 1700885 See table 13
    Gm18: 1701854 G 1701854 See table 13
    Gm18: 1702482 G 1702482 See table 13
    Gm18: 1702563 G 1702563 See table 13
    Gm18: 1702741 G 1702741 See table 13
    Gm18: 1703321 G 1703321 See table 13
    Gm18: 1706708 G 1706708 See table 13
    Gm18: 1706842 G 1706842 See table 13
    Gm18: 1707082 G 1707082 See table 13
    Gm18: 1707115 G 1707115 See table 13
    Gm18: 1707377 G 1707377 See table 13
    Gm18: 1708549 G 1708549 See table 13
    Gm18: 1717352 G 1717352 See table 13
    Gm18: 1721829 G 1721829 See table 13
    Gm18: 1723649 G 1723649 See table 13
    Gm18: 1723650 G 1723650 See table 13
    Gm18: 1724082 G 1724082 See table 13
    Gm18: 1725538 G 1725538 See table 13
    Gm18: 1725630 G 1725630 See table 13
    Gm18: 1725815 G 1725815 See table 13
    Gm18: 1725932 G 1725932 See table 13
    Gm18: 1725991 G 1725991 See table 13
    Gm18: 1726068 G 1726068 See table 13
    Gm18: 1727330 G 1727330 See table 13
    Gm18: 1727343 G 1727343 See table 13
    Gm18: 1727903 G 1727903 See table 13
    Gm18: 1728146 G 1728146 See table 13
    Gm18: 1728824 G 1728824 See table 13
    Gm18: 1729347 G 1729347 See table 13
    Gm18: 1729673 G 1729673 See table 13
    Gm18: 1729866 G 1729866 See table 13
    Gm18: 1730855 G 1730855 See table 13
    Gm18: 1731068 G 1731068 See table 13
    Gm18: 1731184 G 1731184 See table 13
    Gm18: 1731725 G 1731725 See table 13
    Gm18: 1731938 G 1731938 See table 13
    Gm18: 1734691 G 1734691 See table 13
    Gm18: 1735510 G 1735510 See table 13
    Gm18: 1740118 G 1740118 See table 13
    Gm18: 1747766 G 1747766 See table 13
    Gm18: 1751156 G 1751156 See table 13
    Gm18: 1752808 G 1752808 See table 13
    Gm18: 1754310 G 1754310 See table 13
    Gm18: 1754895 G 1754895 See table 13
    Gm18: 1759167 G 1759167 See table 13
    Gm18: 1759307 G 1759307 See table 13
    Gm18: 1761263 G 1761263 See table 13
    Gm18: 1762686 G 1762686 See table 13
    Gm18: 1763519 G 1763519 See table 13
    Gm18: 1768783 G 1768783 See table 13
    Gm18: 1768805 G 1768805 See table 13
    Gm18: 1769619 G 1769619 See table 13
    Gm18: 1773903 G 1773903 See table 13
    Gm18: 1773911 G 1773911 See table 13
    Gm18: 1778021 G 1778021 See table 13
    Gm18: 1783028 G 1783028 See table 13
    Gm18: 1783194 G 1783194 See table 13
    Gm18: 1783357 G 1783357 See table 13
    Gm18: 1785320 G 1785320 See table 13
    Gm18: 1787549 G 1787549 See table 13
    Gm18: 1789215 G 1789215 See table 13
    Gm18: 1789352 G 1789352 See table 13
    Gm18: 1789553 G 1789553 See table 13
    Gm18: 1789934 G 1789934 See table 13
    Gm18: 1805509 G 1805509 See table 13
    Gm18: 1859739 G 1859739 See table 13
    Gm18: 1863987 G 1863987 See table 13
    Gm18: 1864738 G 1864738 See table 13
    Gm18: 1877951 G 1877951 See table 13
    Gm18: 1881755 G 1881755 See table 13
    Gm18: 1607524 G 1607524 See table 15
    Gm18: 1888247 G 1845911 See table 15
    Gm18: 1845911 G 1845911 See table 15
    Gm18: 1846008 G 1846008 See table 15
    Gm18: 1565826 G 1565826 See table 15
    Gm18: 1918014 G 1918014 See table 15
  • TABLE 1A
    Non-limiting examples of markers closely linked
    to various markers set forth in Table 1.
    Linkage GmConsensus
    Marker ID group 4.0 (cM) Phys Map
    BARC-020027-04405 G_(18) 0.00 181,064
    BARC-052957-11678 G_(18) 0.00 187,414
    BARC-064665-18774 G_(18) 0.11 224,648
    BARC-043197-08552 G_(18) 0.92 305,200
    BARC-060195-16470 G_(18) 1.64 470,340
    BARC-018387-03171 G_(18) 7.01 488,479
    BARC-022431-04323 G_(18) 7.43 734,360
    BARC-020839-03962 G_(18) 8.12 981,378
    BARC-900558-00952 G_(18) 8.12 999,063
    BARC-049013-10791 G_(18) 8.39 1,277,303
    BARC-015371-01813 G_(18) 8.63 1,431,827
    S06821-1 G_(18) 9.19 1,563,924
    S06820-1 G_(18) 9.22 1,571,774
    S06818-3 G_(18) 9.23 1,573,060
    S08051-1 G_(18) 9.26 1,579,708
    S16001-001 G_(18) 9.38 1,607,524
    BARCSOYSSR_18_0093 G_(18) 9.44 1,621,261
    Sat_210 G_(18) 9.44 1,621,261
    BARC-048245-10515 G_(18) 9.94 1,718,204
    BARC-G00219-00248 G_(18) 9.96 1,726,610
    BARCSOYSSR_18_0102 G_(18) 10.10 1,736,324
    Satt309 G_(18) 10.10 1,736,324
    S08271-1 G_(18) 10.16 1,749,394
    BARC-012285-01798 G_(18) 11.01 1,945,192
    BARC-010917-01706 G_(18) 11.09 1,955,436
    BARC-012289-01799 G_(18) 11.12 1,957,590
    BARC-028299-05817 G_(18) 11.86 1,958,726
    BARC-061523-17249 G_(18) 12.10 1,979,049
    BARC-030055-06792 G_(18) 12.15 2,033,662
    S07159-1 G_(18) 12.33 2,095,977
    S07158-1 G_(18) 12.34 2,098,742
    BARC-025777-05064 G_(18) 12.92 2,296,490
    BARCSOYSSR_18_0142 G_(18) 13.98 2,409,497
    Sat_141 G_(18) 13.98 2,409,497
    BARC-004952-00267 G_(18) 14.20 2,664,887
    BARCSOYSSR_18_0158 G_(18) 14.70 2,665,098
    Satt610 G_(18) 14.70 2,665,098
    BARC-047665-10370 G_(18) 15.97 2,833,064
    BARC-047787-10396 G_(18) 16.14 2,853,047
    BARCSOYSSR_18_0177 G_(18) 17.19 3,162,740
    Satt570 G_(18) 17.19 3,162,740
    BARC-014395-01348 G_(18) 19.48 3,448,063
    BARCSOYSSR_18_0195 G_(18) 20.57 3,603,119
    AW734137 G_(18) 20.57 3,603,119
    BARC-003432-00279 G_(18) 21.48 3,643,846
    BARCSOYSSR_18_0250 G_(18) 22.22 4,692,375
    Satt217 G_(18) 22.22 4,692,375
    BARCSOYSSR_18_0257 G_(18) 24.96 4,800,515
    Satt235 G_(18) 24.96 4,800,515
    BARCSOYSSR_18_0295 G_(18) 29.20 5,330,646
    Sat_315 G_(18) 29.20 5,330,646
    BARCSOYSSR_18_0305 G_(18) 31.02 5,470,147
    Sat_290 G_(18) 31.02 5,470,147
    BARCSOYSSR_18_0316 G_(18) 32.88 5,675,379
    Sat_131 G_(18) 32.88 5,675,379
    BARCSOYSSR_18_0324 G_(18) 35.43 5,890,285
    Satt324 G_(18) 35.43 5,890,285
    BARCSOYSSR_18_0348 G_(18) 36.97 6,169,586
    Sat_403 G_(18) 36.97 6,169,586
    BARC-040265-07700 G_(18) 39.86 7,275,891
    BARC-901121-00988 G_(18) 40.41 8,415,710
    BARC-063985-18522 G_(18) 40.41 8,791,883
    BARC-039993-07626 G_(18) 40.81 9,012,214
    BARCSOYSSR_18_0550 G_(18) 43.03 11,400,889
    Sat_308 G_(18) 43.03 11,400,889
    BARC-053419-11845 G_(18) 44.99 12,638,074
    BARC-056521-14449 G_(18) 47.51 14,167,067
    BARC-059783-16090 G_(18) 47.51 14,285,415
    BARC-054849-12183 G_(18) 47.51 14,335,308
    BARC-049885-09225 G_(18) 48.21 14,570,865
    BARC-064283-18606 G_(18) 48.21 14,893,358
    BARC-017647-02654 G_(18) 48.33 15,242,485
    BARC-059485-15839 G_(18) 48.95 15,676,568
    BARC-040485-07753 G_(18) 48.95 15,723,524
    BARC-018333-03580 G_(18) 50.04 16,483,354
    BARC-018333-03581 G_(18) 50.24 16,483,354
    BARC-019465-03616 G_(18) 50.88 16,505,062
    BARC-013677-01228 G_(18) 52.04 16,668,537
    BARC-061001-16998 G_(18) 52.04 16,797,216
    BARC-047404-12924 G_(18) 52.04 17,550,827
    BARC-046912-12782 G_(18) 52.04 17,553,931
    BARC-046994-12826 G_(18) 52.04 17,575,698
    BARC-046874-12778 G_(18) 52.04 17,592,240
    BARC-046872-12776 G_(18) 52.04 17,600,728
    BARC-046920-12786 G_(18) 52.04 17,603,029
    BARC-046930-12795 G_(18) 52.04 17,611,727
    BARC-046926-12788 G_(18) 52.04 17,626,176
    BARC-046922-12787 G_(18) 52.04 17,630,432
    BARC-057295-14678 G_(18) 52.04 17,781,283
    BARC-020159-04488 G_(18) 52.04 17,925,069
    BARC-060837-16930 G_(18) 52.04 18,410,099
    BARC-058413-15279 G_(18) 53.38 20,526,141
    BARC-060825-16919 G_(18) 54.45 21,121,950
    BARC-047150-12874 G_(18) 54.45 21,364,220
    BARC-047112-12860 G_(18) 54.45 21,365,038
    BARC-047096-12838 G_(18) 54.45 21,384,584
    BARC-063705-18440 G_(18) 54.45 21,701,030
    BARC-055557-13432 G_(18) 54.45 21,724,083
    BARC-062097-17654 G_(18) 54.45 22,120,170
    BARCSOYSSR_18_0845 G_(18) 54.97 22,150,302
    Satt303 G_(18) 54.97 22,150,302
    BARC-060189-16468 G_(18) 55.60 22,483,339
    BARC-047504-12947 G_(18) 55.60 22,535,676
    BARC-061785-17386 G_(18) 55.60 22,585,948
    BARC-047502-12946 G_(18) 55.60 22,588,708
    BARC-047102-12842 G_(18) 55.60 22,603,647
    BARC-055855-13794 G_(18) 55.60 23,123,288
    BARC-061111-17050 G_(18) 55.60 24,129,395
    BARC-058369-15257 G_(18) 55.60 27,610,750
    BARC-060613-16749 G_(18) 55.60 27,931,082
    BARC-013825-01251 G_(18) 55.60 30,313,907
    BARC-061647-17305 G_(18) 55.60 31,080,816
    BARC-056139-14122 G_(18) 55.60 31,828,672
    BARC-059397-15790 G_(18) 55.60 33,110,626
    BARC-062783-18056 G_(18) 55.60 33,753,070
    BARC-030691-06926 G_(18) 55.60 34,178,194
    BARC-057565-14836 G_(18) 55.60 34,232,818
    BARC-056267-14204 G_(18) 55.60 36,963,309
    BARC-061197-17134 G_(18) 55.60 39,413,323
    BARC-051485-11122 G_(18) 55.60 39,512,471
    BARC-014783-01660 G_(18) 55.60 41,560,487
    BARC-061717-17358 G_(18) 55.60 41,730,041
    BARC-044235-08650 G_(18) 55.60 42,206,429
    BARC-059239-15686 G_(18) 56.18 43,529,731
    BARC-056035-13999 G_(18) 56.71 45,468,441
    BARC-050493-09699 G_(18) 56.82 45,951,229
    BARCSOYSSR_18_1146 G_(18) 57.07 46,265,580
    Satt533 G_(18) 57.07 46,265,580
    BARCSOYSSR_18_1210 G_(18) 57.82 48,532,689
    Satt504 G_(18) 57.82 48,532,689
    BARCSOYSSR_18_1348 G_(18) 59.89 52,189,343
    Sat_185 G_(18) 59.89 52,189,343
    BARCSOYSSR_18_1349 G_(18) 59.90 52,210,836
    Sat_203 G_(18) 59.90 52,210,836
    BARCSOYSSR_18_1364 G_(18) 60.60 52,465,758
    Satt199 G_(18) 60.60 52,465,758
    BARCSOYSSR_18_1385 G_(18) 60.97 52,746,490
    Sat_260 G_(18) 60.97 52,746,490
    BARCSOYSSR_18_1418 G_(18) 63.44 53,445,942
    Satt012 G_(18) 63.44 53,445,942
    BARC-056635-14538 G_(18) 63.92 53,471,513
    BARCSOYSSR_18_1426 G_(18) 65.78 53,656,489
    Sat_164 G_(18) 65.78 53,656,489
    BARCSOYSSR_18_1431 G_(18) 66.39 53,769,539
    Satt517 G_(18) 66.39 53,769,539
    BARC-027694-06635 G_(18) 67.91 54,764,508
    BARC-050613-09770 G_(18) 69.50 54,942,320
    BARC-024489-04936 G_(18) 70.62 55,001,002
    BARC-055139-13077 G_(18) 71.46 55,458,709
    BARC-061783-18883 G_(18) 72.02 55,506,257
    BARC-048761-10703 G_(18) 72.84 56,086,706
    BARC-016867-02359 G_(18) 73.34 56,429,486
    BARC-018441-03188 G_(18) 73.80 56,429,542
    BARC-052045-11324 G_(18) 75.00 57,071,922
    BARC-026013-05225 G_(18) 75.64 57,185,832
    BARC-015063-02553 G_(18) 76.88 57,353,963
    BARC-008223-00022 G_(18) 78.05 57,436,269
    BARC-032277-08935 G_(18) 79.40 57,462,526
    BARC-041705-08069 G_(18) 80.96 57,781,784
    BARC-032785-09037 G_(18) 80.96 57,781,833
    BARCSOYSSR_18_1703 G_(18) 85.66 58,093,491
    Sct_199 G_(18) 85.66 58,093,491
    BARCSOYSSR_18_1708 G_(18) 85.98 58,136,286
    Satt472 G_(18) 85.98 58,136,286
    BARC-048095-10484 G_(18) 86.59 58,177,377
    BARC-038873-07372 G_(18) 87.30 58,438,994
    BARCSOYSSR_18_1750 G_(18) 89.37 58,722,839
    Satt191 G_(18) 89.37 58,722,839
    BARCSOYSSR_18_1767 G_(18) 91.08 58,879,563
    Sat_117 G_(18) 91.08 58,879,563
    BARC-010491-00654 G_(18) 93.00 59,279,444
    BARC-010495-00656 G_(18) 93.23 59,283,702
    BARC-024251-04812 G_(18) 94.30 59,472,425
    BARC-020069-04425 G_(18) 96.31 59,797,088
    BARC-062677-18004 G_(18) 97.32 59,995,654
    BARC-062769-18043 G_(18) 100.16 60,441,813
    BARCSOYSSR_18_1853 G_(18) 100.37 60,463,067
    Sct_187 G_(18) 100.37 60,463,067
    BARC-044363-08678 G_(18) 100.44 60,487,624
    BARCSOYSSR_18_1858 G_(18) 101.82 60,612,599
    Sat_064 G_(18) 101.82 60,612,599
    BARC-054735-12156 G_(18) 102.33 60,802,269
    BARC-013647-01216 G_(18) 103.22 60,909,921
    BARC-055537-13406 G_(18) 103.40 61,041,397
    BARC-039397-07314 G_(18) 103.55 61,188,102
    BARC-043995-08576 G_(18) 104.09 61,306,670
    BARC-064703-18782 G_(18) 105.53 61,480,202
    BARC-049989-09280 G_(18) 105.85 61,591,089
    BARC-017669-03102 G_(18) 107.09 62,046,576
    BARC-013305-00475 G_(18) 107.09 62,259,025
  • In certain embodiments, multiple marker loci that collectively make up the soybean cyst nematode resistance haplotype of interest are investigated. For example, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the various marker loci provided herein can comprise a soybean cyst nematode resistance haplotype. In some embodiments, the haplotype comprises: two or more marker locus comprising (a) at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G; (b) at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (0 at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group 0; (h) at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G; (i) at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G; (j) at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G; (k) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (l) at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (n) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or (o) at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
  • In one embodiment, the method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or in the genome of the first soybean germplasm at least one haplotype that is associated with the resistance, wherein the at least one haplotype comprises at least two of the various marker loci provided herein. For example, one is more likely to get PI88788 Rhg1 if A, T is selected at S08271-1 and P7659-2 respectively. S07158-1 and S07159-1 are used in combination with S08051-1 to distinguish PI437654 and Peking haplotype.
  • In certain embodiments, two or more marker loci or haplotypes can collectively make up a marker profile. The marker profile can comprise any two or more marker loci comprising: (a) at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G; (b) at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (f) at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G; (h) at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G; (i) at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G; (j) at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G; (k) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (l) at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (n) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (o) at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G; (p) any marker loci associated with the rhg1 locus on linkage group G; (q) any marker loci associated with the rhg2 locus on linkage group M; (r) any marker loci associated with the rhg4 locus on linkage group A2; and/or (s) any marker loci associated with resistance to soybean cyst nematode.
  • Any of the marker loci in any of the genomic loci disclosed herein can be combined in the marker profile. For example, the marker profile can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more marker loci or haplotypes associated with resistance to soybean cyst nematode provided herein.
  • In one embodiment, a method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or in the genome of the first soybean germplasm at least one marker profile that is associated with the resistance, wherein the at least one marker profile comprises at least two of the various marker loci provided herein.
  • Not only can one detect the various markers provided herein, it is recognized that one could detect any markers that are closely linked to the various markers discussed herein.
  • In addition to the markers discussed herein, information regarding useful soybean markers can be found, for example, on the USDA's Soybase website, available at www.soybase.org. One of skill in the art will recognize that the identification of favorable marker alleles may be germplasm-specific. The determination of which marker alleles correlate with resistance (or susceptibility) is determined for the particular germplasm under study. One of skill will also recognize that methods for identifying the favorable alleles are routine and well known in the art, and furthermore, that the identification and use of such favorable alleles is well within the scope of the invention.
  • Various methods are provided to identify soybean plants and/or germplasm with improved resistance to soybean cyst nematode. In one embodiment, the method of identifying comprises detecting at least one marker locus associated with resistance to soybean cyst nematode. The term “associated with” in connection with a relationship between a marker locus and a phenotype refers to a statistically significant dependence of marker frequency with respect to a quantitative scale or qualitative gradation of the phenotype. Thus, an allele of a marker is associated with a trait of interest when the allele of the marker locus and the trait phenotypes are found together in the progeny of an organism more often than if the marker genotypes and trait phenotypes segregated separately.
  • Any combination of the marker loci provided herein can be used in the methods to identify a soybean plant or soybean germplasm that displays improved resistance to soybean cyst nematode. Any one marker locus or any combination of the markers set forth in Table 1, or any closely linked marker can be used to aid in identifying and selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.
  • In one embodiment, a method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode is provided. The method comprises detecting in the genome of the first soybean plant or first soybean germplasm at least one marker locus that is associated with resistance. In such a method, the at least one marker locus comprises (a) at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G; (b) at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G; (c) at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G; (d) at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G; (e) at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G; (f) at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G; (g) at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G; (h) at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G; (i) at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G; (j) at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G; (k) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (l) at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; (n) at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or (o) at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
  • In other embodiments, two or more marker loci are detected in the method. In a specific embodiment, the germplasm is a soybean variety.
  • In other embodiments, the method further comprises crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm. In a further embodiment of the method, the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
  • In specific embodiments, the first soybean plant or first soybean germplasm comprises a soybean variety. Any soybean line known to the art or disclosed herein may be used. Non-limiting examples of soybean varieties and their associated soybean cyst nematode resistance alleles encompassed by the methods are provided herein.
  • In another embodiment, the detection method comprises amplifying at least one marker locus and detecting the resulting amplified marker amplicon. In such a method, amplifying comprises (a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm such that the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and (b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon. In such a method, the primer or primer pair can comprise a variant or fragment of one or more of the genomic loci provided herein.
  • In one embodiment, the method involves amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 1-171 or variants or fragments thereof. In one embodiment, the primer or primer pair can comprise a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof. In specific embodiments, the primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOS: SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 or variants or fragments thereof.
  • In a specific embodiment, the primer pair comprises SEQ ID NOS: 81 and 82; SEQ ID NOS: 87 and 88; SEQ ID NOS: 89 and 90; SEQ ID NOS: 91 and 92; SEQ ID NOS: 93 and 94; SEQ ID NOS:95 and 96; SEQ ID NOS: 97 and 98; SEQ ID NOS: 99 and 100; SEQ ID NOS: 101 and 102, SEQ ID NOS: 121 and 122; SEQ ID NO: 121 and 123; SEQ ID NO:124 and 125; SEQ ID NO: 126 and 127; SEQ ID NO: 128 and 129; SEQ ID NO: 130 and 131, SEQ ID NOS: 136 and 137; SEQ ID NOS: 140 and 141; SEQ ID NOS: 144 and 145; SEQ ID NOS: 148 and 149; SEQ ID NOS: 152 and 153; SEQ ID NOS: 156 and 157; SEQ ID NOS: 160 and 161; SEQ ID NOS: 164 and 165; or SEQ ID NOS:168 and 169.
  • In another embodiment, the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified. In such a method, the labeled nucleic acid probe can comprise a sequence comprising a variant or fragment of one or more of the genomic loci provided herein. In one embodiment, the labeled nucleic acid probe can comprise a sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof. In specific embodiments, the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOS: 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, 135 or variants or fragments thereof.
  • Non-limiting examples of primers, probes, genomic loci and amplicons that can be used in the methods and compositions provided herein are summarized in Tables 3, 4, 5 and 6, respectively.
  • TABLE 3
    Non-Limiting Examples of Primer Sequences.
    Linkage
    Group Primer SEQ ID Allele
    (ch) Marker ID Name NO Primer Sequence (Res/Sus)
    G S08271-1-Q2 A/T
    (P10355B-1)
    S08271-1  1 CATTGTTGCCAAGTAATAC
    F1 TACTATATAAATTC
    S08271-  2 TCAAGTATCGCGCAAGCTC
    R1
    S08271-  3 attcgcccttcatggtttct
    F2
    S08271-  4 ctgagtcttatcattctgtggattg
    F3
    S08271-  5 gcaagctcctgcaaggtatt
    R2
    S08271-  6 Catggtttctcttatcttatracattg
    R3a
    S08271-  7 CAATTCATGGTTTCTCTTAT
    R3a RACATT
    137362-  8 TCAAGTATCGCGCAAGCTC
    1
    137363-  9 CATGGTTTCTCTTATCTTAT
    2 RACATTG
    137364- 10 CAATTCATGGTTTCTCTTAT
    3 RACATT
    137365- 11 GCAAGCTCCTGCAAGGTAT
    F2 TAT
    72625- 12 CTTATCTTATRACATTGTTG
    R2 CCAAG
    137366- 13 TCTCTTATRACATTGTTGCC
    R2-2 AAG
    137367- 14 CCACTGTCCCTGCTCCTG
    F3
    137368- 15 GGTTTCTCTTATCTTATRAC
    R3 ATTGTTG
    137369- 16 CATGGTTTCTCTTATRACAT
    R3-3 TGTTG
    89472 17 CGCGCAAGCTCCTGCAAG
    GTATTATAT
    19392 18 CATGGTTTCTCTTATCTTAT
    RACATTGTTGCCAAG
    19393 19 CAATTCATGGTTTCTCTTAT
    RACATTGTTGCCAAG
    P10366B- 20 GACCTTGCGCGATACTTGA
    1R
    S08271- 21 tcaagtatcgcgcaagctc
    F4
    S08271- 22 cattgttgccaagtaatactactatataaat
    F1 tc
    S08271- 23 attcgcccttcatggtttct
    F2
    S08271- 24 ctgagtcttatcattctgtggattg
    F3
    S08271- 25 cattgttgccaagtaatactactatataaat
    F1 tc
    S08271- 26 Catggtttctcttatcttatracattg
    R3
    S08271- 27 CAATTCATGGTTTCTCTT
    R3 ATRACATT
    S08271- 28 tcaagtatcgcgcaagctc
    R1
    S08271- 29 gcaagctcctgcaaggtatt
    R2
    S08271- 30 gcaagctcctgcaaggtatt
    R2
    S08271- 31 tcaagtatcgcgcaagctc
    R1
    G P7659a-2 A/G
    (S08052-1-Q1)
    136879 32 ATGAAGCTCCACCATTTGC
    T
    136880 33 TGGGGGAACATATACCTTG
    AA
    136881 34 TGTCGGGTATGTTTCCATG
    A
    136882 35 CATGGGGGAACATATACCT
    TG
    136883 36 TGTGGTACATGGGGGAAC
    A
    88258 37 TTTCCATGAAGCTCCACCA
    TTTGCT
    88260 38 TGTCTATCCTGTAGGTGGC
    TATTAAGATGCTGA
    G 508051-1-Q1 GA/AC
    136874 39 TGGCAACAAAATCAGAACC
    A
    136875 40 TGTTTTTAAGCCCGATGGA
    G
    82585 41 TCCAGAAAGTGGGGTAAG
    AATGTCTGAGAA
    82586 42 GGCATGTTTTTAAGCCCGA
    antisense TGGAGTA
    82586 43 TACTCCATCGGGCTTAAAA
    ACATGCC
    136876, 44 ATGGCAACAAAATCAGAAC
    p7659A- CA
    1-F3
    136877, 45 TGGAAATTTCTCTGCAACC
    p7659A- A
    1-R3
    136878, 46 TGTTGATCTCGTGGTGGAA
    p7659A- A
    1-R4
    G S07158-1-Q1 TG/GT
    137377 47 AAGTTCCAATTGTTTCATCT
    AAATCC
    137378 48 CCGTCAATCACATGAGTCC
    A
    137375, 49 ACCACTTACTGTCATTTTGG
    p5219A- TTCTT
    1-F1
    137376, 50 TCCGTCAATCACATGAGTC
    p5219A- C
    1-R1
    137379, 51 CACCTTGTCACATTAGTTG
    p5219A- CTGA
    1-F3
    137380, 52 TCACATGAGTCCAAAATGA
    p5219A- AAAA
    1-R3
    G S07159-1-Q1 T/A
    136857,F 53 TGGTACCATGCCTCCCTTTA
    2
    136858, 54 CCATTTTGTATTCCCTCATG
    R2 C
    82575 55 TGTGGGCAGGAGGTTTAT
    GAGTTTATGGTA
    82576 56 CAATGAAGTTAAGCAAGTT
    AATGATGACCATTTTG
    136859, 57 TGGGCAGGAGGTTTATGA
    F3 GT
    136860, 58 GGCAATGGGGTACGAAGT
    R3 TT
    136861, 59 TTCTGTGGGCAGGAGGTTT
    F4 A
    136862, 60 GAAGAGCCTCTGGGCAAT
    R4 G
    G S06818-3-Q2 C/G
    142732 61 TCATTTGATCCTTATACCTG
    CACA
    142733 62 ACTTTTTAATCCGTTTTAAT
    CTCTGC
    S06818- 63 CATTTGATCCTTATACCTGC
    3-Q1F ACA
    S06818- 64 TGCAGTGTAGGACTAATAT
    3-Q1R GCGTTA
    S06818- 65 GAAGGATGATGACTGTTAT
    3-Q3F TCAGAATTT
    S06818- 66 GCAGTGTAGGACTAATATG
    3-Q3R CGTTAAAA
    G S06820-1-Q3 C/T
    142736 67 TGGGACTGACTGCTATGAC
    TGA
    142737 68 AGCTCGTGTACCAGCCTGA
    A
    S06820- 69 TTGGGAAAAGAAGTGCAT
    1-Q1F GG
    S06820- 70 CGTGTACCAGCCTGAAATG
    1-Q1R A
    S06820- 71 CATGTGGGACTGACTGCTA
    1-Q2F TG
    S06820- 72 TCGTGTACCAGCCTGAAAT
    1-Q2R G
    G S06821-1-Q2 A/C
    142740 73 GCCAAATTGAATCTAGGCA
    AA
    142741 74 TCACGTGTCCTCTCCAGAA
    A
    S06821- 75 AAAACTATAAATGAACTTG
    1-Q1F GGGTGA
    S06821- 76 GCTTTTCACGTGTCCTCTCC
    1-Q1R
    S06821- 77 TCATCACCTGATATGATCTT
    1-Q3F AATGGA
    S06821- 78 TGATGCTAGCTTTTCACGT
    1-Q3R GTC
    G S16001-001- C/A
    Q001
    S16001- 79 TTCCACCAACAAACTGGTG
    F001 A
    S16001- 80 CATTTTGACCATGCCCTTG
    R001
  • TABLE 4
    Non-Limiting Examples of Probe Sequences.
    (R) SEQ ID (R) SEQ ID
    Probe 1 or Probe 1 NO for Probe 2 or Probe 2 NO for
    Markers Name (S) Sequence Probe 1 Name (S) Sequence Probe 2
    S08271-1-Q2
    (P10355B-1)
    S08271- R TGGGTTTCAG  81 S08271-1- S TGGGTTTCTG  82
    1-PB1 ATAAC PB2 ATAACC
    S08271-1- 6FAM-  83
    PB1 TGGGTTTCA
    GATAAC
    S08271-1- 6FAM-  84
    PB3 accacggttatcTg
    aa
    S08271-1- VIC-  85
    PB2 TGGGTTTCT
    GATAACC
    S08271-1- VIC-  86
    PB4 accacggttatcAg
    aa
    P7659A-2
    (S08052-1-
    Q1)
    137434 R CTACATCTCC  87 137435 S TCTACATTTCC  88
    TCTTTG TCTTTG
    S08051-1-Q1
    (P7659A-1)
    141803 R CATTTTTCAT  89 141804 S CATTTTTCAGT  90
    CGCACTTT GCACTTT
    S07158-1-Q1
    (P5219A-1)
    125317 S CATATGTCAG  91 125318 R CATATTGCAG  92
    TACTATAAC TACTATAA
    S07159-1-Q1
    (P5219A-2)
    102398 S TGTTGATAAA  93 102399 R TGTTGATAAA  94
    CCATATATG CCTTATATG
    S06818-3-Q2
    142734 R CTTGCCTACA  95 142735 S CTTGCGTACA  96
    CATACA CATAC
    S06820-1-Q3
    142738 R TATCACGCAA  97 142739 S ATCACACAAC  98
    CCAGTTC CAGTTC
    S06821-1-Q2
    142742 R TCCTCTATTG  99 142743 S ATCCTCGATT 100
    AATCTT GAATCT
    S16001-001-
    Q001
    S16001- R atatgctaccaAt 101 S16001- S atatgctaccaCt 102
    001- acagc 001-X001 acagct
    X002
  • TABLE 5
    Non-Limiting Examples of Genomic Loci Comprising the Various Marker Loci
    Provided Herein.
    SEQ ID
    Marker NO
    Name (Res/Sus) Reference Sequence [Res/Sus] SEQ ID NO
    S08271-1- A/T CTGAAATGCAACGCAAATTCGAGTTTAGTAGAAACTTATCATCCAAAAT 103, 104
    Q2 TAAAATTGAAAACTTTAATACAAATGCACATTTTGGAGCCATTCATGTS respectively
    (P10355B- ATCTCTTGGTCTGAGTCTTATCATTCTGTGGATTGAATTCATGGTTTCTC
    1) TTATVACATTGTTGCCAAGTAATACTACTATATAAATTCAGATTTGGGTT
    TC[A/T]GATAACCGTGGTCGTTARTACTATATATATAATACCTTGCAGG
    AGCTTGCGCGATACTTGAAACAGGAGCAGGGACAGTGGAAAATAAAG
    GAGCCATAGCRCCATCTGCTTGCTTATGTAATGTAACCCAATCTGTCTAT
    ATTTYAATACACACCCCATTACGATAAAATTATGCTAGGGCCTAATTTG
    AATTGATTTCT
    P7659A-2 T/C CTCTGTATTTTATGGATGCTCATTGCTTGTGAATCATCATTGGGGGGTT 105, 106
    (S08052-1- GTAATAGCATGAAATGATGGAGAACAGGTGATTGAAGGCATATCTCAT respectively
    Q1 GTGGTACATGGGGGAACATATACCTTGAAAACTCACAGAACTATATAT
    TTTATTGAACTGTCTATCCTGTAGGTGGCTATTAAGATGCTGAGTTAAT
    CTACAT[T/C]TCCTCTTTGTATTAAAAAGTTGTTTCATGTACTAGCAAAT
    GGTGGAGCTTCATGGAAACATACCCGACATCTAAATTTCTTATTATTGT
    TGCTTTATCATTATTTTCTGTGGCCCAATTGATGTATTATGCCCCTATGTT
    TTACTATCTTATTGAATTCAGAAGTATTGATTGCAGGTGGATAATAAAG
    CTGCAGTCCTT
    S08051-1- GT/TC AATAGATCTAATTTGTTAAGCTTTATTTACCAGAGTTACCAAACCATCTG 107, 108
    Q1 TGAGAAATATCCTTCATTCCGTGAAAGATCTGAAAATGTTGATCTCGTG respectively
    (P7659A-1) GTGGAAATTTCTCTGCAACCATGGCATGTTTTTAAGCCCGATGGAGTAA
    GATAACTCTCTGGCACTCTTTAATTTATTTATGCTTTTTCAGGCATTTTTC
    A[GT][TC]GCACTTTTTGTGATATGGTTCTGATTTTGTTGCCATTAACAAT
    TTGCTTGGTACTTATTCTGTGACAGGTGATTTTATTCTCAGACATTCTTA
    CCCCACTTTCTGGAATGAATATACCCTTTGATATTGTGAAGGGTAAGGG
    TCCTGTTATATTTGATCCTATTCACACAGCTGCCCAGGTTGATCAAGTG
    AGGGAGTT
    S07158-1- GT/TG TTAAACAGTTAACAATATGTTTGCTAGCCTACACACAAATCATGATTCA 109, 110
    Q1 GTACACAACCATTTTGGTCCCTGAAAGTATATCACCTTGTCACATTAGTT respectively
    (P5219A-1) GCTGAAACTAAGGAAATACTAAATAAGTTCTAAAAGTTCCAATTGTTTC
    ATCTAAATCCTAAATTTAACCACTTACTGTCATTTTGGTTCTTAAACATAT
    [GT][TG]CAGTACTATAACTTAAATCAAACATTTTTTTTTTTTCATTTTGG
    ACTCATGTGATTGACGGATTTTACTTCGAAGAACTTATTTAGAAGTTTC
    ATAGGTAGTATGTGACAGCACCGTACAGTGTACACTTTCACAAACTAAA
    ACTAAATCGGTGGTTTACTCAATCATACTCAATAATTCAGAAAAGAATC
    ATACATAAA
    S07159-1- T/A AGACAGCCTATGTGTAACACTTAAAAGTTATCACCATGTGACCATGAAG 111, 112
    Q1 TCACAGGTTTGAGTTGTGGAATCAGCCTCTTGAAAATGCAAGGAAAGG respectively
    (P5219A-2) CTGTCTACTATACAGTATAAACCCACACAGAGATCTGACCGTTCTGTGG
    GCAGGAGGTTTATGAGTTTATGGTRCATGCCTCCCTTTATTTTGTTGATA
    AACC[T/A]TATATGGTACTAATAGCATGAGGGAATCAAAATGGTCATCA
    TTAACTTGCTTAACTTCATTGACGTATGTTATCTTGTCAAAGATATCATG
    AGGCATATAATAATGTTATAAAAAACTTACACACTATCAACACCTATTG
    GTGACCATTGTACAAGTGYCTATAATAAAGCCTGTAAACATAACKTACC
    AATGTTGAAAG
    S06818-3- G/C TACATATAGCATAAATTATCTAATTCTCTAATCTATACAAATCAAGGTTT 113, 114
    Q2 AATTACTCATTTGGTCTCTTTACCTGCACAATCTTTATGCTTTATTCCTTG respectively
    TATCTAGAAACTACTTGTTTTAATCTMTACACATATACTTTTTAATCCGT
    TTTAATCTCTGCAGTGTAGGACTAATATGCGTTAAAAAGTGTATGTGTA
    [G/C]GCAAGTAGTTTCTAGGCATAGGAACTAAAACGTAAAGATTGTGC
    AGGTATAAGGATCAAATGAGTAATTAAACCTAAAAAAAATTCTGAATA
    ACAGTCATCATCCTTCTATGAACTATCCTACCCTAGCATTTTTGGGATTG
    ACCGCTACATGCTACCATMCAAGATTGATAACTATGATTACCATATGCA
    GGAAAGGAT
    S06820-1- G/A TAGTTTTAGGGTTAGAATGAACCATGCTAGATTGTTGTCTTTACTTTAGT 115, 116
    Q3 ATTTTTTCATGTTTTTGAAATGTTAAGTGATGCTAGTTGAGTTTATGTTG respectively
    AAGATTTTTATTGTTCAGGCTGTTAATTACATGTGGGACTGACTGCTAT
    GACTGAGTCTTGGGAAAAGAAGTGCATGGCTTTATGTTTATGTAATATC
    AC[G/A]CAACCAGTTCATTTAAATCAATTTCCTGATAAAAGCATGCAAT
    TCATTTCAGGCTGGTACACGAGCTCTGAAAAGGAAGGCATGGGAGCA
    GCTGGCCTTTGAAGAGGGTATGTTAATTGTTATACGTYATTACTTTGGG
    GCTTTAGATGGGATGATCTTCAAAGATGTGCTCTTTTAGATGAATGGTA
    CAAAATAGAAAT
    S06821-1- T/G TATGAAGAAGCTGGAACTCCTGTTATTAAGGAGAAGGATGAGGAMAA 117, 118
    Q2 TTGTGGAAATATTGTCAATGATGAAGAACAGGTGATGCAAATTCCAAG respectively
    CCCATGCTCTATGTCATCATCACCTGATATGATCTTAATGGAGTTGAAA
    AAAGCCAAATTGAATCTAGGCAAAACTATAAATGAACTTGGGGTGATA
    CAATCCTC[T/G]ATTGAATCTTTGAATAAGAAGATGAAGAAGGAGAAA
    AATTTTCTGGAGAGGACACGTGAAAAGCTAGCATCAAAGTTTGCAGCA
    GAATCTGCTCAAGAGAGGGTCCAAGAGCAAACAAGATTGAATCCACCG
    GCCCCTCATGTAGAGTTCACCTTTGGTAACCCTGCWAATAATTTCAATT
    CTGATTCTGGGCAGTGCAA
    S16001- C/A CTCCTTTGCCAAGTCCCTKCAGAGCAAGTGCCCCAGAAGTGGAAATGA 119, 120
    001-Q001 CGATTTACTCGAACCCCTTGACCTTCAAACTCCTACCCATTTTGATAACC respectively
    TATACTTCCAGAATTTACTGGACAAAAAGGGTCTTCTCCATTCCGATCW
    GAAGCTGTTCAATGGTGATTCCACCAACAAACTGGTGAAGAAATATGC
    TACCA[C/A]TACAGCTGCATTCTTTAAAGACTTTGCCAAGGGCATGGTC
    AAAATGAGCAATATCAAGCCTCTAACAGGAAGCGAGGGGCAGATCAG
    AATCAATTGCAGRAAAGTCAATTAAGCATTAGCGTACTATATATGTCTA
    TCCATRCTTATATTTATCTCCAATGATCCATCTTTCTTTACAAAATTATGT
    ATTCTCTAATCTM
  • TABLE 6
    Non-limiting Examples of Amplicons Comprising the Various Marker
    Amplicon
    Linkage SEQ ID Amplicon
    Marker Group Primer Primer NO Amplicon Sequence Size
    Name (cm) 1 2 (R/S) [Res/Sus] (bp)
    S08271-1- G CATTGTT TCAAGTAT CATTGTTGCCAAGTAATACTACTATA 108
    Q2 GCCAAGT CGCGCAAG TAAATTCAGATTTGGGTTTC[A/T]GA
    (P10355B- AATACTA CTC (SEQ TAACCGTGGTCGTTARTACTATATAT
    1) CTATATA ID NO: ATAATACCTTGCAGGAGCTTGCGCG
    AATTC 137) ATACTTGA (SEQ ID NO: 138,
    (SEQ ID 139 respectively)
    NO 136)
    P7659A-2 G ATGAAGC TGGGGGA TGGGGGAACATATACCTTGAAAACT 149
    TCCACCA ACATATAC CACAGAACTATATATTTTATTGAACT
    TTTGCT CTTGAA GTCTATCCTGTAGGTGGCTATTAAG
    (SEQ ID (SEQ ID ATGCTGAGTTAATCTACAT[T/C]TCC
    NO 140)  NO 141) TCTTTGTATTAAAAAGTTGTTTCATG
    TACTAGCAAATGGTGGAGCTTCAT
    (SEQ ID NO 142, 143
    respectively)
    S08051-1- G TGGCAAC TGTTTTTAA TGTTTTTAAGCCCGATGGAGTAAGA 112
    Q1 AAAATCA GCCCGATG TAACTCTCTGGCACTCTTTAATTTAT
    (P7659A- GAACCA GAG (SEQ TTATGCTTTTTCAGGCATTTTTCA[GT]
    1) (SEQ ID ID NO  [TC]GACTTTTTGTGATATGGTTCT
    NO 144) 145) GATTTTGTTGCCA (SEQ ID NO 
    146, 147 respectively)
    S07158-1- G AAGTTCC CCGTCAAT AAGTTCCAATTGTTTCATCTAAATCC 130
    Q1 AATTGTT CACATGAG TAAATTTAACCACTTACTGTCATTTT
    (P5219A- TCATCTA TCCA (SEQ GGTTCTTAAACATAT[GT][TG]CAGT
    1) AATCC(SEQ ID NO  ACTATAACTTAAATCAAACATTTTTT
    ID NO 149) TTTTTTCATTTTGGACTCATGTGATT
    148) GACGG (SEQ ID NO 150, 151
    respectively)
    S07159-1- G TGGTACC CCATTTTGT TGGTRCATGCCTCCCTTTATTTTGTT  70
    Q1 ATGCCTC ATTCCCTC GATAAACC[T/A]TATATGGTACTAAT
    (P5219A- CCTTTA ATGC (SEQ AGCATGAGGGAATCAAAATGG
    2) (SEQ ID ID NO  (SEQ ID NO 154, 155 
    NO 152) 153) respectively)
    S06818-3- G TCATTTG ACTTTTTAA ACTTTTTAATCCGTTTTAATCTCTGC 127
    Q2 ATCCTTAT TCCGTTTTA AGTGTAGGACTAATATGCGTTAAAA
    ACCTGCA ATCTCTGC AGTGTATGTGTA[G/C]GCAAGTAGT
    CA (SEQ (SEQ ID  TTCTAGGCATAGGAACTAAAACGTA
    ID NO NO 157) AAGATTGTGCAGGTATAAGGATCAA
    156) ATGA (SEQ ID NO 158, 159
    respectively)
    506820-1- G TGGGACT AGCTCGTG TGGGACTGACTGCTATGACTGAGTC 135
    Q3 GACTGCT TACCAGCC TTGGGAAAAGAAGTGCATGGCTTTA
    ATGACTG TGAA TGTTTATGTAATATCAC[G/A]CAACC
    A (SEQ ID (SEQ ID  AGTTCATTTAAATCAATTTCCTGATA
    NO 160) NO 161) AAAGCATGCAATTCATTTCAGGCTG
    GTACACGAGCT (SEQ ID NO 
    162, 163 respectively)
    S06821-1- G GCCAAAT TCACGTGT GCCAAATTGAATCTAGGCAAAACTA 113
    Q2 TGAATCT CCTCTCCA TAAATGAACTTGGGGTGATACAATC
    AGGCAAA GAAA (SEQ CTC[T/G[ATTGAATCTTTGAATAAGA
    (SEQ ID ID NO  AGATGAAGAAGGAGAAAAATTTTCT
    NO 164) 165) GGAGAGGACACGTGA (SEQ ID NO
    166, 167 respectively)
    S16001- G TTCCACC CATTTTGA TTCCACCAACAAACTGGTGAAGAAA  82
    001-Q001 AACAAAC CCATGCCC TATGCTACCA[C/A]TACAGCTGCATT
    TGGTGA TTG (SEQ CTTTAAAGACTTTGCCAAGGGCATG
    (SEQ ID  ID NO  GTCAAAATG (SEQ ID NO 
    NO 168) 169) 170, 171, respectively)
  • In another embodiment, the method of detecting comprises DNA sequencing of at least one of the marker loci provided herein. As used herein, “sequencing” refers to sequencing methods for determining the order of nucleotides in a molecule of DNA. Any DNA sequencing method known in the art can be used in the methods provided herein. Non-limiting examples of DNA sequencing methods useful in the methods provided herein include Next Generation Sequencing (NGS) technologies, for example, as described in Egan, A. N, et al. (2012) American Journal of Botany 99(2):175-185; genotyping by sequencing (GBS) methods, for example, as described in Elshire, R. J., et al. (2011) PLoS ONE 6(5):e19379; Molecular Inversion Probe (MIP) genotyping, as described, for example, in Hardenbol, P., et al. (2003) Nature Biotechnology 21(6):673-678; or high throughput genotyping by whole-genome resequencing, as described, for example in Huang, X et al., (2009) Genome Research 19:1068-1076. Each of the above references is incorporated by reference in their entirety herein.
  • An active variant of any one of SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 can comprise a polynucleotide having at least 75%, 80% 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, or 135 as long as it is capable of amplifying and/or detecting the marker locus of interest. By “fragment” is intended a portion of the polynucleotide. A fragment or portion can comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, 100, 150, 200, 250, 300, 350, 400 contiguous nucleotides of SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 as long as it is capable of amplifying and/or detecting the marker locus of interest.
  • Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
  • Traits or markers are considered to be linked if they co-segregate. A 1/100 probability of recombination per generation is defined as a map distance of 1.0 centiMorgan (1.0 cM). Genetic elements or genes located on a single chromosome segment are physically linked. Two loci can be located in close proximity such that recombination between homologous chromosome pairs does not occur between the two loci during meiosis with high frequency, e.g., such that linked loci co-segregate at least about 90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more of the time. Genetic elements located within a chromosome segment are also genetically linked, typically within a genetic recombination distance of less than or equal to 50 centimorgans (cM), e.g., about 49, 40, 30, 20, 10, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25 cM or less. That is, two genetic elements within a single chromosome segment undergo recombination during meiosis with each other at a frequency of less than or equal to about 50%, e.g., about 49%, 40%, 30%, 20%, 10%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less. Closely linked markers display a cross over frequency with a given marker of about 10% or less (the given marker is within about 10 cM of a closely linked marker). In specific embodiments, a closely linked marker is within 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM or 1 cM of any given marker disclosed herein. In further embodiments, a marker associated with one of the markers disclosed herein can be within 75 Kb, 60 Kb, 50 Kb, 40 Kb, 30 Kb, 20K, 10 Kb, 5 Kb or less of the disclosed marker. Put another way, closely linked loci co-segregate at least about 90% of the time. Genetic linkage as evaluated by recombination frequency is impacted by the chromatin structure of the region comprising the loci. Typically, the region is assumed to have a euchromatin structure during initial evaluations. However, some regions, such are regions closer to centrosomes, have a heterochromatin structure. Without further information, the predicted physical distance between genetic map positions is based on the assumption that the region is euchromatic, however if the region comprises heterochromatin the markers may be physically closer together. With regard to physical position on a chromosome, closely linked markers can be separated, for example, by about 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb; 1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100 Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 2 Kb, about 1 Kb, about 500 nucleotides, about 250 nucleotides, or less.
  • When referring to the relationship between two genetic elements, such as a genetic element contributing to resistance and a proximal marker, “coupling” phase linkage indicates the state where the “favorable” allele at the resistance locus is physically associated on the same chromosome strand as the “favorable” allele of the respective linked marker locus. In coupling phase, both favorable alleles are inherited together by progeny that inherit that chromosome strand. In “repulsion” phase linkage, the “favorable” allele at the locus of interest (e.g., a QTL for resistance) is physically linked with an “unfavorable” allele at the proximal marker locus, and the two “favorable” alleles are not inherited together (i.e., the two loci are “out of phase” with each other).
  • Markers are used to define a specific locus on the soybean genome. Each marker is therefore an indicator of a specific segment of DNA, having a unique nucleotide sequence. Map positions provide a measure of the relative positions of particular markers with respect to one another. When a trait is stated to be linked to a given marker it will be understood that the actual DNA segment whose sequence affects the trait generally co-segregates with the marker. More precise and definite localization of a trait can be obtained if markers are identified on both sides of the trait. By measuring the appearance of the marker(s) in progeny of crosses, the existence of the trait can be detected by relatively simple molecular tests without actually evaluating the appearance of the trait itself, which can be difficult and time-consuming because the actual evaluation of the trait requires growing plants to a stage and/or under environmental conditions where the trait can be expressed. Molecular markers have been widely used to determine genetic composition in soybeans.
  • Favorable genotypes associated with at least trait of interest may be identified by one or more methodologies. In some examples one or more markers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs, SNPs, indels, padlock probes, molecular inversion probes, microarrays, sequencing, and the like. In some methods, a target nucleic acid is amplified prior to hybridization with a probe. In other cases, the target nucleic acid is not amplified prior to hybridization, such as methods using molecular inversion probes (see, for example Hardenbol et al. (2003) Nat Biotech 21:673-678). In some examples, the genotype related to a specific trait is monitored, while in other examples, a genome-wide evaluation including but not limited to one or more of marker panels, library screens, association studies, microarrays, gene chips, expression studies, or sequencing such as whole-genome resequencing and genotyping-by-sequencing (GBS) may be used. In some examples, no target-specific probe is needed, for example by using sequencing technologies, including but not limited to next-generation sequencing methods (see, for example, Metzker (2010) Nat Rev Genet. 11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such as sequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina Genome Analyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation (e.g., SOLiD from Applied Biosystems, and Polnator system from Azco Biotech), and single molecule sequencing (SMS or third-generation sequencing) which eliminate template amplification (e.g., Helicos system, and PacBio RS system from Pacific BioSciences). Further technologies include optical sequencing systems (e.g., Starlight from Life Technologies), and nanopore sequencing (e.g., GridION from Oxford Nanopore Technologies). Each of these may be coupled with one or more enrichment strategies for organellar or nuclear genomes in order to reduce the complexity of the genome under investigation via PCR, hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoS ONE 6:e19379), and expression methods. In some examples, no reference genome sequence is needed in order to complete the analysis.
  • The use of marker assisted selection (MAS) to select a soybean plant or germplasm which has a certain marker locus, haplotype or marker profile is provided. For instance, in certain examples a soybean plant or germplasm possessing a certain predetermined favorable marker locus or haplotype will be selected via MAS. In certain other examples, a soybean plant or germplasm possessing a certain predetermined favorable marker profile will be selected via MAS.
  • Using MAS, soybean plants or germplasm can be selected for markers or marker alleles that positively correlate with soybean cyst nematode resistance, without actually raising soybean and measuring for resistance (or, contrawise, soybean plants can be selected against if they possess markers that negatively correlate with resistance). MAS is a powerful tool to select for desired phenotypes and for introgressing desired traits into cultivars of soybean (e.g., introgressing desired traits into elite lines). MAS is easily adapted to high throughput molecular analysis methods that can quickly screen large numbers of plant or germplasm genetic material for the markers of interest and is much more cost effective than raising and observing plants for visible traits.
  • In some embodiments, the molecular markers or marker loci are detected using a suitable amplification-based detection method. In these types of methods, nucleic acid primers are typically hybridized to the conserved regions flanking the polymorphic marker region. In certain methods, nucleic acid probes that bind to the amplified region are also employed. In general, synthetic methods for making oligonucleotides, including primers and probes, are well known in the art. For example, oligonucleotides can be synthesized chemically according to the solid phase phosphoramidite triester method described by Beaucage and Caruthers (1981) Tetrahedron Letts 22:1859-1862, e.g., using a commercially available automated synthesizer, e.g., as described in Needham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168. Oligonucleotides, including modified oligonucleotides, can also be ordered from a variety of commercial sources known to persons of skill in the art.
  • It will be appreciated that suitable primers and probes to be used can be designed using any suitable method. It is not intended that the invention be limited to any particular primer, primer pair or probe. For example, primers can be designed using any suitable software program, such as LASERGENE® or Primer3.
  • It is not intended that the primers be limited to generating an amplicon of any particular size. For example, the primers used to amplify the marker loci and alleles herein are not limited to amplifying the entire region of the relevant locus. In some embodiments, marker amplification produces an amplicon at least 20 nucleotides in length, or alternatively, at least 50 nucleotides in length, or alternatively, at least 100 nucleotides in length, or alternatively, at least 200 nucleotides in length.
  • Non-limiting examples of polynucleotide primers useful for detecting the marker loci provided herein are provided in Table 3 and include, for example, SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 or variants or fragments thereof.
  • PCR, RT-PCR, and LCR are in particularly broad use as amplification and amplification-detection methods for amplifying nucleic acids of interest (e.g., those comprising marker loci), facilitating detection of the markers. Details regarding the use of these and other amplification methods are well known in the art and can be found in any of a variety of standard texts. Details for these techniques can also be found in numerous journal and patent references, such as Mullis, et al. (1987) U.S. Pat. No. 4,683,202; Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47; Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173; Guatelli, et al., (1990) Proc. Natl. Acad. Sci. USA87:1874; Lomeli, et al., (1989) J. Clin. Chem. 35:1826; Landegren, et al., (1988) Science 241:1077-1080; Van Brunt, (1990) Biotechnology 8:291-294; Wu and Wallace, (1989) Gene 4:560; Barringer, et al., (1990) Gene 89:117, and Sooknanan and Malek, (1995) Biotechnology 13:563-564.
  • Such nucleic acid amplification techniques can be applied to amplify and/or detect nucleic acids of interest, such as nucleic acids comprising marker loci. Amplification primers for amplifying useful marker loci and suitable probes to detect useful marker loci or to genotype SNP alleles are provided. For example, exemplary primers and probes are provided in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 and in Tables 3 and 4, and the genomic loci comprising the various marker loci provided herein are provided in SEQ ID NOS: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 and in Table 5. Non-limiting examples of amplicon sequences comprising the marker loci provided herein are provided in Table 6. However, one of skill will immediately recognize that other primer and probe sequences could also be used. For instance primers to either side of the given primers can be used in place of the given primers, so long as the primers can amplify a region that includes the allele to be detected, as can primers and probes directed to other SNP marker loci. Further, it will be appreciated that the precise probe to be used for detection can vary, e.g., any probe that can identify the region of a marker amplicon to be detected can be substituted for those examples provided herein. Further, the configuration of the amplification primers and detection probes can, of course, vary. Thus, the compositions and methods are not limited to the primers and probes specifically recited herein.
  • In certain examples, probes will possess a detectable label. Any suitable label can be used with a probe. Detectable labels suitable for use with nucleic acid probes include, for example, any composition detectable by spectroscopic, radioisotopic, photochemical, biochemical, immunochemical, electrical, optical, or chemical means. Useful labels include biotin for staining with labeled streptavidin conjugate, magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetric labels. Other labels include ligands, which bind to antibodies labeled with fluorophores, chemiluminescent agents, and enzymes. A probe can also constitute radiolabelled PCR primers that are used to generate a radiolabelled amplicon. Labeling strategies for labeling nucleic acids and corresponding detection strategies can be found, e.g., in Haugland (1996) Handbook of Fluorescent Probes and Research Chemicals Sixth Edition by Molecular Probes, Inc. (Eugene Oreg.); or Haugland (2001) Handbook of Fluorescent Probes and Research Chemicals Eighth Edition by Molecular Probes, Inc. (Eugene Oreg.).
  • Detectable labels may also include reporter-quencher pairs, such as are employed in Molecular Beacon and TaqMan™ probes. The reporter may be a fluorescent organic dye modified with a suitable linking group for attachment to the oligonucleotide, such as to the terminal 3′ carbon or terminal 5′ carbon. The quencher may also be an organic dye, which may or may not be fluorescent, depending on the embodiment. Generally, whether the quencher is fluorescent or simply releases the transferred energy from the reporter by non-radiative decay, the absorption band of the quencher should at least substantially overlap the fluorescent emission band of the reporter to optimize the quenching. Non-fluorescent quenchers or dark quenchers typically function by absorbing energy from excited reporters, but do not release the energy radiatively.
  • Selection of appropriate reporter-quencher pairs for particular probes may be undertaken in accordance with known techniques. Fluorescent and dark quenchers and their relevant optical properties from which exemplary reporter-quencher pairs may be selected are listed and described, for example, in Berlman, Handbook of Fluorescence Spectra of Aromatic Molecules, 2nd ed., Academic Press, New York, 1971, the content of which is incorporated herein by reference. Examples of modifying reporters and quenchers for covalent attachment via common reactive groups that can be added to an oligonucleotide in the present invention may be found, for example, in Haugland, Handbook of Fluorescent Probes and Research Chemicals, Molecular Probes of Eugene, Oreg., 1992, the content of which is incorporated herein by reference.
  • In certain examples, reporter-quencher pairs are selected from xanthene dyes including fluoresceins and rhodamine dyes. Many suitable forms of these compounds are available commercially with substituents on the phenyl groups, which can be used as the site for bonding or as the bonding functionality for attachment to an oligonucleotide. Another useful group of fluorescent compounds for use as reporters are the naphthylamines, having an amino group in the alpha or beta position. Included among such naphthylamino compounds are 1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include 3-phenyl-7-isocyanatocoumarin; acridines such as 9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide; benzoxadiazoles; stilbenes; pyrenes and the like. In certain other examples, the reporters and quenchers are selected from fluorescein and rhodamine dyes. These dyes and appropriate linking methodologies for attachment to oligonucleotides are well known in the art.
  • Suitable examples of reporters may be selected from dyes such as SYBR green, 5-carboxyfluorescein (5-FAM™ available from Applied Biosystems of Foster City, Calif.), 6-carboxyfluorescein (6-FAM), tetrachloro-6-carboxyfluorescein (TET), 2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein, hexachloro-6-carboxyfluorescein (HEX), 6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TET™ available from Applied Biosystems), carboxy-X-rhodamine (ROX), 6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOE™ available from Applied Biosystems), VIC™ dye products available from Molecular Probes, Inc., NED™ dye products available from Applied Biosystems, and the like. Suitable examples of quenchers may be selected from 6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoic acid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0™, BHQ-1™, BHQ-2™, and BHQ-3™, each of which are available from Biosearch Technologies, Inc. of Novato, Calif., QSY-7™, QSY-9™, QSY-21™ and QSY-35™, each of which are available from Molecular Probes, Inc., and the like.
  • In one aspect, real time PCR or LCR is performed on the amplification mixtures described herein, e.g., using molecular beacons or TaqMan™ probes. A molecular beacon (MB) is an oligonucleotide which, under appropriate hybridization conditions, self-hybridizes to form a stem and loop structure. The MB has a label and a quencher at the termini of the oligonucleotide; thus, under conditions that permit intra-molecular hybridization, the label is typically quenched (or at least altered in its fluorescence) by the quencher. Under conditions where the MB does not display intra-molecular hybridization (e.g., when bound to a target nucleic acid, such as to a region of an amplicon during amplification), the MB label is unquenched. Details regarding standard methods of making and using MBs are well established in the literature and MBs are available from a number of commercial reagent sources. See also, e.g., Leone, et al., (1995) Molecular beacon probes combined with amplification by NASBA enable homogenous real-time detection of RNA, Nucleic Acids Res. 26:2150-2155; Tyagi and Kramer, (1996) Molecular beacons: probes that fluoresce upon hybridization, Nature Biotechnology 14:303-308; Blok and Kramer, (1997) Amplifiable hybridization probes containing a molecular switch, Mol Cell Probes 11:187-194; Hsuih. et al., (1997) Novel, ligation-dependent PCR assay for detection of hepatitis C in serum, J Clin Microbiol 34:501-507; Kostrikis, et al., (1998) Molecular beacons: spectral genotyping of human alleles, Science 279:1228-1229; Sokol, et al., (1998) Real time detection of DNA:RNA hybridization in living cells, Proc. Natl. Acad. Sci. U.S.A. 95:11538-11543; Tyagi, et al., (1998) Multicolor molecular beacons for allele discrimination, Nature Biotechnology 16:49-53; Bonnet, et al. (1999) Thermodynamic basis of the chemical specificity of structured DNA probes, Proc. Natl. Acad. Sci. U.S.A. 96:6171-6176; Fang, et al. (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies, J. Am. Chem. Soc. 121:2921-2922; Marras, et al., (1999) Multiplex detection of single-nucleotide variation using molecular beacons, Genet. Anal. Biomol. Eng. 14:151-156; and Vet, et al. (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons, Proc. Natl. Acad. Sci. U.S.A. 96:6394-6399. Additional details regarding MB construction and use is found in the patent literature, e.g., U.S. Pat. Nos. 5,925,517; 6,150,097; and 6,037,130.
  • Another real-time detection method is the 5′-exonuclease detection method, also called the TaqMan™ assay, as set forth in U.S. Pat. Nos. 5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is hereby incorporated by reference in its entirety. In the TaqMan™ assay, a modified probe, typically 10-25 nucleic acids in length, is employed during PCR which binds intermediate to or between the two members of the amplification primer pair. The modified probe possesses a reporter and a quencher and is designed to generate a detectable signal to indicate that it has hybridized with the target nucleic acid sequence during PCR. As long as both the reporter and the quencher are on the probe, the quencher stops the reporter from emitting a detectable signal. However, as the polymerase extends the primer during amplification, the intrinsic 5′ to 3′ nuclease activity of the polymerase degrades the probe, separating the reporter from the quencher, and enabling the detectable signal to be emitted. Generally, the amount of detectable signal generated during the amplification cycle is proportional to the amount of product generated in each cycle.
  • It is well known that the efficiency of quenching is a strong function of the proximity of the reporter and the quencher, i.e., as the two molecules get closer, the quenching efficiency increases. As quenching is strongly dependent on the physical proximity of the reporter and quencher, the reporter and the quencher are preferably attached to the probe within a few nucleotides of one another, usually within 30 nucleotides of one another, more preferably with a separation of from about 6 to 16 nucleotides. Typically, this separation is achieved by attaching one member of a reporter-quencher pair to the 5′ end of the probe and the other member to a nucleotide about 6 to 16 nucleotides away, in some cases at the 3′ end of the probe.
  • Separate detection probes can also be omitted in amplification/detection methods, e.g., by performing a real time amplification reaction that detects product formation by modification of the relevant amplification primer upon incorporation into a product, incorporation of labeled nucleotides into an amplicon, or by monitoring changes in molecular rotation properties of amplicons as compared to unamplified precursors (e.g., by fluorescence polarization).
  • Further, it will be appreciated that amplification is not a requirement for marker detection—for example, one can directly detect unamplified genomic DNA simply by performing a Southern blot on a sample of genomic DNA. Procedures for performing Southern blotting, amplification e.g., (PCR, LCR, or the like), and many other nucleic acid detection methods are well established and are taught, e.g., in Sambrook, et al., Molecular Cloning—A Laboratory Manual (3d ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”)) and PCR Protocols A Guide to Methods and Applications (Innis, et al., eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Additional details regarding detection of nucleic acids in plants can also be found, e.g., in Plant Molecular Biology (1993) Croy (ed.) BIOS Scientific Publishers, Inc.
  • Other techniques for detecting SNPs can also be employed, such as allele specific hybridization (ASH). ASH technology is based on the stable annealing of a short, single-stranded, oligonucleotide probe to a completely complementary single-stranded target nucleic acid. Detection is via an isotopic or non-isotopic label attached to the probe. For each polymorphism, two or more different ASH probes are designed to have identical DNA sequences except at the polymorphic nucleotides. Each probe will have exact homology with one allele sequence so that the range of probes can distinguish all the known alternative allele sequences. Each probe is hybridized to the target DNA. With appropriate probe design and hybridization conditions, a single-base mismatch between the probe and target DNA will prevent hybridization.
  • Real-time amplification assays, including MB or TaqMan™ based assays, are especially useful for detecting SNP alleles. In such cases, probes are typically designed to bind to the amplicon region that includes the SNP locus, with one allele-specific probe being designed for each possible SNP allele. For instance, if there are two known SNP alleles for a particular SNP locus, “A” or “C,” then one probe is designed with an “A” at the SNP position, while a separate probe is designed with a “C” at the SNP position. While the probes are typically identical to one another other than at the SNP position, they need not be. For instance, the two allele-specific probes could be shifted upstream or downstream relative to one another by one or more bases. However, if the probes are not otherwise identical, they should be designed such that they bind with approximately equal efficiencies, which can be accomplished by designing under a strict set of parameters that restrict the chemical properties of the probes. Further, a different detectable label, for instance a different reporter-quencher pair, is typically employed on each different allele-specific probe to permit differential detection of each probe. In certain examples, each allele-specific probe for a certain SNP locus is 11-20 nucleotides in length, dual-labeled with a florescence quencher at the 3′ end and either the 6-FAM (6-carboxyfluorescein) or VIC (4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′ end.
  • To effectuate SNP allele detection, a real-time PCR reaction can be performed using primers that amplify the region including the SNP locus, for instance the sequences listed in Table 5, the reaction being performed in the presence of all allele-specific probes for the given SNP locus. By then detecting signal for each detectable label employed and determining which detectable label(s) demonstrated an increased signal, a determination can be made of which allele-specific probe(s) bound to the amplicon and, thus, which SNP allele(s) the amplicon possessed. For instance, when 6-FAM- and VIC-labeled probes are employed, the distinct emission wavelengths of 6-FAM (518 nm) and VIC (554 nm) can be captured. A sample that is homozygous for one allele will have fluorescence from only the respective 6-FAM or VIC fluorophore, while a sample that is heterozygous at the analyzed locus will have both 6-FAM and VIC fluorescence.
  • The KASPar® and Illumina® Detection Systems are additional examples of commercially-available marker detection systems. KASPar® is a homogeneous fluorescent genotyping system which utilizes allele specific hybridization and a unique form of allele specific PCR (primer extension) in order to identify genetic markers (e.g. a particular SNP locus associated with soybean cyst nematode resistance). Illumina® detection systems utilize similar technology in a fixed platform format. The fixed platform utilizes a physical plate that can be created with up to 384 markers. The Illumina® system is created with a single set of markers that cannot be changed and utilizes dyes to indicate marker detection.
  • These systems and methods represent a wide variety of available detection methods which can be utilized to detect markers associated with improved resistance to soybean cyst nematode, but any other suitable method could also be used.
  • Introgression of soybean cyst nematode resistance into non-resistant or less-resistant soybean germplasm is provided. Any method for introgressing one or more marker loci into soybean plants known to one of skill in the art can be used. Typically, a first soybean germplasm that contains soybean cyst nematode resistance derived from a particular marker locus, haplotype or marker profile and a second soybean germplasm that lacks such resistance derived from the marker locus, haplotype or marker profile are provided. The first soybean germplasm may be crossed with the second soybean germplasm to provide progeny soybean germplasm. These progeny germplasm are screened to determine the presence of soybean cyst nematode resistance derived from the marker locus, haplotype or marker profile, and progeny that tests positive for the presence of resistance derived from the marker locus, haplotype or marker profile are selected as being soybean germplasm into which the marker locus, haplotype or marker profile has been introgressed. Methods for performing such screening are well known in the art and any suitable method can be used.
  • One application of MAS is to use the resistance markers, haplotypes or marker profiles to increase the efficiency of an introgression or backcrossing effort aimed at introducing a resistance trait into a desired (typically high yielding) background. In marker assisted backcrossing of specific markers from a donor source, e.g., to an elite genetic background, one selects among backcross progeny for the donor trait and then uses repeated backcrossing to the elite line to reconstitute as much of the elite background's genome as possible.
  • Thus, the markers and methods can be utilized to guide marker assisted selection or breeding of soybean varieties with the desired complement (set) of allelic forms of chromosome segments associated with superior agronomic performance (resistance, along with any other available markers for yield, disease tolerance, etc.). Any of the disclosed marker loci, marker alleles, haplotypes, or marker profiles can be introduced into a soybean line via introgression, by traditional breeding (or introduced via transformation, or both) to yield a soybean plant with superior agronomic performance. The number of alleles associated with resistance that can be introduced or be present in a soybean plant ranges from 1 to the number of alleles disclosed herein, each integer of which is incorporated herein as if explicitly recited.
  • The markers and methods provided herein can also be utilized to guide marker assisted selection or breeding of soybean varieties comprising other soybean cyst nematode resistance markers or alleles to create a molecular stack for soybean cyst nematode resistance. For example, any of the marker loci provided herein can be introduced into a soybean line having one or more of the soybean cyst nematode resistance loci rhg1, rhg2, rhg3 or rhg5. In one embodiment, any one or more of the marker loci provided herein can be stacked with the rhg1 locus. In another embodiment, any one or more of the marker loci provided herein can be stacked with the rhg2 locus. In a further embodiment, any one or more of the marker loci provided herein can be stacked with the rhg1 and rhg2 loci.
  • This also provides a method of making a progeny soybean plant and these progeny soybean plants, per se. The method comprises crossing a first parent soybean plant with a second soybean plant and growing the female soybean plant under plant growth conditions to yield soybean plant progeny. Methods of crossing and growing soybean plants are well within the ability of those of ordinary skill in the art. Such soybean plant progeny can be assayed for alleles associated with resistance and, thereby, the desired progeny selected. Such progeny plants or seed can be sold commercially for soybean production, used for food, processed to obtain a desired constituent of the soybean, or further utilized in subsequent rounds of breeding. At least one of the first or second soybean plants is a soybean plant in that it comprises at least one of the marker loci or marker profiles, such that the progeny are capable of inheriting the marker locus or marker profile.
  • Often, a method is applied to at least one related soybean plant such as from progenitor or descendant lines in the subject soybean plants pedigree such that inheritance of the desired resistance can be traced. The number of generations separating the soybean plants being subject to the methods provided herein will generally be from 1 to 20, commonly 1 to 5, and typically 1, 2, or 3 generations of separation, and quite often a direct descendant or parent of the soybean plant will be subject to the method (i.e., 1 generation of separation).
  • Genetic diversity is important for long term genetic gain in any breeding program. With limited diversity, genetic gain will eventually plateau when all of the favorable alleles have been fixed within the elite population. One objective is to incorporate diversity into an elite pool without losing the genetic gain that has already been made and with the minimum possible investment. MAS provides an indication of which genomic regions and which favorable alleles from the original ancestors have been selected for and conserved over time, facilitating efforts to incorporate favorable variation from exotic germplasm sources (parents that are unrelated to the elite gene pool) in the hopes of finding favorable alleles that do not currently exist in the elite gene pool.
  • For example, the markers, haplotypes, primers, probes, and marker profiles can be used for MAS in crosses involving elite×exotic soybean lines by subjecting the segregating progeny to MAS to maintain major yield alleles, along with the resistance marker alleles herein.
  • As an alternative to standard breeding methods of introducing traits of interest into soybean (e.g., introgression), transgenic approaches can also be used to create transgenic plants with the desired traits. In these methods, exogenous nucleic acids that encode a desired marker loci, marker profile or haplotype are introduced into target plants or germplasm. For example, a nucleic acid that codes for a resistance trait is cloned, e.g., via positional cloning, and introduced into a target plant or germplasm.
  • Experienced plant breeders can recognize resistant soybean plants in the field, and can select the resistant individuals or populations for breeding purposes or for propagation. In this context, the plant breeder recognizes “resistant” and “non-resistant” or “susceptible” soybean plants. However, plant resistance is a phenotypic spectrum consisting of extremes in resistance and susceptibility, as well as a continuum of intermediate resistance phenotypes. Evaluation of these intermediate phenotypes using reproducible assays are of value to scientists who seek to identify genetic loci that impart resistance, to conduct marker assisted selection for resistant populations, and to use introgression techniques to breed a resistance trait into an elite soybean line, for example.
  • By “improved resistance” is intended that the plants show a decrease in the disease symptoms that are the outcome of plant exposure to soybean cyst nematode. That is, the damage caused by soybean cyst nematode is prevented, or alternatively, the disease symptoms caused by soybean cyst nematode is minimized or lessened. Thus, improved resistance to soybean cyst nematode can result in reduction of the disease symptoms by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater. Hence, the methods provided herein can be utilized to protect plants from soybean cyst nematode.
  • Screening and selection of soybean cyst nematode resistant soybean plants may be performed, for example, by exposing plants to soybean cyst nematode and selecting those plants showing resistance to soybean cyst nematode. Various assays can be used to measure resistance or improved resistance to soybean cyst nematode. For example, soybean cyst nematode resistance can be determined by visual observations after plant exposure to a particular race of soybean cyst nematode, such as race 1, 2, 3, 5 or 14. Scores range from 1 to 9 and indicate visual observations of resistance as compared to other genotypes in the test. A score of 1 indicates soybean cyst nematode are able to infect the plant and cause yield loss, while a score of 9 indicates soybean cyst nematode resistance. Preliminary scores are reported as double digits, for example, ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.
  • Non-limiting examples of soybean cyst nematode resistance phenotypic screening are described in detail below.
  • Multiple populations of Heterodera glycines are maintained and increased on host plants. These populations are used to identify, purify, and characterize elite soybean varieties for resistance to soybean cyst nematode. The following races of soybean cyst nematode are maintained: Race 1 (Type HG 2.5), Race 2 (Type HG 1.2.5.7), Race 3 (Type HG 0 or Type HG 7), Race 5 (Type HG 2.5.7), and Race 14 (Type HG 1.3.6.7).
  • Eggs or second stage juveniles (J2) are used to inoculate host plants to increase their population. Soybean cyst nematode infestation requires a minimum 35 days before the cysts reach maturity and can be used to inoculate soybean experiments. Cyst eggs/J2 inoculant is harvested through a series of washings, grindings, and screenings. Screens are used progressing from larger to smaller sizes, ending with a #500 (25 μm) screen.
  • Soybean plants are grown in cones. Cones are long containers approximately 12 inches long and 1.5 inches in diameter at the top (e.g., Ray Leach Cone-Tainers™). The cone is designed to easily remove the root mass. Three to seven days after planting, an inoculum channel is made in the cone containing the experimental line by poking a 4 inch hole with a 10 ml pipette tip. One ml of inoculum is dispensed into the channel. The plants are watered manually for the duration of the test, with watering being moderately light during the first 3-5 days until J2 infects the roots.
  • Plants are scored approximately 28-35 days following inoculation when cyst reproduction on susceptible checks is sufficiently high. Plants are removed from their cones and the soil is removed from the roots by gently dipping the roots into a bucket of water. The plants are screened to identify native resistance to one or more of the five races of soybean cyst nematode inoculated using a combination of three methods (1) visual 9-6-1 score; (2) visual full count; and/or (3) microscope count score depending on the stage of the line when screened. In general, lines earlier in the development cycle (R1-R2) are screened by the visual 9-6-1 method, and lines that have progressed to later development phases (R3-R5) are screened by the visual full count and/or microscope count method(s).
  • One typical phenotyping method is a visual evaluation of the roots. Susceptible checks are first evaluated for the development of cysts on the root system. These counts are recorded and averaged across the experiment to determine the susceptible (SUS) check average. Roots from the test plants are then scored based on a comparison with the average of the susceptible checks as follows:
  • 9=0-15% of the susceptible checks average
  • 6=16-40% of the susceptible checks average
  • 1=≧41% of the susceptible checks average
    • Visual Counts:
  • In this method, known checks are counted and reported in full. Observed cysts on the test plants are counted for comparison to the susceptible check plant scores. Cyst counts are converted to 1-9 scores based on the female index (FI). The female index (FI) is the percentage of the number of females cysts produced on each experimental line divided by the number produced on a standard susceptible soybean check, then the result is multiplied by 100. A low FI (<10) means that the soybean cyst nematode population is not able to reproduce well on the test line, a high FI means that the soybean cyst nematode population is able to reproduce well on the test line.
    • Microscope Counts:
  • Cysts counts for soybean cyst nematode assays for checks and experimental line are determined by washing cysts from roots and counting the number of cysts under the microscope.
  • At about 28-35 days after inoculation, roots from the susceptible check controls are examined for yellow cysts to assess whether to begin the process of evaluating the test. Experimental lines are compared with known standard checks. Once adequate levels of cysts are detected on the check varieties, plants from the test lines are removed from cones one at a time. Soil is removed from roots by gently dipping the roots into a bucket of water. The root tissue is placed on a 850 micron (#20) pore sieve stacked over a 250 micron (#60) pore sieve and sprayed with a jet of water to dislodge cysts from the roots. Collected cysts are rinsed from the #60 sieve into a clean labeled cup using no more than 30 mls of additional water.
  • Once all the samples are collected, each sample is counted using a gridded counting dish under a stereo microscope. The number of cysts counted are recorded for each sample. Cyst counts on the test plants are converted to the 1-9 scoring scale based on the female index (FI) described above.
  • The following exemplary soybean cyst nematode checks can be planted and used to monitor cyst development:
  • TABLE 7
    Exemplary soybean cyst nematode checks.
    Race 1 Race 2 Race 3 Race 5 Race 14
    92B12 RES 95M60 RES 9182 RES 92B12 RES 9182 RES
    9281 SUS 9281 SUS 9281 SUS 9281 SUS 9281 SUS
    9234 RES PI437654 RES 9234 RES 9234 RES 9234 SUS
    9392 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS
    91M12 MR 9234 MR 93B15 MR 91M12 SUS 93B15 MR
    RES = Resistant; SUS = Susceptible; and, MR = Moderately Resistant
  • In some examples, a kit or an automated system for detecting marker loci, haplotypes, and marker profiles, and/or correlating the marker loci, haplotypes, and marker profiles with a desired phenotype (e.g., soybean cyst nematode resistance) are provided. As used herein, “kit” refers to a set of reagents for the purpose of performing the various methods of detecting or identifying herein, more particularly, the identification and/or the detection of a soybean plant or germplasm having improved resistance to soybean cyst nematode.
  • In one embodiment, a kit for detecting or selecting at least one soybean plant or soybean germplasm with improved resistance to soybean cyst nematode is provided. Such a kit comprises (a) primers or probes for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein at least one of the primers and probes in the kit are capable of detecting a marker locus comprising one or more of S08271-1-Q2, P7659A-2, S08051-1-Q1, S07158-1-Q1, S07159-1-Q1, S06818-3-Q2, S06820-1-Q3, S06821-1-Q2, S16001-001-Q001 or a marker closely linked thereto on linkage group G; and, (b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
  • Thus, a typical kit or system can include a set of marker probes or primers configured to detect at least one favorable allele of one or more marker loci associated with resistance to soybean cyst nematode, for instance a favorable marker locus, haplotype or marker profile. These probes or primers can be configured, for example, to detect the marker loci noted in the tables and examples herein, e.g., using any available allele detection format, such as solid or liquid phase array based detection, microfluidic-based sample detection, etc. The systems and kits can further include packaging materials for packaging the probes, primers, or instructions, controls such as control amplification reactions that include probes, primers or template nucleic acids for amplifications, molecular size markers, or the like.
  • A typical system can also include a detector that is configured to detect one or more signal outputs from the set of marker probes or primers, or amplicon thereof, thereby identifying the presence or absence of the allele. A wide variety of signal detection apparatus are available, including photo multiplier tubes, spectrophotometers, CCD arrays, scanning detectors, phototubes and photodiodes, microscope stations, galvo-scans, microfluidic nucleic acid amplification detection appliances and the like. The precise configuration of the detector will depend, in part, on the type of label used to detect the marker allele, as well as the instrumentation that is most conveniently obtained for the user. Detectors that detect fluorescence, phosphorescence, radioactivity, pH, charge, absorbance, luminescence, temperature, magnetism or the like can be used. Typical detector examples include light (e.g., fluorescence) detectors or radioactivity detectors. For example, detection of a light emission (e.g., a fluorescence emission) or other probe label is indicative of the presence or absence of a marker allele. Fluorescent detection is generally used for detection of amplified nucleic acids (however, upstream and/or downstream operations can also be performed on amplicons, which can involve other detection methods). In general, the detector detects one or more label (e.g., light) emission from a probe label, which is indicative of the presence or absence of a marker allele. The detector(s) optionally monitors one or a plurality of signals from an amplification reaction. For example, the detector can monitor optical signals which correspond to “real time” amplification assay results.
  • System or kit instructions that describe how to use the system or kit or that correlate the presence or absence of the favorable allele with the predicted resistance are also provided. For example, the instructions can include at least one look-up table that includes a correlation between the presence or absence of the favorable alleles, haplotypes, or marker profiles and the predicted resistance. The precise form of the instructions can vary depending on the components of the system, e.g., they can be present as system software in one or more integrated unit of the system (e.g., a microprocessor, computer or computer readable medium), or can be present in one or more units (e.g., computers or computer readable media) operably coupled to the detector. As noted, in one typical example, the system instructions include at least one look-up table that includes a correlation between the presence or absence of the favorable alleles and predicted resistance. The instructions also typically include instructions providing a user interface with the system, e.g., to permit a user to view results of a sample analysis and to input parameters into the system.
  • Isolated polynucleotides comprising the nucleic acid sequences of the primers and probes provided herein are also encompassed herein. In one embodiment, the isolated polynucleotide comprises a polynucleotide capable of detecting a marker locus of the soybean genome comprising a marker locus comprising one or more of S08271-1-Q2, P7659A-2, S08051-1-Q1, S07158-1-Q1, S07159-1-Q1, S06818-3-Q2, S06820-1-Q3, S06821-1-Q2, S16001-001-Q001 or a marker closely linked thereto on linkage group G.
  • In specific embodiments, the isolated polynucleotide comprises: (a) a polynucleotide comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171; (b) a polynucleotide having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171; or (c) a polynucleotide comprising at least 10 contiguous nucleotides of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.
  • In certain embodiments, the isolated nucleic acids are capable of hybridizing under stringent conditions to nucleic acids of a soybean cultivar resistant to soybean cyst nematode, for instance to particular SNPs that comprise a marker locus, haplotype or marker profile.
  • As used herein, a substantially identical or complementary sequence is a polynucleotide that will specifically hybridize to the complement of the nucleic acid molecule to which it is being compared under high stringency conditions. A polynucleotide is said to be the “complement” of another polynucleotide if they exhibit complementarity. As used herein, molecules are said to exhibit “complete complementarity” when every nucleotide of one of the polynucleotide molecules is complementary to a nucleotide of the other. Two molecules are said to be “minimally complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional “low-stringency” conditions. Similarly, the molecules are said to be “complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional “high-stringency” conditions.
  • Appropriate stringency conditions which promote DNA hybridization, for example, 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2×SSC at 50° C., are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Typically, stringent conditions for hybridization and detection will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
  • Non-limiting examples of the methods and compositions disclosed herein are as follows:
  • 1. A method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode, the method comprising detecting in the genome of said first soybean plant or in the genome of said first soybean germplasm at least one marker locus that is associated with the resistance, wherein:
  • (a) the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
  • (b) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
  • (c) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
  • (d) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G;
  • (e) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
  • (f) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
  • (g) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
  • (h) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
  • (i) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
  • (j) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
  • (k) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
  • (l) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
  • (m) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
  • (n) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or
  • (o) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
  • 2. The method of embodiment 2, wherein at least two marker loci are detected.
    3. The method of embodiment 2, wherein the at least two marker loci comprise a haplotype that is associated with said resistance.
    4. The method of embodiment 2, wherein the at least two marker loci comprise a marker profile that is associated with said resistance.
    5. The method of any one of embodiments 1-4, wherein the germplasm is a soybean variety.
    6. The method of any one of embodiments 1-5, wherein the method further comprises selecting the first soybean plant or first soybean germplasm or a progeny thereof having the at least one marker locus.
    7. The method of embodiment 6, further comprising crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm.
    8. The method of embodiment 7, wherein the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
    9. The method of any one of embodiments 1-8, wherein the detecting comprises amplifying at least one of said marker loci and detecting the resulting amplified marker amplicon.
    10. The method of embodiment 9, wherein the amplifying comprises:
  • a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm, wherein the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and
  • b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon.
  • 11. The method of embodiment 10, wherein said method comprises amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.
    12. The method of embodiment 10, wherein said primer or primer pair comprises a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.
    13. The method of embodiment 10, wherein said primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 or variants or fragments thereof.
    14. The method of embodiment 10, wherein said primer pair comprises:
  • a) SEQ ID NOS: 81 and 82; b) SEQ ID NOS: 87 and 88; c) SEQ ID NOS: 89 and 90; d) SEQ ID NOS: 91 and 92; e) SEQ ID NOS: 93 and 94; f) SEQ ID NOS:95 and 96; g) SEQ ID NOS: 97 and 98; h) SEQ ID NOS: 99 and 100; i) SEQ ID NOS: 101 and 102; j) SEQ ID NOS: 121 and 122; k) SEQ ID NOS: 121 and 123; l) SEQ ID NOS: 124 and 125; m) SEQ ID NOS: 126 and 127; n) SEQ ID NOS: 128 and 129; o) SEQ ID NOS: 130 and 131; p) SEQ ID NOS: 136 and 137; q) SEQ ID NOS: 140 and 141; r) SEQ ID NOS: 144 and 145; s) SEQ ID NOS: 148 and 149; t) SEQ ID NOS: 152 and 153; u) SEQ ID NOS: 156 and 157; v) SEQ ID NOS: 160 and 161; w) SEQ ID NOS: 164 and 165; or, x) SEQ ID NOS: 168 and 169.
  • 15. The method of embodiment 10, wherein the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified.
    16. The method of embodiment 15, wherein said labeled nucleic acid probe comprises a nucleic acid sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof.
    17. The method of embodiment 15, wherein the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, or 135.
    18. The method of any one of embodiments 1-19, wherein the detecting comprises DNA sequencing of at least one of said marker loci.
    19. An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising
  • (a) the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
  • (b) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
  • (c) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
  • (d) the at least one marker locus comprises 507158-1-Q1 or a marker closely linked thereto on linkage group G;
  • (e) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
  • (f) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
  • (g) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
  • (h) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
  • (i) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
  • (j) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
  • (k) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
  • (l) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
  • (m) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
  • (n) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or
  • (o) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
  • 20. The isolated polynucleotide of embodiment 19, wherein the polynucleotide comprises:
  • (a) a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169;
  • (b) a polynucleotide having at least 90% sequence identity to the polynucleotides set forth in part (a); or
  • (c) a polynucleotide comprising at least 10 contiguous nucleotides of the polynucleotides set forth in part (a).
  • 21. A kit for detecting or selecting at least one soybean plant or soybean germplasm with improved resistance to soybean cyst nematode, the kit comprising:
  • a) a primer or a probe for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein the primer or probe are capable of detecting a marker locus, wherein:
      • (i) the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
      • (ii) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
      • (iii) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
      • (iv) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G;
      • (v) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
      • (vi) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
      • (vii) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
      • (iix) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
      • (ix) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
      • (x) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
      • (xi) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
      • (xii) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
      • (xiii) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
      • (xiv) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or
      • (xv) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G; and,
  • b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
    • EXPERIMENTAL
  • The following examples are offered to illustrate, but not to limit the claimed invention. It is understood that the examples and embodiments described herein are for illustrative purposes only, and persons skilled in the art will recognize various reagents or parameters that can be altered without departing from the spirit of the invention or the scope of the appended claims.
  • Soybean Sequence and SNP Marker Assays Associated with Soybean Cyst Nematode Resistance, Rhg1
  • SNP markers for the Rhg1 locus (Soybean Cyst Nematode Resistance) on Linkage Group G have been produced, as well as, markers genetically linked to these markers. Markers from this region are relevant in breeding populations and will facilitate selection of soybean plants with resistance to SCN at the Rhg1 locus tracing back to PI437654, Peking, and/or PI88788, as well as stacks with other marker assisted traits, including yield genes.
  • Previously, bioassay procedures for screening soybean plants against a reference list Soybean Cyst nematode races were used to determine resistance allele state. These assays are expensive and somewhat variable. These markers and their association with the trait phenotype in relevant breeding populations have been optimized. The markers, and additional SNPs linked to these markers, allow for a much more efficient process of selecting and breeding. Markers also facilitate stacking sources of resistance and stacks with other important traits in soybeans, including yield. These markers and those linked to these markers, allow for identification and selection of plants in a highly efficient manner, without the need for bioassay work.
    • Example 1
  • Markers were developed to characterize, identify, and/or select resistant or susceptible alleles at the Rhg1 locus on linkage group G (ch 18). Markers were screened against various known resistant and susceptible parents.
  • Marker S08271-1-Q2 was developed to identify alleles associated with SCN phenotype, this marker detects an A/T polymorphism at position 1749394 on ch 18, which is likely derived from PI88788. During development, this marker was validated against SCN resistant line BSR101, and susceptible line P1437654. The marker was further validated and confirmed against a panel of 31 varieties which included proprietary experimental lines, proprietary commercial lines, and public lines.
  • TABLE 8
    Assay conditions:
    H20  4.28 ul
    Hot Tub buffer  0.5 ul
    Rox Dye (50X) 0.075 ul
    DNTPs(24 mM each) 0.039 ul
    Primer(100 uM) 0.0375 ul 
    Primer(100 uM) 0.0375 ul 
    Primer(100 uM) 0.0375 ul 
    FAM Probe(100 uM 0.005 ul
    VIC Probe(100 uM 0.005 ul
    Hot Tub enzyme 0.025 ul
    Total volume 5.005 ul
  • Further development and testing was done to optimize the marker system for high throughput analysis of soybean. From this testing, S08271-1-Q2 was chosen for high throughput analysis needs, but other versions can be used to detect the polymorphism. There is a 5 bp deletion in the region, the S08271 forward primer is inside of this indel, and avoids any assay difficulties that may arise from this deletion.
  • TABLE 9
    Optimization:
    S08271- S08271- Tcaagtatcgcgcaagctc S08271- Catggtttctcttatcttatracattg S08271- S08271-
    1-Q1 F4 (SEQ ID NO: 121) R3 (SEQ ID NO: 122 ) and 1-PB3 1-PB4
    CAATTCATGGTTTCTCTTATRACATT
    (SEQ ID NO: 123)
    S08271- S08271- Cattgttgccaagtaatactactatataaattc S08271- Tcaagtatcgcgcaagctc S08271- S08271-
    1-Q2 F1 (SEQ ID NO: 124) R1 (SEQ ID NO: 125) 1-PB1 1-PB2
    S08271- S08271- Attcgcccttcatggtttct S08271- Gcaagctcctgcaaggtatt S08271- S08271-
    1-Q3 F2 (SEQ ID NO: 126) R2 (SEQ ID NO: 127) 1-PB1 1-PB2
    S08271- S08271- Ctgagtcttatcattctgtggattg S08271- Gcaagctcctgcaaggtatt S08271- S08271-
    1-Q4 F3 (SEQ ID NO: 128) R2 (SEQ ID NO: 129) 1-PB1 1-PB2
    S08271- S08271- Cattgttgccaagtaatactactatataaattc S08271- Tcaagtatcgcgcaagctc S08271- S08271-
    1-Q5 F1 (SEQ ID NO: 130) R1 (SEQ ID NO: 131) 1-PB3 1-PB4
    F4 and R1 are the same primer.
    Note:
  • TABLE 10
    S08271-1- 6FAM- S08271-1- VIC-
    PB1 TGGGTTTCAGATAAC PB2 TGGGTTTCTGATAACC
    (SEQ ID NO: 132) (SEQ ID NO: 133)
    S08271-1- 6FAM-accacggttatcTgaa S08271-1- VIC-accacggttatcAgaa
    PB3 (SEQ ID NO: 134) PB4 (SEQ ID NO: 135)
  • Similar development, testing and analysis was done to produce additional markers to detect polymorphisms associated with the Rhg1 locus and soybean cyst nematode resistance, with the results of this work summarized in the Tables provided herein. The markers were validated against the panel of SCN resistant or susceptible varieties described above. The markers are capable of detecting SCN loci likely derived from one or more of PI88788, Peking, PI437654, as well markers from other sources. These markers may have further been optimized for robust and consistent performance in high throughput assay conditions.
  • These markers can be used in other assays or with other assay conditions, Some markers were assayed under additional conditions. For example, S06818-3-Q2, S06820-Q3, and S06821-1-Q2 were tested under the following conditions.
  • The parameters used for the TaqMan assay are as follows:
  • TABLE 11
    Cycle Settings
    94° C. 120 sec  1 cycle
    60° C. 60 sec
    72° C.  1 sec 40 cycles
    94° C. 30 sec
  • TABLE 12
    Assay Mix 1x (ul)
    DNA (1.5 ng) - dried down in assay plate —
    ddH20 3.95
    Hottub buffer 0.5
    dNTP (2.5 mM) 0.375
    Primer 1 + Primer 2 (100 uM F + R) 0.02
    Probe 1 (10 uM) 0.05
    Probe 2 (10 uM) 0.05
    Hottub enzyme 0.025
    Rox dye (50x) 0.075
    Total 5.05
    • Example 2
  • Using a case-control association analysis, the Rhg1 locus from Peking associated with resistance to soybean cyst nematode (SCN) was fine-mapped to a region between 1548716-1881755 bp on Gm18 (Lg G). A set of 158 SNPs were identified in this region that perfectly differentiate highly tolerate from susceptible lines. These markers are ideal for marker-assisted selection of SCN resistance.
  • Phenotypic data for selected case group lines was based on lab screening and pedigree information. DNA was prepped using standard Illumina TruSeq chemistry. Selected resistant and susceptible soybean lines formed the case group and were sequenced to ˜0.5-40× genome coverage on an Illumina HiSeq2000. SNPs were called using a proprietary software to automate the process, missing data was imputed using a separate proprietary software. Haploview was used to conduct a case-control association analysis on a set of 12,449 SNPs identified in the region from 688871-2675880 bp on Gm18. The case group comprised 41 public and proprietary soybean lines susceptible to SCN and the control group comprised 7 public and proprietary lines with resistance derived from Peking. Following Haploview filtering using the settings noted below, 12,093 SNPs remained in the analysis.
    • Haploview Settings:
  • Do Association Test
  • Case/Control Data
  • Ignore Pairwise comparisons of markers >10 kb apart
  • Exclude individuals with >50% missing genotypes
  • HW p-value cutoff: 0.0
  • Min genotype %:50
  • Max # mendel errors: 1
  • Minimum minor allele freq.: 0.05
  • *Physical positions are based on the Glymal Williams82 soybean reference assembly from JGI.
  • The case-control analysis identified several SNPs in linkage disequilibrium with Rhg1 (Peking) phenotypic scores. The case-control association analysis using 12,093 SNPs reveals a peak of allele to phenotype association between 1548716-1881755 bp on Gm18 (Lg G), suggesting that Rhg1 from Peking is in this region, as evaluated using a plot of chi square values. 158 SNPs have a perfect association between 41 susceptible (case) and 7 resistant (control) lines (Table 13). These markers are ideal for TaqMan assay design, or for evaluation by other methods, including sequencing, hybridization, or other technologies. Numerous additional SNPs analyzed here that are linked to region but are not in perfect LD with trait could be very informative markers when used in select germplasm.
  • TABLE 13
    Phys Case, Control Case, Control Chi P
    SNP Name Pos sus Peking Ratio Counts Frequencies square value Marker
    Gm18: 926125 926125 T A 46:0, 0:2 1.000, 0.000 48 4.26E−12
    Gm18: 1138152 1138152 G A 54:0, 0:2 1.000, 0.000 56 7.25E−14
    Gm18: 1517146 1517146 G C 72:0, 0:10 1.000, 0.000 82 1.36E−19
    Gm18: 1518206 1518206 A G 72:0, 0:12 1.000, 0.000 84 4.95E−20
    Gm18: 1520624 1520624 A T 60:0, 0:6 1.000, 0.000 66 4.51E−16
    Gm18: 1520675 1520675 C T 64:0, 0:8 1.000, 0.000 72 2.15E−17
    Gm18: 1520743 1520743 G A 68:0, 0:8 1.000, 0.000 76 2.84E−18
    Gm18: 1524498 1524498 G T 64:0, 0:12 1.000, 0.000 76 2.84E−18
    Gm18: 1548716 1548716 C T 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1550153 1550153 T A 74:0, 0:8 1.000, 0.000 82 1.36E−19
    Gm18: 1550231 1550231 A T 64:0, 0:8 1.000, 0.000 72 2.15E−17
    Gm18: 1552799 1552799 C A 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1554392 1554392 T G 68:0, 0:10 1.000, 0.000 78 1.03E−18
    Gm18: 1554570 1554570 A C 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1554604 1554604 A G 70:0, 0:14 1.000, 0.000 84 4.95E−20
    Gm18: 1554689 1554689 T C 66:0, 0:10 1.000, 0.000 76 2.84E−18
    Gm18: 1555210 1555210 C G 60:0, 0:6 1.000, 0.000 66 4.51E−16
    Gm18: 1560043 1560043 T A 68:0, 0:10 1.000, 0.000 78 1.03E−18
    Gm18: 1560088 1560088 C T 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1560390 1560390 A C 66:0, 0:12 1.000, 0.000 78 1.03E−18
    Gm18: 1560442 1560442 T A 66:0, 0:12 1.000, 0.000 78 1.03E−18
    Gm18: 1560784 1560784 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1561009 1561009 G A 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1561190 1561190 T A 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1561429 1561429 C T 64:0, 0:8 1.000, 0.000 72 2.15E−17
    Gm18: 1561725 1561725 A T 62:0, 0:10 1.000, 0.000 72 2.15E−17
    Gm18: 1562884 1562884 A G 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1563153 1563153 G T 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1564092 1564092 A T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1565225 1565225 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1565646 1565646 T G 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1566882 1566882 C T 72:0, 0:8 1.000, 0.000 80 3.74E−19
    Gm18: 1567685 1567685 C T 72:0, 0:8 1.000, 0.000 80 3.74E−19
    Gm18: 1567843 1567843 T A 72:0, 0:10 1.000, 0.000 82 1.36E−19
    Gm18: 1568490 1568490 A C 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1568999 1568999 C T 72:0, 0:14 1.000, 0.000 86 1.80E−20
    Gm18: 1569035 1569035 G T 70:0, 0:12 1.000, 0.000 82 1.36E−19
    Gm18: 1569146 1569146 C T 66:0, 0:12 1.000, 0.000 78 1.03E−18
    Gm18: 1570660 1570660 T C 78:0, 0:12 1.000, 0.000 90 2.38E−21
    Gm18: 1572368 1572368 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1577559 1577559 T A 62:0, 0:2 1.000, 0.000 64 1.24E−15
    Gm18: 1578727 1578727 G T 70:0, 0:14 1.000, 0.000 84 4.95E−20
    Gm18: 1579201 1579201 G A 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1579270 1579270 A G 72:0, 0:14 1.000, 0.000 86 1.80E−20
    Gm18: 1579707 1579707 T G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1579708 1579708 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21 S08051-1
    Gm18: 1581688 1581688 T A 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1583772 1583772 G A 70:0, 0:12 1.000, 0.000 82 1.36E−19
    Gm18: 1584054 1584054 A G 78:0, 0:12 1.000, 0.000 90 2.38E−21
    Gm18: 1584659 1584659 G C 72:0, 0:14 1.000, 0.000 86 1.80E−20
    Gm18: 1589032 1589032 C T 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1595321 1595321 T C 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1598101 1598101 G T 70:0, 0:10 1.000, 0.000 80 3.74E−19
    Gm18: 1599717 1599717 G A 66:0, 0:14 1.000, 0.000 80 3.74E−19
    Gm18: 1599752 1599752 A G 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1599841 1599841 C T 56:0, 0:2 1.000, 0.000 58 2.62E−14
    Gm18: 1600011 1600011 C T 56:0, 0:10 1.000, 0.000 66 4.51E−16
    Gm18: 1600033 1600033 C T 50:0, 0:8 1.000, 0.000 58 2.62E−14
    Gm18: 1600179 1600179 A T 54:0, 0:12 1.000, 0.000 66 4.51E−16
    Gm18: 1601192 1601192 T C 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1601614 1601614 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1602244 1602244 C G 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1603722 1603722 C T 64:0, 0:12 1.000, 0.000 76 2.84E−18
    Gm18: 1604031 1604031 A G 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1605443 1605443 A T 60:0, 0:10 1.000, 0.000 70 5.93E−17
    Gm18: 1606442 1606442 T A 66:0, 0:14 1.000, 0.000 80 3.74E−19
    Gm18: 1606566 1606566 A T 56:0, 0:14 1.000, 0.000 70 5.93E−17
    Gm18: 1606647 1606647 C T 56:0, 0:8 1.000, 0.000 64 1.24E−15
    Gm18: 1609397 1609397 C A 76:0, 0:10 1.000, 0.000 86 1.80E−20
    Gm18: 1610935 1610935 A G 58:0, 0:10 1.000, 0.000 68 1.64E−16
    Gm18: 1612466 1612466 G A 68:0, 0:8 1.000, 0.000 76 2.84E−18
    Gm18: 1612553 1612553 G A 70:0, 0:4 1.000, 0.000 74 7.81E−18
    Gm18: 1614300 1614300 T A 68:0, 0:10 1.000, 0.000 78 1.03E−18
    Gm18: 1614960 1614960 A T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1618118 1618118 T A 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1626263 1626263 T G 52:0, 0:4 1.000, 0.000 56 7.25E−14
    Gm18: 1626278 1626278 G A 54:0, 0:8 1.000, 0.000 62 3.43E−15
    Gm18: 1627202 1627202 A T 50:0, 0:2 1.000, 0.000 52 5.55E−13
    Gm18: 1627204 1627204 C A 48:0, 0:2 1.000, 0.000 50 1.54E−12
    Gm18: 1629930 1629930 T C 54:0, 0:12 1.000, 0.000 66 4.51E−16
    Gm18: 1634611 1634611 A T 64:0, 0:2 1.000, 0.000 66 4.51E−16
    Gm18: 1643225 1643225 C G 70:0, 0:12 1.000, 0.000 82 1.36E−19
    Gm18: 1653887 1653887 C T 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1654681 1654681 T A 70:0, 0:12 1.000, 0.000 82 1.36E−19
    Gm18: 1654687 1654687 G C 70:0, 0:10 1.000, 0.000 80 3.74E−19
    Gm18: 1657025 1657025 A T 66:0, 0:14 1.000, 0.000 80 3.74E−19
    Gm18: 1680507 1680507 T C 74:0, 0:8 1.000, 0.000 82 1.36E−19
    Gm18: 1700832 1700832 C T 62:0, 0:14 1.000, 0.000 76 2.84E−18
    Gm18: 1700885 1700885 G A 58:0, 0:8 1.000, 0.000 66 4.51E−16
    Gm18: 1701854 1701854 A G 64:0, 0:14 1.000, 0.000 78 1.03E−18
    Gm18: 1702482 1702482 C T 62:0, 0:10 1.000, 0.000 72 2.15E−17
    Gm18: 1702563 1702563 C A 46:0, 0:12 1.000, 0.000 58 2.62E−14
    Gm18: 1702741 1702741 T C 68:0, 0:10 1.000, 0.000 78 1.03E−18
    Gm18: 1703321 1703321 T A 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1706708 1706708 G A 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1706842 1706842 C G 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1707082 1707082 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1707115 1707115 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1707377 1707377 T C 68:0, 0:10 1.000, 0.000 78 1.03E−18
    Gm18: 1708549 1708549 G A 64:0, 0:12 1.000, 0.000 76 2.84E−18
    Gm18: 1717352 1717352 G T 64:0, 0:12 1.000, 0.000 76 2.84E−18
    Gm18: 1721829 1721829 A T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1723649 1723649 C A 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1723650 1723650 A T 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1724082 1724082 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1725538 1725538 T G 60:0, 0:6 1.000, 0.000 66 4.51E−16
    Gm18: 1725630 1725630 G C 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1725815 1725815 G A 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1725932 1725932 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1725991 1725991 A G 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1726068 1726068 G T 78:0, 0:12 1.000, 0.000 90 2.38E−21
    Gm18: 1727330 1727330 T C 72:0, 0:12 1.000, 0.000 84 4.95E−20
    Gm18: 1727343 1727343 A C 72:0, 0:12 1.000, 0.000 84 4.95E−20
    Gm18: 1727903 1727903 C T 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1728146 1728146 C A 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1728824 1728824 G A 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1729347 1729347 T C 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1729673 1729673 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1729866 1729866 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1730855 1730855 A T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1731068 1731068 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1731184 1731184 T A 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1731725 1731725 T C 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1731938 1731938 G A 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1734691 1734691 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1735510 1735510 T A 78:0, 0:12 1.000, 0.000 90 2.38E−21
    Gm18: 1740118 1740118 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1747766 1747766 A T 74:0, 0:12 1.000, 0.000 86 1.80E−20
    Gm18: 1751156 1751156 C T 70:0, 0:12 1.000, 0.000 82 1.36E−19
    Gm18: 1752808 1752808 A T 54:0, 0:10 1.000, 0.000 64 1.24E−15
    Gm18: 1754310 1754310 A G 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1754895 1754895 T A 50:0, 0:12 1.000, 0.000 62 3.43E−15
    Gm18: 1759167 1759167 G A 72:0, 0:12 1.000, 0.000 84 4.95E−20
    Gm18: 1759307 1759307 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1761263 1761263 A C 62:0, 0:14 1.000, 0.000 76 2.84E−18
    Gm18: 1762686 1762686 A G 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1763519 1763519 T A 76:0, 0:12 1.000, 0.000 88 6.55E−21
    Gm18: 1768783 1768783 C A 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1768805 1768805 A G 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1769619 1769619 T A 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1773903 1773903 T C 72:0, 0:6 1.000, 0.000 78 1.03E−18
    Gm18: 1773911 1773911 A T 74:0, 0:6 1.000, 0.000 80 3.74E−19
    Gm18: 1778021 1778021 A G 72:0, 0:12 1.000, 0.000 84 4.95E−20
    Gm18: 1783028 1783028 G A 70:0, 0:10 1.000, 0.000 80 3.74E−19
    Gm18: 1783194 1783194 C T 62:0, 0:12 1.000, 0.000 74 7.81E−18
    Gm18: 1783357 1783357 G T 70:0, 0:14 1.000, 0.000 84 4.95E−20
    Gm18: 1785320 1785320 T G 78:0, 0:10 1.000, 0.000 88 6.55E−21
    Gm18: 1787549 1787549 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1789215 1789215 G A 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1789352 1789352 G C 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1789553 1789553 C T 78:0, 0:12 1.000, 0.000 90 2.38E−21
    Gm18: 1789934 1789934 T A 78:0, 0:12 1.000, 0.000 90 2.38E−21
    Gm18: 1805509 1805509 T C 54:0, 0:4 1.000, 0.000 58 2.62E−14
    Gm18: 1859739 1859739 C G 68:0, 0:12 1.000, 0.000 80 3.74E−19
    Gm18: 1863987 1863987 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21
    Gm18: 1864738 1864738 A G 78:0, 0:14 1.000, 0.000 92 8.67E−22
    Gm18: 1877951 1877951 T C 74:0, 0:14 1.000, 0.000 88 6.55E−21
    Gm18: 1881755 1881755 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21
  • Additionally, the markers on LG G summarized in Table 14 were also included in this study.
  • TABLE 14
    Case, Control
    Phys Ratio Case, Control Chi
    Marker Genetic Pos SUS Peking Counts Frequencies square P value Source
    S08271-1-Q2 10.2 1749394 A T 42:28, 0:14 0.600, 0.000 16.8 4.15E−05 Pi88788
    (P10355B-1)
    P7659A-2 12.3 1580305 C T Pi88788
    S08051-1-Q1 9.3 1579707 T G  76:0, 0:14 1.000, 0.000 90 2.38E−21 Peking,
    (P7659A-1) 1579708 C T  76:0, 0:14 1.000, 0.000 90 2.38E−21 PI437654
    S07158-1-Q1 12.3 2098742 G T 24:54, 2:12 0.308, 0.143 1.591 0.2072 PI437654,
    (P5219A-1) 2098741 T G 24:54, 2:12 0.308, 0.143 1.591 0.2072 Pi88788,
    Peking
    S07159-1-Q1 12.3 2095977 A A  2:76, 0:14 0.026, 0.000 0.367 0.5447 PI437654
    (P5219A-2)
    S06818-3-Q2 9.2 1573060 C G 66:10, 0:12 0.868, 0.000 41.684 1.07E−10 Peking or
    Pi88788
    S06820-1-Q3 9.2 1571774 A G 66:10, 0:14 0.868, 0.000 45.592 1.46E−11 Peking or
    Pi88788
    S06821-1-Q2 9.2 1563924 G T 64:10, 0:14 0.865, 0.000 44.396 2.68E−11 Peking or
    Pi88788
    S16001-001- 9.4 1607524 A A Pi88788
    Q001
    • Example 3
  • Using a case-control association analysis, the Rhg1 locus from P188788 associated with resistance to soybean cyst nematode (SCN) was fine-mapped to a region between 1477584-1933546 bp on Gm18 (Lg G). A set of 6 SNPs were identified in this region that perfectly differentiate highly PI88788 derived lines from susceptible lines. These markers are ideal for marker-assisted selection of SCN resistance.
  • Phenotypic data for selected case group lines was based on lab screening and pedigree information. DNA was prepped using standard Illumina TruSeq chemistry. Selected resistant and susceptible soybean lines formed the case group and were sequenced to ˜0.5-40× genome coverage on an Illumina HiSeq2000. SNPs were called using a proprietary software to automate the process, missing data was imputed using a separate proprietary software. Haploview was used to conduct a case-control association analysis on a set of 13,147 SNPs identified in the region from 688871-2675880 bp on Gm18. The case group comprised 41 public and proprietary soybean lines susceptible to SCN and the control group comprised 78 proprietary lines with resistance derived from P188788. Following Haploview filtering using the settings noted below, 10,872 SNPs remained in the analysis.
    • Haploview Settings:
  • Do Association Test
  • Case/Control Data
  • Ignore Pairwise comparisons of markers >10 kb apart
  • Exclude individuals with >50% missing genotypes
  • HW p-value cutoff: 0.0
  • Min genotype %:50
  • Max # mendel errors: 1
  • Minimum minor allele freq.: 0.05
  • *Physical positions are based on the Glymal Williams82 soybean reference assembly from JGI.
  • The case-control analysis identified several SNPs in linkage disequilibrium with Rhg1 (Peking) phenotypic scores. The case-control association analysis using 10,872 SNPs reveals a peak of allele to phenotype association between 1477584-1933546 bp on Gm18 (Lg G), suggesting that Rhg1 from P188788 is in this region, as evaluated using a plot of chi square values. 158 SNPs have a perfect association between 41 susceptible (case) and 78 resistant (control) lines (Table A). These markers are ideal for TaqMan assay design, or for evaluation by other methods, including sequencing, hybridization, or other technologies. Numerous additional SNPs analyzed here that are linked to region but are not in perfect LD with trait could be very informative markers when used in select germplasm.
  • TABLE 15
    Case, Control Case, Control Chi Marker
    Name Phys Pos SUS Pi88788 Ratio Counts Frequencies square P value Assay
    Gm18: 1607524 1607524 A C 76:0, 0:124 1.000, 0.000 200 2.09E−45 S16001-
    001-Q001
    Gm18: 1888247 1845911 A T 68:0, 0:108 1.000, 0.000 176 3.62E−40
    Gm18: 1845911 1845911 T C 56:0, 0:108 1.000, 0.000 164 1.51E−37
    Gm18: 1846008 1846008 A G 54:0, 0:100 1.000, 0.000 154 2.32E−35
    Gm18: 1565826 1565826 T G 74:0, 0:64 1.000, 0.000 138 7.29E−32
    Gm18: 1918014 1918014 G A 58:0, 0:80 1.000, 0.000 138 7.29E−32

    Additionally, the markers on LG G summarized in Table B were also included in this study.
  • TABLE 16
    Case, Control
    Production Phys Ratio Case, Control Chi P
    Marker Lg Genetic Pos SUS Pi88788 Counts Frequencies square value Source
    S08271-1- G 10.2 1749394 A or T A 28:42, 0:106 0.400, 0.000 50.422 1.24E−12 PI88788
    Q2
    (P10355B-
    1)
    P7659A-2 G 12.3 1580305 C or T T 64:10, 4:134 0.865, 0.029 154.477 1.82E−35 PI88788
    S08051-1- G 9.3 1579707 Peking,
    Q1 and PI437654
    (P7659A-1) 1579708
    S07158-1- G 12.3 2098742 T or G G 54:24, 0.692, 0.086 87.315 9.26E−21 PI437654,
    Q1 12:128 PI88788,
    (P5219A-1) 2098741 G or T T 54:24, 0.692, 0.086 87.315 9.26E−21 Peking
    12:128
    S07159-1- G 12.3 2095977 PI437654
    Q1
    (P5219A-2)
    S06818-3- G 9.2 1573060 C or G G 66:10, 0:128 0.868, 0.000 164.32 1.29E−37 Peking or
    Q2 PI88788
    S06820-1- G 9.2 1571774 A or G 66:10, 2:114 0.868, 0.017 145.44 1.72E−33 Peking or
    Q3 PI88788
    S06821-1- G 9.2 1563924 G or T T 64:10, 2:142 0.865, 0.014 167.686 2.37E−38 Peking or
    Q2 PI88788
    S16001- G 9.4 1607524 A C 76:0, 0:124 1.000, 0.000 200 2.09E−45 PI88788
    001-Q001
  • All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
  • Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

Claims (21)

That which is claimed:
1. A method of identifying a first soybean plant or a first soybean germplasm that displays improved resistance to soybean cyst nematode, the method comprising detecting in the genome of said first soybean plant or in the genome of said first soybean germplasm at least one marker locus that is associated with the resistance, wherein:
(a) the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
(b) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
(c) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
(d) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G;
(e) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
(f) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
(g) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
(h) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
(i) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
(j) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
(k) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
(l) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
(m) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
(n) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or
(o) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
2. The method of claim 1, wherein at least two marker loci are detected.
3. The method of claim 1, wherein the at least two marker loci comprise a haplotype that is associated with said resistance.
4. The method of claim 1, wherein the at least two marker loci comprise a marker profile that is associated with said resistance.
5. The method of claim 1, wherein the germplasm is a soybean variety.
6. The method of claim 1, wherein the method further comprises selecting the first soybean plant or first soybean germplasm or a progeny thereof having the at least one marker locus.
7. The method of claim 6, further comprising crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm.
8. The method of claim 7, wherein the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
9. The method of claim 1, wherein the detecting comprises amplifying at least one of said marker loci and detecting the resulting amplified marker amplicon.
10. The method of claim 9, wherein the amplifying comprises:
a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm, wherein the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and
b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon.
11. The method of claim 10, wherein said method comprises amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.
12. The method of claim 10, wherein said primer or primer pair comprises a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.
13. The method of claim 10, wherein said primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 or variants or fragments thereof.
14. The method of claim 10, wherein said primer pair comprises:
a) SEQ ID NOS: 81 and 82;
b) SEQ ID NOS: 87 and 88;
c) SEQ ID NOS: 89 and 90;
d) SEQ ID NOS: 91 and 92;
e) SEQ ID NOS: 93 and 94;
f) SEQ ID NOS:95 and 96;
g) SEQ ID NOS: 97 and 98;
h) SEQ ID NOS: 99 and 100;
i) SEQ ID NOS: 101 and 102;
j) SEQ ID NOS: 121 and 122;
k) SEQ ID NOS: 121 and 123;
l) SEQ ID NOS: 124 and 125;
m) SEQ ID NOS: 126 and 127;
n) SEQ ID NOS: 128 and 129;
o) SEQ ID NOS: 130 and 131;
p) SEQ ID NOS: 136 and 137;
q) SEQ ID NOS: 140 and 141;
r) SEQ ID NOS: 144 and 145;
s) SEQ ID NOS: 148 and 149;
t) SEQ ID NOS: 152 and 153;
u) SEQ ID NOS: 156 and 157;
v) SEQ ID NOS: 160 and 161;
w) SEQ ID NOS: 164 and 165; or,
x) SEQ ID NOS: 168 and 169.
15. The method of claim 10, wherein the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified.
16. The method of claim 15, wherein said labeled nucleic acid probe comprises a nucleic acid sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof.
17. The method of claim 15, wherein the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOs: 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, or 135.
18. The method of claim 1, wherein the detecting comprises DNA sequencing of at least one of said marker loci.
19. An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising
(a) the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
(b) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
(c) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
(d) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G;
(e) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
(f) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
(g) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
(h) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
(i) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
(j) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
(k) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
(l) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
(m) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
(n) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or
(o) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G.
20. The isolated polynucleotide of claim 19, wherein the polynucleotide comprises:
(a) a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169;
(b) a polynucleotide having at least 90% sequence identity to the polynucleotides set forth in part (a); or
(c) a polynucleotide comprising at least 10 contiguous nucleotides of the polynucleotides set forth in part (a).
21. A kit for detecting or selecting at least one soybean plant or soybean germplasm with improved resistance to soybean cyst nematode, the kit comprising:
a) a primer or a probe for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein the primer or probe are capable of detecting a marker locus, wherein:
(i) the at least one marker locus comprises S08271-1-Q2 or a marker closely linked thereto on linkage group G;
(ii) the at least one marker locus comprises P7659A-2 or a marker closely linked thereto on linkage group G;
(iii) the at least one marker locus comprises S08051-1-Q1 or a marker closely linked thereto on linkage group G;
(iv) the at least one marker locus comprises S07158-1-Q1 or a marker closely linked thereto on linkage group G;
(v) the at least one marker locus comprises S07159-1-Q1 or a marker closely linked thereto on linkage group G;
(vi) the at least one marker locus comprises S06818-3-Q2 or a marker closely linked thereto on linkage group G;
(vii) the at least one marker locus comprises S06820-1-Q3 or a marker closely linked thereto on linkage group G;
(iix) the at least one marker locus comprises S06821-1-Q2 or a marker closely linked thereto on linkage group G;
(ix) the at least one marker locus comprises S16001-001-Q001 or a marker closely linked thereto on linkage group G;
(x) the at least one marker locus is between about marker Satt309 and BARC-012285-01798 on linkage group G;
(xi) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
(xii) the at least one marker locus is between about marker BARC-030055-06792 and BARC-025777-05064 on linkage group G;
(xiii) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G;
(xiv) the at least one marker locus is between about marker BARC-015371-01813 and BARCSOYSSR—18—0093 on linkage group G; or
(xv) the at least one marker locus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto on linkage group G; and,
b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
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