CN109055604A - One kind haplotype molecular labeling relevant to corn yield and its application - Google Patents

One kind haplotype molecular labeling relevant to corn yield and its application Download PDF

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CN109055604A
CN109055604A CN201811197778.0A CN201811197778A CN109055604A CN 109055604 A CN109055604 A CN 109055604A CN 201811197778 A CN201811197778 A CN 201811197778A CN 109055604 A CN109055604 A CN 109055604A
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snp
haplotype
indel
corn
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高世斌
罗博文
张啸
马鹏
钟海旭
苏顺宗
吴玲
刘丹
陈圳
冯信
王怡凯
高多江
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Sichuan Agricultural University
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Abstract

The invention discloses a kind of haplotype molecular labeling relevant to corn yield and its applications, the haplotype-tag is located on the 2nd article of chromosomal gene GRMZM2G039588 of corn, the primer pair of amplification or the above-mentioned haplotype-tag of detection is additionally provided simultaneously, can be used for improving that corncob is thick, fringe is thick, the application in spike length, row grain number and stem phosphorus content, stem phosphorus absorption efficiency and stem P uptake by plants.

Description

One kind haplotype molecular labeling relevant to corn yield and its application
Technical field
The invention belongs to field of molecular biotechnology, and in particular to a kind of haplotype molecular labeling relevant to corn yield And its application.
Background technique
Functional marker (functional markers) is based on functional nucleic acid polymorphism in target gene motif One kind New molecular marker made of the exploitation of site.Association analysis method dependent on genome allelic haplotype it is non-with Linkage disequilibrium based on machine, this method can be used for identifying the function motif of phenotype relevant gene and gene internal.With The germ plasm resource of some mutual affinity-less relations, pure line cultivar or self-mating system are material, are carried out for candidate gene section Sequence polymorphism analysis, the phenotypic data of materials for binding biological, using statistical method, to examine phenotypic variation and candidate Association and a kind of approach (Whitt S R, Buckler for examining candidate gene phenotypic function between gene sequence diversity E S.Using natural allelic diversity to evaluate gene function[J].Plant Functional Genomics,2003:123-139;Wilson L M,Whitt S R,A M,et al.Dissection of maize kernel composition and starch production by candidate gene association[J].The Plant Cell,2004,16(10):2719-2733.).If existing therebetween significant Association then derives from the multifarious molecular labeling for examining the sequence in the site, becomes corresponding functional label.This side Method can make full use of Genetic Recombination accumulated in natural evolution and artificial evolution's process, thus high score rate examine existing species Relationship between the genetic diversity and phenotypic variation of middle candidate gene, polymorphism and interaction (the Bao J of final identification function S,Corke H,Sun M.Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice(Oryza sativa L.)[J] .Theoretical and Applied Genetics, 2006,113 (7): 1171-1183.), and then obtain functional label.It closes Connection, which is analyzed, provides statistical circumstantial evidence, therefore the functional label of referred to as indirect type.
Summary of the invention
In view of this, utilizing RIL the present invention provides a kind of haplotype molecular labeling relevant to corn yield and application The separation of (Recombinant Inbred Lines, recombinant inbred lines) group's GRMZM2G039588 gene and the RIL group Phenotypic variation data, thus it is speculated that the hereditary effect of the haplotype-tag.
The invention also discloses a kind of above-mentioned haplotype-tags, and corncob is thick, fringe is thick, spike length, row grain number and stem improving Application in phosphorus content, stem phosphorus absorption efficiency and stem P uptake by plants.
The present invention is realized especially by following technical scheme:
A kind of haplotype molecular labeling relevant to corn yield, the haplotype-tag are located at the 2nd article of dye of corn Colour solid gene GRMZM2G039588, since initiation codon ATG, there is following variation in physical location downstream: InDel 328、SNP 655、InDel 656、SNP 680、SNP 682、SNP 686、SNP 689、SNP 692、InDel 696、SNP 700、SNP 701、SNP 704、SNP 706、SNP 708、SNP 709、SNP 713、SNP 714、SNP 715、 InDel 717、SNP 756、SNP 761、SNP 1384、InDel 1418、SNP 1426、SNP 1447、InDel 1451、 SNP 1469、SNP 1474、SNP 1475、SNP 1477、SNP 1478、InDel 1484、InDel 1549、SNP 1609、 SNP 1610, SNP 1612, InDel 1617, SNP 1631, SNP 1661, SNP 1693, SNP 1696,1761 and of SNP SNP 1763。
The present invention also provides the primer pair for expanding or detecting above-mentioned haplotype-tag, the primer pair is as follows:
Upstream primer: TCTGCGGCTTCCTGTGAGTGA;
Downstream primer: GCCACGCTTGCCTTCTAATGC.
The present invention also provides the application of the haplotype molecular labeling, primer pair in identification corn yield, in corn Application in high yield improvement.
The application in high yield corn germ plasm resource is being identified or screened to the haplotype molecular labeling simultaneously.
Haplotype molecular labeling described in another aspect in corn breeding application also protection scope of the present invention it It is interior.
The present invention also provides a kind of methods for detecting above-mentioned haplotype molecular labeling relevant to corn yield, are drawn with above-mentioned Object is to PCR amplification corn gene group DNA to be detected is carried out, with above-mentioned primer pair PCR amplification corn material genome to be detected DNA, according to amplified production, there are above-mentioned haplotype molecular labelings when determining maize seed to be detected.
The PCR amplification system is 25 μ L:10ng/ μ L DNA profiling, 1 μ L, Max Super-Fidelity DNA 0.5 μ L of Polymerase, mix primer 2 μ L, ddH28 μ L, Phanta Max Buffer of O, 12.5 μ L, Dntp Mix (10mM each)1μL。
The PCR response procedures are as follows: 95 DEG C of initial denaturation 3min;95 DEG C of denaturation 15s, Tm annealing 15s, 72 DEG C of extension 2kb/ Min, totally 38 recycle;72 DEG C extend 5min eventually;12 DEG C of preservations.
The invention has the benefit that
The present invention passes through phosphorous to 3 years 4 points of Correlated Yield Characters of RIL group and two independent seedling stages for repeating experiment It measures correlated traits and carries out gene GRMZM2G039588 comparison discovery, except the corncob under Chongzhou City's collating condition is slightly other each Its corresponding RIL family of 178 haplotype type is substantially less than the corresponding RIL family of 9782 haplotypes (178 correspondences under a environmental condition Haplotype character thick for axis for be excellent haplotype);Except the corn ear length under the treatment conditions of the gorge Bi Feng is other each The corresponding RIL family of its 178 haplotype is considerably longer than the corresponding RIL family of 9782 haplotypes (178 is corresponding under a environmental condition Haplotype is excellent haplotype for spike length);Its 178 haplotype is corresponding under the treatment conditions of four environment of Ear Width of Maize RL family is substantially lower than the corresponding RIL family of 9782 haplotypes, and (9782 haplotypes are for fringe is thick under the conditions of low-phosphorus stress It performs better than);Corn tassel row number corresponding RIL family of 178 haplotypes under the conditions of Chongzhou City and the low-phosphorous gorge Bi Feng is substantially less than The corresponding RIL family of 9782 haplotypes (9782 haplotypes are corresponded to and performed better than for tassel row number under the conditions of low-phosphorous);For in stem Phosphorus content and stem in P uptake by plants, the corresponding RIL family of 178 haplotypes is all significantly higher than 9782 haplotypes under control conditions Corresponding RIL family and stem phosphorus utilization are on the contrary, explanation is under conditions of normal phosphorus content, and 178 haplotypes are to the phosphorus in stem Content and P uptake by plants are advantageous, and 9728 haplotypes are advantageous to the phosphorus utilization of stem.
Specific embodiment
Below in conjunction with specific embodiment of the present invention, technical solution of the present invention is clearly and completely described, is shown So, described embodiments are only a part of the embodiments of the present invention, instead of all the embodiments.Based on the reality in the present invention Example is applied, every other embodiment obtained by those of ordinary skill in the art without making creative efforts all belongs to In the scope of protection of the invention.
Embodiment 1
To RIL group parent 1 (corn Tolerant to low P self-mating system 178), parent 2 (corn low-phosphorous sensitive self-mating system 9782) and During the GRMZM2G039588 gene order of canonical sequence B73 compares, occur 43 single times be made of SNP and InDel altogether Type.Two allelotypes that material is divided by the present invention according to this haplotype, in 271 parts of RIL groups (178 × 9782) Design primer (F:TCTGCGGCTTCCTGTGAGTGA in DNA;R:GCCA CGCTTGCCTTCTAATGC), PCP amplification includes this The segment of a haplotype;PCR, electrophoresis and sequencing approach are as follows:
1) PCR amplification
PCR amplification GRMZM2G039588 gene InDel is marked in 200 parts of RIL Meta-genomic DNAs.Amplification usesMax Super-Fidelity DNA Polymerase enzyme.The PCR amplification system of the enzyme is as follows:
PCR response procedures: 95 DEG C of initial denaturation 3min;95 DEG C of denaturation 15s, Tm anneal 15s, 72 DEG C of extension 2kb/min, and totally 38 A circulation;72 DEG C extend 5min eventually;12 DEG C of preservations.
2) amplified production send sequencing
According to sequencing result, the number and each group number of two kinds of Genotypes of separation are counted.
According to the RIL population material of electrophoresis and each genotype of sequencing result classified statistic.
3) experimental result
By counted on two genotype groupings and 2013,2014 and 2015 RIL groups in two kinds of horizontal phosphorus Handle (CK and T) yield Relevant phenotype data (including row grain number, tassel row number, prominent sharp length, spike length, fringe is thick, axis is thick, 100-grain weight, Fringe weight and axis weight) and the nitrogen and phosphorus content phenotypic data for repeating experiment independent twice (including stem/root nitrogen content, stem/root are phosphorous Amount, stem/root amount of nitrogen sucking, stem/root P uptake by plants, stem/root nitrogen use efficiency and stem/root phosphorus utilization) combine, independent sample T- Test is examined under two kinds of horizontal phosphorus processing, is chosen and is counted horizontal P < 0.05 phenotype below (table 1).It is wrapped in total in the haplotype Containing 43 sites, wherein SNP site 34,9, the site InDel.Wherein in 198 RIL familys for being used to Genotyping, belong to It is 85 in family's coefficient of 9782 haplotype of self-mating system, the family quantity for belonging to 178 haplotype of self-mating system is 113.
Under the conditions of the low-phosphorous and normal phosphorus of table 1 between two kinds of haplotypes significant difference character
Application test of the haplotype-tag of the present invention of embodiment 2 on corn yield
178,9782 and RIL of parent group, 271 familys are planted on Wenjiang in April, 2014 farm.Test uses random district's groups Design, the uniline area long 2m of row, spacing in the rows 0.4m, line-spacing 0.7m, every row plant 5 caves, and 2 plants of every cave compares and handle 2 weights of each setting It is multiple.Collating condition is to apply 50kg/hm in the form of potassium dihydrogen phosphate prior to seeding2P and 63kg/hm2K;In the form of urea Apply 180kg/hm2N, wherein applying 60kg/hm in seedling stage2, 120kg/hm is applied in the jointing stage2.Under the conditions of low-phosphorus stress, sowing Preceding not apply phosphate fertilizer, nitrogen fertilizer application and potash fertilizer, wherein potash fertilizer is that 63kg/hm is applied in the form of potassium chloride2K;3 periods of nitrogenous fertilizer point Fertilising, fertilization time is with dose as collating condition.In the corn jointing stage to the listed number of each cell, field management is omited Higher than general field management.
The fertilising of in April, 2014 and in April, 2015 plantation RIL family and parent are consistent with management condition and 2013.
The investigation of field plant type economical character, every cell are carried out after the entire experimental plot plant blossom phase as unit of cell It chooses uniform 5 plants of a growing way to be investigated, after fruit ear is mature, uniform 5 fruit ears, sunning to perseverance is collected among every cell Weight carries out indoor species test, and species test character has: row grain number, tassel row number, spike length, fringe are thick, axis is thick, fringe is heavy, axis is heavy, 100-grain weight, investigation Statistical method is specifically shown in Table 2.All character investigation methods are referring to [84] " corn germ plasm resource Description standard sum numbers such as Shi Yunsu According to standard " book.
The investigation method of 2 yield traits of table
The 4-6 month in 2012, seminar's early period refined Anduo County battalion the 219 parts of familys in farm this RIL group, river sand medium into The low-phosphorous potting culture with control of row, control is identical with processing growth time, and two repetitions are arranged in control and processing interval 2 days, Be spaced 7 days between repeating, sowing is sowed by random sequence, collection material when culture is to 61 heart of leaf, 2 plants of each family, root system with Cauline leaf is dispensed into two paper bags, paper bag is put into 105 DEG C of water-removing 30min in baking oven, then be transferred to 80 DEG C of dry 72h, measures root It is that dry weight and cauline leaf dry weight save later.Population material weight of root system and cauline leaf dry weight are successively ground with small-sized crushing type sample grinding machine 0.200g after thin, is weighed and (cross 1mm sieve), 50mL is placed in and disappears and boil in pipe and (sample is not adhered on bottleneck), first instill a small amount of water Wet sample, enriching sulfuric acid 5mL shake up and (stand overnight), and the one small funnel of curved neck of bottle lid first slowly heats on electric furnace, to Concentrated sulfuric acid decomposition increases temperature to 380 DEG C when emitting a large amount of white cigarettes again.Disappear when boiling to solution in uniform brownish black after about 1h, removes and disappear Pipe is boiled, curved neck funnel is lifted after slightly cold, 30%H is added dropwise2O22ml, and constantly shake to disappear and boil pipe, 380 DEG C of heating (slightly boiled) 30min, It removes, 30%H is added dropwise in slightly cold rear repetition2O21ml, 380 DEG C disappear boil 30min again, disappear and boil to solution in after colourless or limpid, remove Disappear and boil pipe cooling, rinses funnel with a small amount of water, washing lotion inflow, which disappears, boils in pipe.The boil liquid that will disappear nondestructively washes in 100ml volumetric flask, With water constant volume, shake up.It is measured after placing clarification after filtering for nitrogen, phosphorus.It synchronizes to disappear and boils blank control.
Points for attention: (1) fire when boiling the beginning that disappears wants small;(2) add H2O2When to wait vessel it is few it is cold after, lift small funnel, directly By H2O2It instills in solution;(3) disappearing, it is thorough to boil.The well-done mark that disappears is: solution is in colourless or limpid color;(4) boil liquid that disappears is last Catch up with most H2O2Otherwise it will affect the colorimetric estimation of nitrogen, phosphorus.Method is to disappear boil liquid in boiling 5-10 points after limpid color again.Also observable Most H is caught up in the fluctuation of liquid level2O2Liquid level is tranquiler afterwards.
Flow Analyzer surveys concentration of nitrogen and phosphorus and correlated traits calculates
Using Continuous Flow Analysis instrument (Alliance Integral Futura), open instrument and its associated with calculate Machine, and it is switched to operating system, advanced distilled water switches to the reaction reagent surveyed nitrogen or survey phosphorus after baseline is steady respectively, to Sample introduction is analyzed for steady rear beginning again for baseline.After analysis, final data processing and output are carried out, nitrogen concentration (mg/ is obtained L), phosphorus concentration (mg/l).Thus cauline leaf nitrogen content (SNC), cauline leaf amount of nitrogen sucking (SNU), cauline leaf nitrogen use efficiency (SNUE), stem are calculated Leaf phosphorus content (SPC), cauline leaf P uptake by plants (SPU), cauline leaf phosphorus utilization (SPUE), root nitrogen content (RNC), root amount of nitrogen sucking (RNU), Root nitrogen use efficiency (RNUE), root phosphorus content (RPC), root P uptake by plants (RPU), root phosphorus utilization (RPUE).
Calculation method are as follows: tissue nitrogen content=nitrogen concentration of measurement ×, which disappears, boils rear constant volume/weighing dry weight, and tissue inhales nitrogen Amount=tissue nitrogen content × tissue dry weight organizes nitrogen use efficiency=tissue dry weight/plant amount of nitrogen sucking, plant amount of nitrogen sucking=cauline leaf Amount of nitrogen sucking+root system amount of nitrogen sucking;Tissue phosphorus content=phosphorus concentration of measurement ×, which disappears, boils rear constant volume/weighing dry weight, and tissue inhales phosphorus Amount=tissue phosphorus content × tissue dry weight organizes phosphorus use efficiency=tissue dry weight/plant P uptake by plants, plant P uptake by plants=cauline leaf P uptake by plants+root system P uptake by plants.After nitrogen, phosphorus use efficiency refer to absorbance units the content of nitrogen and phosphorous, the fertile biomass of institute, nitrogen, phosphorus benefit It is higher with efficiency, show that absorbance units the content of nitrogen and phosphorous biological quality produced is more.
Under the conditions of low-phosphorous and normal phosphorus, corncob slightly two kinds of lists times under the conditions of phosphorus normal in addition to the base of Chongzhou City in 2015 Type mean value independent sample T-test examines difference not significant, all significant in Wenjiang base, the gorge Bi Feng farm and the farm Fen Jiang difference, And 9782 haplotypes are all significantly higher than 178 haplotypes.Corn ear length is two under the conditions of in addition to the farm of the gorge Bi Feng in 2014 is low-phosphorous Kind haplotype mean value independent sample T-test examines difference not significant, in Wenjiang base, Chongzhou City base and the farm Fen Jiang difference It is all significant, and 178 haplotypes are all significantly higher than 9782 haplotypes.And Ear Width of Maize is under the conditions of low-phosphorous in all 4 places Two kinds of haplotype mean value independent sample T-test examine difference significant, and 178 haplotypes are lower than 9782 haplotypes, especially Under the conditions of significant difference is only present in low-phosphorous in Chongzhou City base and the gorge Bi Feng farm.Tassel row number also Chongzhou City's base under the conditions of low-phosphorous Significant difference in ground and the gorge Bi Feng farm, 178 haplotypes are lower than 9782 haplotypes.Finally, stem phosphorus content, stem P uptake by plants and stem phosphorus Utilization rate significant difference in the mean value independent sample T-test inspection all under the conditions of normal phosphorus between two kinds of haplotypes.
It although an embodiment of the present invention has been shown and described, for the ordinary skill in the art, can be with Understand without departing from the principles and spirit of the present invention can to these examples carry out it is a variety of variation, modification, replacement and Modification, the scope of the present invention is defined by the appended.

Claims (9)

1. a kind of haplotype molecular labeling relevant to corn yield, which is characterized in that the haplotype-tag is located at corn The 2nd article of chromosomal gene GRMZM2G039588, since initiation codon ATG, physical location downstream occurs following Variation: InDel 328, SNP 655, InDel 656, SNP 680, SNP 682, SNP 686, SNP 689, SNP 692, InDel 696、SNP 700、SNP 701、SNP 704、SNP 706、SNP 708、SNP 709、SNP 713、SNP 714、SNP 715、InDel 717、SNP 756、SNP 761、SNP 1384、InDel 1418、SNP 1426、SNP 1447、InDel 1451、SNP 1469、SNP 1474、SNP 1475、SNP 1477、SNP 1478、InDel 1484、InDel 1549、SNP 1609、SNP 1610、SNP 1612、InDel 1617、SNP 1631、SNP 1661、SNP 1693、SNP 1696、SNP 1761 and SNP 1763.
2. amplification or the primer pair for detecting haplotype-tag described in claim 1, which is characterized in that the primer pair is such as Under:
Upstream primer: TCTGCGGCTTCCTGTGAGTGA;
Downstream primer: GCCACGCTTGCCTTCTAATGC.
3. application of the haplotype-tag described in claim 1 in corn yield improvement.
4. application of the primer pair as claimed in claim 2 in corn yield improvement.
5. the application in high yield corn germ plasm resource is being identified or screened to haplotype molecular labeling described in claim 1.
6. application of the haplotype molecular labeling described in claim 1 in corn breeding.
7. a kind of method for detecting haplotype molecular labeling described in claim 1, which is characterized in that use claim 2 primer To PCR amplification corn gene group DNA to be detected is carried out, with above-mentioned primer pair PCR amplification corn material genome to be detected DNA, according to amplified production, there are above-mentioned haplotype molecular labelings when determining maize seed to be detected.
8. the method according to the description of claim 7 is characterized in that the PCR amplification system is 25 μ L:10ng/ μ L DNA 1 μ L, Max Super-Fidelity DNA Polymerase of template 0.5 μ L, mix primer 2 μ L, ddH2O 8 μ L, Phanta 12.5 μ L, Dntp Mix of Max Buffer, 1 μ L.
9. the method according to the description of claim 7 is characterized in that the PCR response procedures are as follows: 95 DEG C of initial denaturation 3min; 95 DEG C of denaturation 15s, Tm annealing 15s, 72 DEG C of extension 2kb/min, totally 38 recycle;72 DEG C extend 5min eventually;12 DEG C of preservations.
CN201811197778.0A 2018-10-15 2018-10-15 One kind haplotype molecular labeling relevant to corn yield and its application Pending CN109055604A (en)

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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7825308B1 (en) * 2008-04-15 2010-11-02 Pioneer Hi-Bred International, Inc. Maize variety 32D78
CN103451200A (en) * 2012-05-29 2013-12-18 华中农业大学 Molecular marker for controlling corn plant height and applications thereof

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7825308B1 (en) * 2008-04-15 2010-11-02 Pioneer Hi-Bred International, Inc. Maize variety 32D78
CN103451200A (en) * 2012-05-29 2013-12-18 华中农业大学 Molecular marker for controlling corn plant height and applications thereof

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
CHAOBIN LI等: "Genome-Wide Characterization of cis-Acting DNA Targets Reveals the Transcriptional Regulatory Framework of Opaque2 in Maize", 《THE PLANT CELL》 *
FENGKAI WU等: "Molecular Evolution and Association of Natural Variation in ZmARF31 with Low Phosphorus Tolerance in Maize", 《FRONT PLANT SCI》 *
张力天: "玉米苗期耐低磷相关性状全基因组关联分析", 《中国优秀硕士学位论文全文数据库农业科技辑》 *

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