CN105950729A - SNP (single nucleotide polymorphism) marker related to hevea brasiliensis stem girth and application thereof - Google Patents
SNP (single nucleotide polymorphism) marker related to hevea brasiliensis stem girth and application thereof Download PDFInfo
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Abstract
The invention discloses an SNP (single nucleotide polymorphism) marker related to hevea brasiliensis stem girth and application thereof. The SNP marker is shown as in SEQID NO:1, and the base at the 132bpth site from the 5' end of the nucleotide sequence is G or T. The SNP marker is closely related to the stem girth of hevea brasiliensis, and can be effectively used for molecular marker assisted breeding of hevea brasiliensis.
Description
Technical field
The present invention relates to a kind of SNP marker and application thereof, particularly relate to a kind of relevant to rubber tree stem girth
SNP marker and application thereof.
Background technology
Rubber tree is a kind of tropical tree species played an important role in World Economics and military developments, and it produces
Natural rubber tree is a kind of important raw material of industry and strategic materials.At present, the face of China suitable planting rubber tree
Long-pending limited, actual cultivated area has reached the limit, does not the most expand cultivated area to increase the space of yield, greatly
Amplitude improves rubber tree yield per unit area and is an applicable Chinese rubber career development and alleviates natural rubber confession
Need the feasible way of contradiction pressure.
Rubber tree cross-breeding is always the conventional method of Rubber Tree Breeding, but the conventional breeding cycle is long, and
The scarcity of germ plasm resource, all restriction rubber tree prevalent variety cultivation and industry development.Along with Modern Molecular Biotechnology
Development, molecular marker assisted selection breeding can solve the problems referred to above to a certain extent, promotes Rubber Tree Breeding to enter
Journey.Molecular marker assisted selection breeding, i.e. molecular breeding, be that traditional genetic breeding has with modern molecular biology
The breeding method that machine combines, utilizes DNA molecular marker to select breeding material, comprehensive improvement selection-breeding thing
The important economical trait planted.In recent years, rubber tree molecular markers development and utilize work achieved with certain progress,
But far from meeting the demand of rubber tree molecular breeding.
The stem of rubber tree thick (stem girth) growth is to weigh rubber tree growing way, wood volume amount and Rubber Yield
Leading indicator, is also the important evidence planting glue productive technology management and economic management, and present stage excavates effective rubber
The molecular marker that thick (stem girth) character of gum stem is relevant, to realize seed selection in early days and to improve breeding accuracy, from
And obtain bigger breeding and genetic progress.
Summary of the invention
The invention reside in and overcome deficiency of the prior art, it is provided that be a kind of relevant to rubber tree stem girth, it is possible to have
Effectiveness is in the SNP marker of rubber tree selection-breeding and application etc. thereof.
Wherein, SNP (singlenucleotidepolymorphism, SNP, i.e. single nucleotide polymorphism) is
The class proposed by the human genome research center scholar Lander of Massachusetts Institute Technology for 1996 is divided
Sub-genetic marker, is primarily referred to as in genomic level the DNA sequence caused by the variation by single core thuja acid many
State property.The polymorphism that SNP shows relates only to the variation of single base, performance be have conversion, transversion,
Insertion and disappearance etc..
The first aspect of the invention is to provide a kind of SNP marker relevant to rubber tree stem girth, and its feature exists
In, the sequence of described SNP marker as shown in SEQIDNO:1, sequence shown in described SEQIDNO:1
From 5 ' ends, the base of 132bp site is G or T.According to the present invention, core shown in SEQIDNO:1
Nucleotide sequence is as follows:
GAAGCACTAAGACGGTCCATAGTGTACTTCAGAGGCCAACCGGTTG
GCACAATTGCTGCAATTGACCATGCCTCAGAGGAGGTTTTGAACTATGAT
CAGGTAATTCTTTAACTAAAATTTGATACTATAATXGTTTTTCTAGCTTTCAG
TATGATGAATGGGTGTGAGGCTTGGGAAATTTGCTATTGTAGTTTGTATTGT
ATAGAAGGTATGCTGTCAGATTGTAATCTGTCTCC (SEQIDNO:1).
Inventor finds, the site genotype of this SNP marker is heterozygosis GT and the rubber tree of the TT that isozygotys
Stem girth to be significantly coarser than genotype herein be the rubber tree of GG of isozygotying.And then, according to the present invention, by detection
The above-mentioned SNP of rubber tree, it is possible to effectively determine its stem girth character, specifically, as it was previously stated, this SNP
Loci gene type be the stem girth of the rubber tree of heterozygosis GT and the TT that isozygotys significantly be coarser than herein genotype for isozygotying
The genotype of the rubber tree of GG, such as this SNP site be heterozygosis GT or isozygoty TT time, then can determine
Rubber tree to be measured belong to the individuality that stem girth is thick.Thus, inventor determines, the SNP marker of the present invention and rubber
The stem girth character of gum is closely related, it is possible to be effective to the molecular mark of rubber tree.And then can
According to actual breeding demand, Rubber Tree Breeding material is carried out Seedling selection, be further able to be effectively improved breeding
Efficiency and accuracy, improve the genetic level of rubber tree reproductive population such that it is able to select accurately and efficiently
Rubber tree improved seeds.Additionally, utilize the SNP marker of the present invention to carry out rubber tree molecular mark,
There is early screening, the advantage that time-consuming, with low cost, accuracy is high.
The second aspect of the invention is to provide a kind of for detecting the SNP mark described in first aspect of the present invention
The primer pair of note, described primer is to having the nucleotides sequence shown in SEQIDNO:2 and SEQIDNO:3
Row.Specifically, the sequence of described primer pair is as follows:
Forward primer: GAAGCACTA AGACGGTCCATAG (SEQIDNO:2);
Downstream primer: GGAGACAGATTACAATCTGACAGC (SEQIDNO:3).
According to the present invention, utilize the primer of the present invention to can be effectively to the above-mentioned of rubber tree to be measured and stem girth
The fragment at the SNP marker place that shape is relevant carries out PCR amplification, so can effectively be realized by order-checking right
The detection of this SNP marker, determines the genotype in this SNP marker site of rubber tree to be measured, and then can be effective
Determine the stem girth character of rubber tree to be measured.Specifically, this SNP marker site genotype be heterozygosis GT or
It is the rubber tree of GG of isozygotying that the stem girth of rubber tree of TT of isozygotying significantly is coarser than genotype herein, such as this SNP
The genotype in site be heterozygosis GT or isozygoty TT time, then can determine rubber tree to be measured to belong to stem girth thick
Individual.Thus, with the primer pair of the SNP marker detecting the foregoing present invention, it is possible to be effective to rubber
The molecular mark of gum, and then early stage can be assisted to realize short time, low cost, high accuracy ground
Selection-breeding rubber tree improved seeds.
The third aspect of the invention is to provide a kind of for detecting the SNP mark described in first aspect of the present invention
The test kit of note, it comprises the primer pair described in second aspect of the present invention.I.e. the test kit of the present invention comprises
There is the primer pair of the nucleotide sequence shown in SEQIDNO:2 and SEQIDNO:3.According to the present invention,
Utilize the primer pair included in the test kit of the present invention, it is possible to effectively realize first side to rubber tree to be measured
The polymorphic detection of the SNP marker relevant to stem girth character described in face, determines this SNP of rubber tree to be measured
The genotype of marker site, and then can effectively determine the stem girth character of rubber tree to be measured.Specifically, this SNP
At marker site, genotype is that the stem girth of the rubber tree of heterozygosis GT and the TT that isozygotys significantly is coarser than genotype herein and is
Isozygoty the rubber tree of GG, the genotype of such as this SNP site be heterozygosis GT or isozygoty TT time, then can
Enough determine rubber tree to be measured belongs to the individuality that stem girth is thick.Thus, the present invention be used for detect the present invention first
The test kit of the SNP marker described in aspect, it is possible to be effective to the molecular mark of rubber tree, enter
And can assist and realize short time, low cost, high accuracy ground selection-breeding rubber tree improved seeds in early days.
The fourth aspect of the invention is to provide the SNP marker as described in terms of the present invention is first, the present invention
Primer described in second aspect to or third aspect of the present invention described in test kit in rubber tree selection-breeding
Purposes.
As it was previously stated, by can be used in detecting the SNP marker relevant to rubber tree stem girth character of the present invention
Reagent, the such as primer described in second aspect of the present invention to or comprise the test kit etc. of this primer pair, it is possible to
Effectively detect the genotype of the above-mentioned SNP marker determining rubber tree to be measured, and then based on the genotype obtained
Can effectively determine the stem girth character of rubber tree to be measured such that it is able to effectively auxiliary rubber tree selection-breeding.
And then, the fifth aspect of the invention is to provide a kind of method detecting rubber tree stem girth character, by right
Rubber tree to be measured carries out the detection of the SNP marker described in first aspect of the present invention, determines described rubber to be measured
The stem girth character of tree.
Specifically, can mark by can be used in detecting the SNP relevant to rubber tree stem girth character of the present invention
The reagent of note, the such as primer described in second aspect of the present invention to or comprise the test kit etc. of this primer pair, right
Rubber tree to be measured carries out PCR amplification, order-checking, in order to detection determines the above-mentioned SNP marker of rubber tree to be measured
Genotype, and then can effectively determine the stem girth character of rubber tree to be measured based on the genotype obtained.Wherein,
As it was previously stated, the stem girth of the rubber tree that this SNP marker site genotype is heterozygosis GT and the TT that isozygotys shows
Writing and being coarser than genotype herein is the rubber tree of GG of isozygotying, such as, be heterozygosis when the genotype of this SNP site
GT or isozygoty TT time, rubber tree the most to be measured belong to the individuality that stem girth is thick.Thus, the detection rubber of the present invention
The method of gum stem girth character, it is possible to detect rubber tree stem girth character quickly, efficiently and accurately, and then can
Be effective to the molecular mark of rubber tree such that it is able to auxiliary realize in early days the short time, low cost,
High accuracy ground selection-breeding rubber tree improved seeds.
Wherein, the method that rubber tree to be measured carries out SNP marker detection is not particularly limited.Order-checking, strand
Conformational polymerphism polymerase chain reaction PCR singlestrandconformationpolymorphism,
PCR-SSCP), restriction fragment length polymorphism polymerase chain reaction
(PCR-restriTCionfragmentlength polymorphism, PCR-RFLP) and flight time matter
The technology such as spectrum all can realize the detection of SNP.Wherein, order-checking is that a kind of accuracy is the highest, motility strong,
The detection technique that flux is big, the detection cycle is short.Pair of primers, amplification only need to be designed in the both sides of SNP site
The product of 200-1000bp, then the genotype of SNP site can be directly detected by order-checking.Thus, this
Invention uses the method for order-checking to carry out SNP marker detection.According to the present invention, by rubber tree to be measured is carried out
The detection of foregoing SNP marker, determines the stem girth character of described rubber tree to be measured, farther includes:
Extract the genomic DNA of rubber tree to be measured;Utilize the primer pair described in second aspect of the present invention, by described
The genomic DNA of rubber tree to be measured carries out PCR amplification, in order to obtain pcr amplification product;To described
Pcr amplification product checks order, in order to obtain sequencing result;Based on described sequencing result, determine described in treat
Survey the genotype of the described SNP marker of rubber tree;And described SNP marker of based on described rubber tree to be measured
Genotype, determine the stem girth character of described rubber tree to be measured.Thereby, it is possible to be effectively improved detection rubber tree stem
Enclose the efficiency of character.
In the present invention, the method for the genomic DNA extracting rubber tree to be measured is not particularly limited, and can use
Any of genome DNA extracting method or test kit are carried out.According to some concrete examples of the present invention,
CTAB method is used to extract the genomic DNA of rubber tree to be measured.Thereby, it is possible to it is good, pure effectively to obtain quality
Spend high genomic DNA, it is simple to subsequent step is carried out.
In the present invention, the genomic DNA of described rubber tree to be measured is carried out the condition of PCR amplification not by spy
Do not limit.According to some concrete examples of the present invention, the amplification system of this PCR amplification is calculated as with 25 μ l:
100-200ng/ μ l masterplate DNA 1 μ l, shown in SEQIDNO:2 and SEQIDNO:3 of 10 μMs
Forward primer and each 1 μ l of reverse primer, 10 × PCR reaction buffer 2.5 μ l, 2.5mM dNTP 2.0 μ l,
The TapDNA polymerase 0.2 μ l of 5U/ μ l, water surplus.This PCR reaction condition is: 95 DEG C of denaturations 5min
After, 94 DEG C of 30s, 60 DEG C of 30s, 72 DEG C of 1min totally 30 circulations, 72 DEG C extend 5min.Thus,
The fragment at the SNP marker place of the present invention can be expanded quickly, efficiently and accurately, it is thus achieved that target amplification is produced
Thing, it is simple to the carrying out of subsequent step.
In the present invention, the method checking order described pcr amplification product is not particularly limited, as long as can
Effectively obtain the pcr amplification product i.e. sequence of the fragment at SNP marker place.According to the present invention one
A little concrete examples, can use selected from sequence measurements such as HISEQ2000, SOLiD, 454 and unimolecules
Described pcr amplification product is checked order by least one.Thereby, it is possible to it is high flux, quick, efficient, accurate
Really obtain sequencing result.
The present invention is based on sequencing result, by comparison rubber tree with reference to genome sequence, it is possible to effectively determine to be measured
The genotype of the described SNP marker of rubber tree is GT, TT or GG.
In the present invention, the GT genotype of described SNP marker and the stem girth of TT genotype individuals are significantly coarser than
GG genotype individuals.The i.e. foregoing SNP marker of the present invention is closely related with the stem girth character of rubber tree.
Thus, based on a determination that the genotype of this SNP marker of rubber tree to be measured, it is possible to determine accurately and effectively and treat
Survey the stem girth character of rubber tree, such as when the genotype of this SNP site is GT or TT, rubber the most to be measured
That sets belongs to the individuality that stem girth is thick.And then the method for the present invention can be effective to the molecular marker auxiliary of rubber tree
Breeding such that it is able to auxiliary realizes short time, low cost, high accuracy ground selection-breeding rubber tree improved seeds in early days.
Beneficial effects of the present invention:
(1) SNP marker that the present invention provides is not limited by the age etc. of rubber tree, can be used for the morning of rubber tree
Phase selection-breeding, can remarkably promote the breeding process of rubber tree;
(2) detection rubber tree as shown in SEQIDNO.1 from 5 ' ends the side of SNP site of 132bp
Method, accurately and reliably, easy to operate;
(3) rubber tree detection of the SNP site of 132bp from 5 ' ends as shown in SEQIDNO.1,
Marker assisted selection for rubber tree stem girth character provides scientific basis.
Summary of the invention
Below in conjunction with specific embodiment, the present invention is further illustrated, to be more fully understood that the present invention.
Embodiment 1: the acquisition of the SNP marker relevant to rubber tree stem girth
1.1 rubber tree germplasm materials obtain
The colony used is rubber tree 1981'IRRDB kind matter, plants in Chinese Academy of Tropical Agricultural Sciences's rubber
Institute country rubber tree Germplasm Resources, its genetic background is mainly derived from Brazil's Amazon river region Acker
In state (Acre), Mato Grosso state (Mato Grosso) and Lang Duoniya stateThree
State.In June, 2014, gathering 34 parts of kind matter young leaflet tablet liquid nitrogen cryopreservations, to take back laboratory standby.
1.2 rubber tree germplasm materials DNA extraction
Take the rubber tree blade of freezen protective, use CTAB method to extract genomic DNA: (1) weighs 1g
Rubber tree tender leaf, grinds to form fine powder after liquid nitrogen flash freezer, transfer in 50ml centrifuge tube.(2) 10ml is added
2 × extract with CTAB buffer the beta-mercaptoethanol of 2% (the most in advance add) of 65 DEG C of preheatings, rotate gently from
Heart pipe makes plant tissue be uniformly dispersed in extraction buffer, 65 DEG C of incubation 1h, and rotates centrifugal the most gently
Pipe.(3) mixture is cooled to room temperature and adds isopyknic Tris-phenol chloroform isoamyl alcohol (25 24 1),
Then overturning centrifuge tube makes it mix, it is to note that do not vibrate, and prevents from interrupting DNA.(4) room temperature, 12000
Rpm is centrifuged 10min and makes its split-phase.(5) draw aqueous phase in another centrifuge tube, add the isopyknic chloroform of people:
Isoamyl alcohol (24 1), reverse mixing.Room temperature, 12000rpm is centrifuged 10min.(6) aqueous phase is drawn extremely
In another centrifuge tube, adding isopyknic isopropanol, reverse mixing, room temperature places 20min.(7) room temperature,
14000rpm is centrifuged 20min.Abandon supernatant, 75% ethanol rinse of precipitation use 1ml ice pre-cooling 2 times.(every
During secondary rinsing, room temperature, 14000rpm is centrifuged 10min).(8) abandon supernatant, superclean bench dries
DNA precipitates.It is then dissolved in 200 μ l TE (pH 8.0) buffer or ddH2O.Add people 1 μ l Rnase
A (10mg/m1), 37 DEG C of water-bath 30min ,-20 DEG C save backup.
1.3 use the order-checking of Sanger method to obtain the SNP marker that rubber tree stem girth is relevant
Based on Sanger method order-checking platform, 9 samples in above-mentioned colony are carried out yield related gene order-checking,
Analyze its nucleotide polymorphic site, use Tassel 3.0_standalone software analysis SNP site with
Know the dependency of economical character, find a SNP site relevant to rubber tree stem girth.This site is positioned at SEQ
The 132bp site of sequence shown in ID NO:1, represents at this with X in SEQ ID NO:1 sequence
Site, and the base in site herein is G or T.This site genotype is heterozygosis GT or the rubber of the TT that isozygotys
It is the rubber tree of GG of isozygotying that the stem girth of gum is significantly coarser than genotype herein.
Embodiment 2: the sequence verification of the SNP marker relevant to rubber tree stem girth and application
2.1 amplifications nucleotide fragments containing SNP site
With the aforementioned genomic DNA of rubber tree each to be measured obtained that extracts as masterplate, utilize forward primer F:
5'-GAA GCA CTA AGA CGG TCC ATA G-3'(SEQ ID NO:2) and reverse primer R:
5'-GGA GAC AGA TTA CAA TCT GAC AGC-3'(SEQ ID NO:3), amplify to be measured
The nucleotide fragments at SNP place.Wherein, PCR reaction system is 25 μ l:100-200ng/ μ l masterplate DNA
The each 1 μ l of 1 μ l, 10 μMs of primers F and R, 10 × PCR reaction buffer 2.5 μ l, 2.5mM dNTP 2.0 μ l,
The Tap archaeal dna polymerase 0.2 μ l of 5U/ μ l, water surplus;PCR reaction condition is: 95 DEG C of denaturations 5min
After, 94 DEG C of 30s, 60 DEG C of 30s, 72 DEG C of 1min totally 30 circulations, 72 DEG C extend 5min.
2.2 order-checkings identify SNP site genotype
By the PCR primer obtained in above-mentioned steps through sepharose electrophoresis detection, reclaim and be inserted into pMD
In 18-T carrier, each sample selects 6 monoclonals to carry out check order (raw work biological engineering Shanghai company limited),
The genotype of (i.e. the SNP marker of the present invention) at 132bp in identification SEQ ID NO:1 sequence.34
Genotype and the stem girth thereof of rubber tree to be measured this SNP site individual are as shown in table 1 below.
The genotype of 1 34 rubber trees to be measured of table this SNP site individual and stem girth thereof
Plant matter numbering | Genotype | (cm) is enclosed in footpath | Plant matter numbering | Genotype | (cm) is enclosed in footpath |
XJA00276 | GG | 82.2 | XJA04002 | GT | 91.9 |
XJA00323 | GG | 67.4 | XJA04071 | GG | 69.8 |
XJA00445 | GG | 75.2 | XJA04075 | GG | 71.2 |
XJA01197 | GG | 46.5 | XJA04152 | GG | 60.4 |
XJA01198 | GG | 64.8 | XJA04210 | GG | 67.1 |
XJA01663 | GG | 65.1 | XJA04285 | GT | 92.7 |
XJA01840 | TT | 80.7 | XJA04314 | GG | 65.8 |
XJA02702 | GG | 60.1 | XJA04397 | GT | 89.3 |
XJA02967 | GG | 60.3 | XJA04634 | TT | 91.6 |
XJA02968 | GG | 65.1 | XJA04971 | GG | 59.4 |
XJA02972 | GT | 77.8 | XJA04975 | GG | 65.4 |
XJA02974 | GT | 88.2 | XJA05006 | GG | 73.4 |
XJA03000 | GG | 82.5 | XJA05190 | GG | 68 |
XJA03019 | GG | 81.7 | XJA05255 | GG | 71.6 |
XJA03642 | GG | 80.6 | XJA05381 | GG | 68.2 |
XJA03765 | GG | 81.4 | XJA05728 | GG | 74.6 |
XJA03788 | GG | 77.9 | XJA05787 | GT | 79.3 |
2.3 SNP site genotype and the association analysis of stem girth
Result based on table 1, utilizes the general linear model analysis of Tassel 3.0_standalone software
The genotype of SNP site and the relatedness of stem girth, find the genotype of this SNP site and the dependency of stem girth
Reach pole significant level (R2=0.28209743, p=0.00606920).Use DPS software analysis SNP
Difference relation between loci gene type frequency and stem girth such as table 2, wherein GT heterozygous and homozygous of TT
Body stem girth average is higher, and the homozygous individual stem girth average of GG is relatively low, and GT heterozygous and homozygous of TT
Body stem girth average reaches pole significant level (P < 0.01) with the difference of GG genotype individuals stem girth average, i.e. contains
Individuality (GT heterozygous and the homozygous individuality of the TT) stem girth of allele T is all coarser than GG genotype individuals.
And then, it was demonstrated that nucleotide sequence shown in SEQ ID NO:1 is the 132nd bit base G or T and rubber from 5 ' ends
Tree stem girth character significant correlation, for the SNP marker that rubber tree stem girth character is relevant, the GT of this SNP marker
The stem girth of heterozygous and the homozygous individuality of TT is significantly coarser than GG genotype individuals, i.e. contains allele T's
Individual (GT heterozygous and the homozygous individuality of TT) stem girth is all coarser than GG genotype individuals.
Difference relation between table 2 SNP site of the present invention genotypic frequency and stem girth
Above the specific embodiment of the present invention is described in detail, but it has been intended only as example, the present invention
It is not restricted to particular embodiments described above.To those skilled in the art, any to the present invention
The equivalent modifications carried out and replacement are the most all among scope of the invention.Therefore, in the essence without departing from the present invention
The impartial conversion made under god and scope and amendment, all should contain within the scope of the invention.
Claims (8)
1. a SNP marker relevant to rubber tree stem girth, it is characterised in that the sequence of described SNP marker
Row are as shown in SEQIDNO:1, and sequence shown in described SEQIDNO:1 is 132bp site from 5 ' ends
The base at place is G or T.
SNP marker the most according to claim 1, it is characterised in that the heterozygosis of described SNP marker
The stem girth of GT genotype and TT genotype rubber tree of isozygotying significantly is coarser than GG genotype rubber tree of isozygotying.
3. the primer pair being used for test right requirement SNP marker described in 1 or 2, it is characterised in that
The nucleotide sequence of described primer pair is as shown in SEQIDNO:2 and SEQIDNO:3.
4. the test kit being used for test right requirement SNP marker described in 1 or 2, it is characterised in that
It comprises the primer pair described in claim 3.
5. primer described in SNP marker, claim 3 as claimed in claim 1 or 2 to or right
Require the purposes in rubber tree selection-breeding of the test kit described in 4.
6. the method detecting rubber tree stem girth character, it is characterised in that by rubber tree to be measured is carried out
The detection of the SNP marker described in claim 1 or 2, determines the stem girth character of described rubber tree to be measured.
Method the most according to claim 6, it is characterised in that by rubber tree to be measured is carried out right
The detection of requirement SNP marker described in 1 or 2, determines the stem girth character of described rubber tree to be measured, further
Including:
Extract the genomic DNA of rubber tree to be measured;
Utilize the primer pair described in claim 3, the genomic DNA of described rubber tree to be measured is carried out PCR
Amplification, in order to obtain pcr amplification product;
Described pcr amplification product is checked order, in order to obtain sequencing result;
Based on described sequencing result, determine the genotype of the described SNP marker of described rubber tree to be measured;And
The genotype of described SNP marker based on described rubber tree to be measured, determines the stem of described rubber tree to be measured
Enclose character.
Method the most according to claim 7, it is characterised in that the heterozygosis GT base of described SNP marker
Because the stem girth of type and TT genotype rubber tree of isozygotying significantly is coarser than GG genotype rubber tree of isozygotying.
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Cited By (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN113846177A (en) * | 2021-07-30 | 2021-12-28 | 中国热带农业科学院橡胶研究所 | SNP molecular marker for rubber tree secondary emulsion tube array number and application thereof |
CN117487950A (en) * | 2022-05-31 | 2024-02-02 | 中国热带农业科学院橡胶研究所 | Construction method of rubber tree variety DNA fingerprint library |
Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN101812433A (en) * | 2009-11-10 | 2010-08-25 | 中国热带农业科学院橡胶研究所 | Use of hevea brasiliensis invertase and coding gene thereof |
CN101812434A (en) * | 2009-11-10 | 2010-08-25 | 中国热带农业科学院橡胶研究所 | Invertase and application of encoding gene thereof |
-
2016
- 2016-05-19 CN CN201610335314.6A patent/CN105950729B/en active Active
Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN101812433A (en) * | 2009-11-10 | 2010-08-25 | 中国热带农业科学院橡胶研究所 | Use of hevea brasiliensis invertase and coding gene thereof |
CN101812434A (en) * | 2009-11-10 | 2010-08-25 | 中国热带农业科学院橡胶研究所 | Invertase and application of encoding gene thereof |
Non-Patent Citations (6)
Title |
---|
DEJUN LI 等: "Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids", 《SCIENTIFIC REPORTS》 * |
LEONARDO RIPPEL SALGADO 等: "De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers", 《BMC GENOMICS》 * |
WIRULDA POOTAKHAM 等: "SINGLE NUCLEOTIDE POLYMORPHISM MARKER DEVELOPMENT IN THE RUBBER TREE, HEVEA BRASILIENSIS (EUPHORBIACEAE)", 《AMERICAN JOURNAL OF BOTANY》 * |
戚继艳 等: "橡胶树胚胎晚期丰富蛋白基因HbLEA1的克隆和表达分析", 《热带作物学报》 * |
林飞鹏 等: "橡胶树HbSUT3的分子进化分析", 《中国农业科学》 * |
龙翔宇 等: "橡胶树糖代谢调控基因HbF2KP的克隆及表达", 《南京林业大学学报(自然科学版)》 * |
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN113846177A (en) * | 2021-07-30 | 2021-12-28 | 中国热带农业科学院橡胶研究所 | SNP molecular marker for rubber tree secondary emulsion tube array number and application thereof |
CN113846177B (en) * | 2021-07-30 | 2023-04-25 | 中国热带农业科学院橡胶研究所 | SNP molecular marker for number of secondary emulsion tubes of rubber tree and application of SNP molecular marker |
CN117487950A (en) * | 2022-05-31 | 2024-02-02 | 中国热带农业科学院橡胶研究所 | Construction method of rubber tree variety DNA fingerprint library |
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