CN105861498B - One kind SNP marker relevant to rubber tree dry incineration method and its application - Google Patents

One kind SNP marker relevant to rubber tree dry incineration method and its application Download PDF

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CN105861498B
CN105861498B CN201610335315.0A CN201610335315A CN105861498B CN 105861498 B CN105861498 B CN 105861498B CN 201610335315 A CN201610335315 A CN 201610335315A CN 105861498 B CN105861498 B CN 105861498B
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rubber tree
snp marker
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incineration method
genotype
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CN105861498A (en
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唐朝荣
龙翔宇
胡彦师
秦云霞
方永军
何斌
赵庆洲
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Rubber Research Institute Chinese Academy Tropical Agricultural Sciences
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    • C12Q2600/156Polymorphic or mutational markers

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Abstract

The invention discloses a kind of SNP marker relevant to rubber tree dry incineration method and its applications.Wherein, it is C or A which, which is base of the nucleotide sequence shown in SEQIDNO:1 from 5 ' ends at the site 120bp,.The dry incineration method of SNP marker and rubber tree of the invention is closely related, can be effective for the molecular mark of rubber tree.

Description

One kind SNP marker relevant to rubber tree dry incineration method and its application
Technical field
The present invention relates to a kind of SNP marker and its applications, more particularly to a kind of SNP mark relevant to rubber tree dry incineration method Note and its application.
Background technique
Rubber tree is a kind of tropical tree species played an important role in world economy and military developments, and what is produced is natural Rubber tree is a kind of important raw material of industry and strategic materials.Currently, the limited area of Chinese suitable planting rubber, practical to plant Area has reached the limit, increases the space of yield without expanding cultivated area, increases substantially the production of rubber tree unit area Amount is a suitable Chinese rubber career development and the feasible way for alleviating natural rubber imbalance between supply and demand pressure.
Rubber tree crossbreeding is always the conventional method of Yield Breeding, however the conventional breeding period is long and germplasm provides The scarcity in source, restriction rubber tree prevalent variety cultivation and industry development.With the development of Modern Molecular Biotechnology, molecular labeling is auxiliary It helps selection and use that can solve the above problems to a certain extent, pushes Rubber Tree Breeding process.Molecular marker assisted selection breeding, That is molecular breeding is traditional genetic breeding and the breeding method that modern molecular biology organically combines, utilizes DNA molecular marker pair Breeding material is selected, the important economical trait of comprehensive improvement breeding species.In recent years, rubber tree molecular markers development and benefit Certain progress has been achieved with work, but far from meeting the needs of rubber tree molecular breeding.
The relevant molecular labeling of effective rubber tree dry incineration method character also to be excavated at this stage, to realize early yield Seed selection and raising Yield Breeding accuracy, to obtain bigger Yield Breeding and genetic progress.
Summary of the invention
The invention reside in deficiency in the prior art is overcome, provide one kind, Neng Gouyou relevant to rubber tree dry incineration method Effectiveness is in the SNP marker of rubber tree breeding and its application etc..
Wherein, SNP (singlenucleotidepolymorphism, SNP, i.e. single nucleotide polymorphism) be 1996 by The molecule genetic marker that the human genome research center scholar Lander of Massachusetts Institute Technology is proposed, is primarily referred to as DNA sequence polymorphism caused by a single nucleotide variation in genomic level.The polymorphism that SNP is shown relates only to The variation of single base, performance is that have conversion, transversion, insertion and missing etc..
The first aspect of the invention is to provide a kind of SNP marker relevant to rubber tree dry incineration method, which is characterized in that As shown in seqid no:1, sequence shown in the SEQIDNO:1 is from 5 ' ends at the site 120bp for the sequence of the SNP marker Base is C or A.According to the present invention, nucleotide sequence shown in SEQIDNO:1 is as follows:
AGTTATCATAATGGAGGATCTTGGCCAGGTTTGTCCATTTTCTCTCTCTATTTAAACTGAATATCTCTCTATTAATA TGATGTTCATGCCGTTAGGATAGCATTCCTGTCATGTTTCACXAGAGGTCTTAGAACATTATTTGGTGTTATTTTGT TGAATAGAGGCTATTGATGAATTATACATAAAATTTATTGTATTCAGCCTAGTTAT ACCCTAGACA (SEQIDNO: 1)。
Inventors have found that genotype is that the dry incineration method of the rubber tree of heterozygosis CA is significantly higher than at the site of the SNP marker Genotype is the rubber tree of homozygosis CC and homozygosis AA herein.In turn, according to the present invention, by detecting the above-mentioned SNP of rubber tree, energy Its dry incineration method character is enough effectively determined, specifically, as previously mentioned, the SNP site genotype is the rubber tree of heterozygosis CA Dry incineration method is significantly higher than the rubber tree that genotype herein is homozygosis CC and homozygosis AA, such as the genotype of the SNP site is miscellaneous When closing CA, then can determine rubber tree to be measured belongs to the high individual of dry incineration method.Inventor determines as a result, SNP of the invention It marks and is closely related with the dry incineration method character of rubber tree, it can be effective for the molecular mark of rubber tree.In turn Seedling selection can be carried out to Rubber Tree Breeding material according to practical breeding demand, be further able to effectively improve the efficiency of breeding And accuracy, the genetic level of rubber tree reproductive population is improved, so as to accurately and efficiently select the excellent product of rubber tree Kind.In addition, carrying out rubber tree molecular mark using SNP marker of the invention, have early screening, save the time, Advantage low in cost, accuracy is high.
The second aspect of the invention is to provide a kind of for detecting drawing for SNP marker described in first aspect of the present invention Object pair, the primer pair have nucleotide sequence shown in SEQIDNO:2 and SEQIDNO:3.Specifically, the sequence of the primer pair Column are as follows:
Upstream primer: AGTTATCATAATGGAGGATCTTGGCC (SEQIDNO:2);
Downstream primer: TGTCTAGGGTATAACTAGGCTGAATACAAT (SEQIDNO:3).
It according to the present invention, can be effectively to the above-mentioned and dry incineration method of rubber tree to be measured using primer pair of the invention Segment where the relevant SNP marker of shape carries out PCR amplification, and then the inspection to the SNP marker can be effectively realized by sequencing It surveys, determines the genotype in the rubber tree to be measured SNP marker site, and then can effectively determine the dry incineration method of rubber tree to be measured Shape.Specifically, the dry incineration method for the rubber tree that genotype is heterozygosis CA at the SNP marker site is significantly higher than genotype herein and is The rubber tree of homozygous CC and homozygosis AA, for example, the SNP site genotype be heterozygosis CA when, then can determine rubber tree to be measured Belong to the high individual of dry incineration method.It, can be effective as a result, with the primer pair for detecting mentioned-above SNP marker of the invention In the molecular mark of rubber tree, and then early stage can be assisted to realize short time, low cost, high accuracy ground breeding rubber Gum excellent variety.
The third aspect of the invention is to provide a kind of for detecting the examination of SNP marker described in first aspect of the present invention Agent box, it includes primer pairs described in the second aspect of the present invention.In kit i.e. of the invention comprising have SEQIDNO:2 and The primer pair of nucleotide sequence shown in SEQIDNO:3.According to the present invention, primer included in kit of the invention is utilized It is right, it can effectively realize the more of the SNP marker relevant to dry incineration method character described in the first aspect of rubber tree to be measured State property detection, determines the genotype in the rubber tree to be measured SNP marker site, and then can effectively determine the dry glue of rubber tree to be measured Yield traits.Specifically, the dry incineration method for the rubber tree that genotype is heterozygosis CA at the SNP marker site is significantly higher than base herein Because of the rubber tree that type is homozygosis CC and homozygosis AA, for example, the SNP site genotype for heterozygosis CA when, then can determine rubber to be measured Gum belongs to the high individual of dry incineration method.It is of the invention for detecting SNP marker described in first aspect of the present invention as a result, Kit, can effective for the molecular mark of rubber tree, and then can assist early stage realize the short time, it is low at This, high accuracy ground breeding rubber tree excellent variety.
The fourth aspect of the invention is to provide SNP marker, the present invention second as described in first aspect of the present invention Purposes of the kit described in primer pair described in aspect or third aspect of the present invention in rubber tree breeding.
As previously mentioned, by can be used in detecting SNP marker relevant to rubber tree dry incineration method character of the invention Reagent, such as primer pair described in the second aspect of the present invention or the kit comprising the primer pair etc., can be effectively detected It determines the genotype of the above-mentioned SNP marker of rubber tree to be measured, and then rubber to be measured can effectively be determined based on the genotype of acquisition The dry incineration method character of tree, so as to effective auxiliary rubber tree breeding.
In turn, the fifth aspect of the invention is to provide a kind of method for detecting rubber tree dry incineration method character, by right Rubber tree to be measured carries out the detection of SNP marker described in first aspect present invention, determines the dry incineration method of the rubber tree to be measured Character.
It specifically, can be by can be used in detecting SNP marker relevant to rubber tree dry incineration method character of the invention Reagent, such as primer pair described in the second aspect of the present invention or the kit comprising the primer pair etc., to rubber tree to be measured PCR amplification, sequencing are carried out, to detect the genotype for the above-mentioned SNP marker for determining rubber tree to be measured, and then the base based on acquisition Because type can effectively determine the dry incineration method character of rubber tree to be measured.Wherein, as previously mentioned, genotype at the SNP marker site It is significantly higher than the rubber tree that genotype herein is homozygous CC He homozygosis AA for the dry incineration method of the rubber tree of heterozygosis CA, such as when this When the genotype of SNP site is heterozygosis CA, then rubber tree to be measured belongs to the high individual of dry incineration method.Inspection of the invention as a result, The method for surveying rubber tree dry incineration method character, can quickly, efficiently and accurately detect rubber tree dry incineration method character, Jin Erneng Enough molecular marks effective for rubber tree, so as to assist early stage to realize short time, low cost, high accuracy Ground breeding rubber tree excellent variety.
Wherein, the method for carrying out SNP marker detection to rubber tree to be measured is not particularly limited.Sequencing, single-strand conformation polymorphism Property polymerase chain reaction PCR singlestrandconformationpolymorphism, PCR-SSCP), restriction fragment Length polymorphism polymerase chain reaction (PCR-restriTCionfragmentlength polymorphism, PCR-RFLP) And the detection of SNP may be implemented in the technologies such as flight time mass spectrum.Wherein, sequencing is a kind of accuracy highest, strong flexibility, is led to The detection technique that amount is big, detection cycle is short.Only pair of primers need to be designed in the two sides of SNP site, expand the production of 200-1000bp Object, then pass through the genotype for being sequenced and can directly detecting SNP site.Thus, the present invention carries out SNP marker using the method for sequencing Detection.According to the present invention, by carrying out the detection of mentioned-above SNP marker to rubber tree to be measured, the rubber to be measured is determined The dry incineration method character of tree further comprises: extracting the genomic DNA of rubber tree to be measured;Utilize the second aspect institute of the present invention The genomic DNA of the rubber tree to be measured is carried out PCR amplification, to obtain pcr amplification product by the primer pair stated;To described Pcr amplification product is sequenced, to obtain sequencing result;Based on the sequencing result, the institute of the rubber tree to be measured is determined State the genotype of SNP marker;And the genotype of the SNP marker based on the rubber tree to be measured, determine the rubber to be measured The dry incineration method character of gum.Thereby, it is possible to effectively improve the efficiency of detection rubber tree dry incineration method character.
In the present invention, the method for extracting the genomic DNA of rubber tree to be measured is not particularly limited, and can be used any known Genome DNA extracting method or kit carry out.Some specific examples according to the present invention extract rubber to be measured using CTAB method The genomic DNA of gum.Thereby, it is possible to effectively obtain genomic DNA high-quality, with high purity, carried out convenient for subsequent step.
In the present invention, the condition that the genomic DNA of the rubber tree to be measured carries out PCR amplification is not particularly limited.Root According to some specific examples of the invention, the amplification system of the PCR amplification is calculated as with 25 μ l: 1 μ l of 100-200ng/ μ l template DNA, Forward primer shown in 10 μM of SEQIDNO:2 and SEQIDNO:3 and each 2.5 μ of 1 μ l, 10 × PCR reaction buffer of reverse primer The 0.2 μ l of TapDNA polymerase of 2.0 μ l, 5U/ μ l of l, 2.5mM dNTP, water surplus.The PCR reaction condition are as follows: 95 DEG C of initial denaturations After 5min, 94 DEG C of 30s, 60 DEG C of 30s, 72 DEG C of 1min are recycled for 30 totally, 72 DEG C of extension 5min.Thereby, it is possible to quick, efficient, quasi- The segment where SNP marker of the invention really is expanded, target amplification product is obtained, convenient for the progress of subsequent step.
In the present invention, the method that the pcr amplification product is sequenced is not particularly limited, as long as can effectively obtain The sequence of segment where pcr amplification product, that is, SNP marker.Some specific examples according to the present invention, can be using choosing The pcr amplification product is sequenced from at least one of the sequencing approaches such as HISEQ2000, SOLiD, 454 and unimolecule.By This, can it is high-throughput, quickly, efficiently and accurately obtain sequencing result.
The present invention is based on sequencing results, refer to genome sequence by comparing rubber tree, can effectively determine rubber to be measured The genotype of the SNP marker of tree is CA, CC or AA.
In the present invention, the dry incineration method of the CA genotype individuals of the SNP marker is significantly higher than CC and AA genotype individuals. Mentioned-above SNP marker i.e. of the invention and the dry incineration method character of rubber tree are closely related.As a result, based on determining rubber to be measured The genotype of the SNP marker of gum can accurately and effectively determine the dry incineration method character of rubber tree to be measured, such as the SNP When the genotype in site is CA, then rubber tree to be measured belongs to the high individual of dry incineration method.And then method of the invention can have Effectiveness is in the molecular mark of rubber tree, so as to assist early stage to realize the short time, low cost, select to high accuracy Educate rubber tree excellent variety.
Beneficial effects of the present invention:
(1) SNP marker provided by the invention is not limited by age of rubber tree etc., can be used for the early stage breeding of rubber tree, It can significantly promote the breeding process of rubber tree;
(2) method of detection rubber tree SNP site of 120bp from 5 ' ends as shown in SEQIDNO.1, accurately and reliably, It is easy to operate;
(3) detection of rubber tree SNP site of 120bp from 5 ' ends as shown in SEQIDNO.1, produces for rubber tree dry glue The marker assisted selection of amount character provides scientific basis.
Summary of the invention
Below with reference to specific embodiment, the present invention is further illustrated, to better understand the invention.
Embodiment 1: the acquisition of SNP marker relevant to rubber tree dry incineration method
1.1 rubber tree germplasm materials obtain
Used group is rubber tree 1981'IRRDB germplasm, is planted in Rubber Institute, Chinese Academy of Agricultural Science National rubber tree Germplasm Resources, genetic background are mainly derived from Brazilian Amazon river region Acree state (Acre), horse Hold in the palm Grosso state (Mato Grosso) and the state Lang DuoniyaThree states.Acquire 34 parts of germplasm childrens in June, 2014 It is spare that leaflet tablet liquid nitrogen cryopreservation takes back laboratory.
1.2 rubber tree germplasm materials DNA are extracted
The rubber tree blade for taking freezen protective extracts genomic DNA using CTAB method: (1) weighing 1g rubber tree tender leaf, liquid It is ground into fine powder after nitrogen is quick-frozen, is transferred in 50ml centrifuge tube.(2) 2 × CTAB that 10ml65 DEG C of preheating is added extracts buffering (2% beta -mercaptoethanol has been added) in liquid in advance, and gently rotating centrifuge tube makes plant tissue be uniformly dispersed in extraction buffer, 65 DEG C of incubation 1h, and centrifuge tube is gently rotated frequently.(3) mixture is cooled to room temperature that isometric Tris- Fen ︰ Lv Fang ︰ is added is different Amylalcohol (25 ︰, 24 ︰ 1), then overturning centrifuge tube makes its mixing, it is to note that not vibrate, prevent from interrupting DNA.(4) room temperature, 12000rpm centrifugation 10min makes its split-phase.(5) water phase is drawn into another centrifuge tube, adds the chloroform that people is isometric: isoamyl alcohol (24 ︰ 1), is mixed by inversion.Room temperature, 12000rpm are centrifuged 10min.(6) water phase is drawn into another centrifuge tube, is added isometric Isopropanol is mixed by inversion, and is placed at room temperature for 20min.(7) room temperature, 14000rpm are centrifuged 20min.Supernatant is abandoned, precipitating is pre- with 1ml ice 75% cold ethyl alcohol rinses 2 times.(every time when rinsing, room temperature, 14000rpm is centrifuged 10min).(8) supernatant, superclean bench are abandoned On dry DNA precipitating.It is then dissolved in 200 μ l TE (pH 8.0) buffers or ddH2O.Add 1 μ l Rnase A (10mg/ of people M1), 37 DEG C of water-bath 30min, -20 DEG C save backup.
1.3 obtain the relevant SNP marker of rubber tree dry incineration method using the sequencing of Sanger method
Based on Sanger method microarray dataset, the sequencing of yield related gene is carried out to 9 samples in above-mentioned group, analyzes its core Nucleotide polymorphism site is related to known economical character using Tassel 3.0_standalone software analysis SNP site Property, find a SNP site relevant to rubber tree dry incineration method.The site is located at the 120bp of sequence shown in SEQ ID NO:1 At site, in SEQ ID NO:1 sequence with X indicate this at site, and the base in site is C or A herein.Gene at the site Type is that be significantly higher than genotype herein be homozygous CC or the rubber tree of homozygosis AA to the dry incineration method of the rubber tree of heterozygosis CA.
Embodiment 2: the sequence verification and application of SNP marker relevant to rubber tree dry incineration method
2.1 nucleotide fragments of the amplification containing SNP site
Using the aforementioned genomic DNA for extracting each rubber tree to be measured obtained as template, forward primer F:5 '-AGT is utilized TAT CAT AAT GGA GGA TCT TGG CC-3 ' (SEQ ID NO:2) and reverse primer R:5 '-TGT CTA GGG TAT AAC TAG GCT GAA TAC AAT-3 ' (SEQ ID NO:3), amplifies the nucleotide fragments where SNP to be measured.Wherein, PCR reaction system is 25 μ l:100-200ng/ μ l template DNA, 1 μ l, 10 μM of primers Fs and each 1 μ l, 10 × PCR reaction buffer of R The 0.2 μ l of Tap archaeal dna polymerase of 2.5 μ l, 2.5mM dNTP, 2.0 μ l, 5U/ μ l, water surplus;PCR reaction condition are as follows: 95 DEG C pre- After being denaturalized 5min, 94 DEG C of 30s, 60 DEG C of 30s, 72 DEG C of 1min are recycled for 30 totally, 72 DEG C of extension 5min.
2.2 sequencing identification SNP site genotype
The PCR product obtained in above-mentioned steps is detected through agarose electrophoresis, recycles and is inserted into pMD 18-T carrier In, each sample selects 6 monoclonals that (raw work bioengineering Shanghai Co., Ltd) is sequenced, and identifies SEQ ID NO:1 sequence In column at 120bp (SNP marker i.e. of the invention) genotype.The genotype of the individual SNP site of 34 rubber trees to be measured and Its dry incineration method is as shown in table 1 below.
The genotype and its dry incineration method of the individual SNP site of 1 34, table rubber trees to be measured
Germplasm number Genotype Dry incineration method (g) Germplasm number Genotype Dry incineration method (g)
XJA00276 CC 14.7 XJA03765 CA 63.8
XJA00323 CC 12.2 XJA03788 CC 40.3
XJA00445 CC 14.3 XJA04002 CC 18.8
XJA01197 CC 29.8 XJA04075 CC 30.1
XJA01198 CC 23.0 XJA04210 CC 16.0
XJA01663 CC 11.0 XJA04314 CC 20.9
XJA01840 CC 31.9 XJA04397 CC 22.6
XJA02534 CC 26.6 XJA04634 CC 44.3
XJA02682 CC 32.5 XJA04971 CC 15.8
XJA02702 CC 15.9 XJA04975 AA 11.7
XJA02967 CC 20.0 XJA05006 CA 55.6
XJA02968 CC 15.9 XJA05190 CC 10.4
XJA02974 CC 26.2 XJA05255 CC 28.4
XJA03000 CC 30.7 XJA05381 CC 26.7
XJA03015 CC 37.1 XJA05539 CC 12.4
XJA03019 CC 32.3 XJA05728 CC 24.4
XJA03642 CC 30.5 XJA05787 CC 44.8
The association analysis of 2.3SNP loci gene type and dry incineration method
It is based on table 1 as a result, using Tassel 3.0_standalone software general linear model analyze SNP site Genotype and dry incineration method relevance, the correlation of the genotype for finding the SNP site and dry incineration method reached extremely aobvious Write level (R2=0.455377, p=0.000045).Using DPS software analyze SNP site genotype frequency and dry incineration method it Between difference relationship such as table 2, wherein CA heterozygous individual dry incineration method mean value highest, the homozygous individual dry incineration method mean value time of CC It, the homozygous dry incineration method mean value of AA is minimum, and CA genotype individuals dry incineration method mean value and CC genotype individuals dry incineration method The difference of mean value reaches extremely significant horizontal (P < 0.01), CA genotype individuals dry incineration method mean value and AA genotype individuals dry incineration method The difference of mean value reaches extremely significant horizontal (P < 0.01).In turn, it was demonstrated that nucleotide sequence shown in SEQ ID NO:1 is the from 5 ' ends Base A or C and rubber tree dry incineration method character at the site 120bp is significant related, is the relevant SNP mark of rubber tree yield traits Note, the dry incineration method of the CA genotype individuals of the SNP marker are significantly higher than CC and AA genotype individuals.
Difference relationship between the SNP site genotype frequency of the present invention of table 2 and dry incineration method
Specific embodiments of the present invention are described in detail above, but it is merely an example, the present invention is simultaneously unlimited It is formed on particular embodiments described above.To those skilled in the art, any couple of present invention carries out equivalent modifications and Substitution is also all among scope of the invention.Therefore, without departing from the spirit and scope of the invention made by equal transformation and Modification, all should be contained within the scope of the invention.

Claims (8)

1. a kind of SNP marker relevant to rubber tree dry incineration method, which is characterized in that the sequence of the SNP marker such as SEQ ID Shown in NO:1, base of the sequence shown in the SEQ ID NO:1 from 5 ' ends at the site 120bp is C or A.
2. SNP marker according to claim 1, which is characterized in that the heterozygosis CA genotype rubber tree of the SNP marker Dry incineration method is significantly higher than homozygous CC and homozygosis AA genotype rubber tree.
3. a kind of primer pair for SNP marker described in detecting as claimed in claim 1 or 22, which is characterized in that the core of the primer pair Nucleotide sequence is as shown in SEQ ID NO:2 and SEQ ID NO:3.
4. a kind of kit for SNP marker described in detecting as claimed in claim 1 or 22, which is characterized in that it includes claims Primer pair described in 3.
5. SNP marker as claimed in claim 1 or 2, primer pair as claimed in claim 3 or reagent as claimed in claim 4 Purposes of the box in rubber tree breeding.
6. a kind of method for detecting rubber tree dry incineration method character, which is characterized in that wanted by carrying out right to rubber tree to be measured The detection of SNP marker described in asking 1 or 2 determines the dry incineration method character of the rubber tree to be measured.
7. according to the method described in claim 6, it is characterized in that, as claimed in claim 1 or 2 by being carried out to rubber tree to be measured SNP marker detection, determine the dry incineration method character of the rubber tree to be measured, further comprise:
Extract the genomic DNA of rubber tree to be measured;
Using primer pair as claimed in claim 3, the genomic DNA of the rubber tree to be measured is subjected to PCR amplification, to obtain Pcr amplification product;
The pcr amplification product is sequenced, to obtain sequencing result;
Based on the sequencing result, the genotype of the SNP marker of the rubber tree to be measured is determined;And
The genotype of the SNP marker based on the rubber tree to be measured determines the dry incineration method character of the rubber tree to be measured.
8. the method according to the description of claim 7 is characterized in that the heterozygosis CA genotype rubber tree of the SNP marker is dry Glue yield is higher than homozygosis CC and homozygosis AA genotype rubber tree.
CN201610335315.0A 2016-05-19 2016-05-19 One kind SNP marker relevant to rubber tree dry incineration method and its application Expired - Fee Related CN105861498B (en)

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