CN109762922A - SNP marker and its screening technique for Germplasm Resources on Phaseolus Vulgaris identification - Google Patents
SNP marker and its screening technique for Germplasm Resources on Phaseolus Vulgaris identification Download PDFInfo
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Abstract
The invention discloses the SNP marker identified for Germplasm Resources on Phaseolus Vulgaris and its screening techniques, using 200 parts of Germplasm Resources on Phaseolus Vulgaris materials as research object, using IIB-RAD technology, it is connect using standard type 5'-NNN-3' connector with digestion label, both-end sequencing is carried out in Illumina Hiseq Xten platform after library Quality Control is qualified, it is suitble to least SNP site combination, the foundation for Germplasm Resources on Phaseolus Vulgaris high throughput authentication technique system needed for identifying 200 parts of Germplasm Resources on Phaseolus Vulgaris to provide technical support to filter out.The big genome coverage rate of SNP marker quantity is high, and parting accuracy easy to operate is high, can form unified standard under various circumstances, SNP is compared with SSR, in terms of Varieties identification and database sharing advantageously.SNP in genome density more it is high more evenly, it is easier to realize that Data Integration compares, it is more high-throughput.
Description
Technical field
The present invention relates to the SNP marker identified for Germplasm Resources on Phaseolus Vulgaris and its screening technique, be related to molecular biology and
Field of bioinformatics.
Background technique
Traditional Germplasm Resources of Farm Crop identification technology is special by interracial feature mainly with field plot field plot test
Sex differernce distinguishes different kinds, this method time-consuming, labour-consuming, and vulnerable to human factor, the influence of environmental weather conditions, can not
Guarantee the accuracy and timeliness of testing result.The electrophoretic techniques that the nineties are risen mainly based on protein, isodynamic enzyme,
But Isozyme and protein is the product of gene expression, mode of inheritance and it is not all show as codominant inheritance, polymorphism compared with
It is few, relatively close and hereditary basis complexity the material of affiliation is difficult to identify.In recent years, using SSR as the molecular labeling skill of representative
Art is widely used to the germ plasm resources such as wheat, barley, corn and soybean, rice, sorghum, watermelon, wild cabbage, cucumber, tomato
Identification, the technology have many advantages, such as that polymorphism is high and quantity is abundant, not affected by environment, detection is quick, have wide application
Prospect.Single nucleotide polymorphism (Single Nucleotide Polymorphism, SNP) is got up as the latest development phase
The emerging molecular marking technique of the third generation, with detection flux is big, distribution density is wide, polymorphism is high, genetic stability is strong, speed
The features such as fast, analysis system high degree of automation are easy to establish normalizing operation, are suitble to extensive SNP research and gene point
Type.
Currently, SNP technology is used primarily in large Germplasm Resources of Farm Crop identification such as wheat, corn, in the kind of small ancestor crop
The identification aspect research of matter resource is less.Kidney bean is a kind of edible leguminous plant, is commonly called as kidney bean, traditional field
Field plot test is time-consuming and laborious at high cost, and very large deviation can also be generated by being protected from environmental, and there are also use SSR molecular marker
Identify Bean Varieties, but SNP is compared with SSR, in terms of Varieties identification and database sharing advantageously.SNP
In genome density more it is high more evenly, it is easier to realize that Data Integration compares, it is more high-throughput.
Summary of the invention
The present invention overcomes above-mentioned the deficiencies in the prior art, provide for Germplasm Resources on Phaseolus Vulgaris identification SNP marker and its
Screening technique, it is intended to identify the genetic resources that SNP marker technology is applied to phaseolus vulgaris seeds, kind intellectual property protection, kind
Identification etc., it is (restricted based on IIB type using IIB-RAD technology using 200 parts of Germplasm Resources on Phaseolus Vulgaris materials as research object
Endonuclease simplify gene), connect using standard type 5'-NNN-3' connector with digestion label, library Quality Control qualification after
Illumina Hiseq Xten platform carries out both-end sequencing, is suitble to needed for identifying 200 parts of Germplasm Resources on Phaseolus Vulgaris most to filter out
Few SNP site combination, the foundation for Germplasm Resources on Phaseolus Vulgaris high throughput authentication technique system provide technical support.
For one group of SNP site of Germplasm Resources on Phaseolus Vulgaris identification, the SNP site is as follows:
The site SNP1 is upper 46683rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP2 is upper 1017737th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP3 is upper 1086014th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP4 is upper 1254713rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP5 is upper 1311225th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP6 is upper 2131483rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP7 is upper 3007865th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP8 is upper 3135424th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP9 is upper 3923914th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP10 is upper 4942315th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP11 is upper 5432345th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP12 is upper 6522078th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP13 is upper 6620054th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP14 is upper 7722620th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP15 is upper 12162033rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP16 is upper 26664238th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP17 is upper 168481st deoxyribonucleotide of chromosome NC_023750.1；
The site SNP18 is upper 890411st deoxyribonucleotide of chromosome NC_023750.1；
The site SNP19 is upper 4491604th deoxyribonucleotide of chromosome NC_023750.1；
The site SNP20 is upper 30328074th deoxyribonucleotide of chromosome NC_023750.1；
The site SNP21 is upper 42337957th deoxyribonucleotide of chromosome NC_023750.1；
The site SNP22 is upper 3674063rd deoxyribonucleotide of chromosome NC_023751.1；
The site SNP23 is upper 28221712nd deoxyribonucleotide of chromosome NC_023751.1；
The site SNP24 is upper 36187449th deoxyribonucleotide of chromosome NC_023751.1；
The site SNP25 is upper 7900898th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP26 is upper 28047209th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP27 is upper 35763840th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP28 is upper 44269374th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP29 is upper 17327453rd deoxyribonucleotide of chromosome NC_023753.1；
The site SNP30 is upper 1206438th deoxyribonucleotide of chromosome NC_023754.1；
The site SNP31 is upper 11184227th deoxyribonucleotide of chromosome NC_023755.1；
The site SNP32 is upper 22706619th deoxyribonucleotide of chromosome NC_023756.1；
The site SNP33 is upper 34249539th deoxyribonucleotide of chromosome NC_023756.1；
The site SNP34 is upper 13974494th deoxyribonucleotide of chromosome NC_023757.1；
The site SNP35 is upper 18532434th deoxyribonucleotide of chromosome NC_023757.1；
The site SNP36 is upper 19472651st deoxyribonucleotide of chromosome NC_023757.1；
The site SNP37 is upper 24331691st deoxyribonucleotide of chromosome NC_023757.1；
The site SNP38 is upper 27358347th deoxyribonucleotide of chromosome NC_023757.1；
The site SNP39 is upper 43130693rd deoxyribonucleotide of chromosome NC_023757.1；
The site SNP40 is upper 8716636th deoxyribonucleotide of chromosome NC_023758.1；
The site SNP41 is upper 8945758th deoxyribonucleotide of chromosome NC_023758.1；
The site SNP42 is upper 21880092nd deoxyribonucleotide of chromosome NC_023758.1；
The site SNP43 is upper 46446342nd deoxyribonucleotide of chromosome NC_023758.1；
The site SNP44 is upper 48062570th deoxyribonucleotide of chromosome NC_023758.1；
The site SNP45 is upper 10896730th deoxyribonucleotide of chromosome NC_023759.1；
The site SNP46 is upper 16082599th deoxyribonucleotide of chromosome NC_023759.1；
The site SNP47 is upper 37515677th deoxyribonucleotide of chromosome NC_023759.1.
A kind of screening technique of one group of SNP site for Germplasm Resources on Phaseolus Vulgaris identification, includes the following steps:
1) genomic DNA is extracted from Kidney bean, using the sequencing library of IIB-RAD technology building Kidney bean, obtains original number
According to；
2) initial data is filtered optimization, obtains RAD sequencing data；
3) the RAD sequencing data obtained in step 2) is counted to and obtained the number of each individual RAD label and is sequenced deep
Degree, obtains the SNP site data A of sample；
4) the SNP site data A obtained in step 3) is subjected to parting and secondary filter optimization obtains SNP site data B；
5) core SNP is selected in the SNP site data B obtained from step 3), obtains minimum SNP used in identification Kidney bean
Sites Combination constructs clustering chadogram.
Further, the condition of the filtering optimization in the step 2) is as follows:
A does not contain the sequence of restriction enzyme (BsaXI) recognition site；
B rejects low quality sequence, i.e. base of the mass value lower than 30 is more than the 15% of series sum, is determined as low
Mass-sequential；
The sequence of c rejecting base containing N.
Further, the condition of the filtering optimization in the step 4) is as follows:
1. rejecting the SNP site of the smallest gene frequency (MAF) less than 0.01；
2. rejecting the site that SNP parting miss rate is higher than 20%；
3. rejecting the data of SNP site more than two on the same label.
Further, parting is carried out to SNP site using maximum likelihood method in the step 4).
Further, the step of selecting core SNP in the step 5) is as follows:
The SNP site for having missing is deleted in the SNP site data B that S1 is obtained in step 4), can obtain SNP site
Data a；
The SNP site data a connection obtained in step S1 is combined into different sequences by S2, using software screening method tag SNP,
Obtain SNP site data b；
The SNP site data b obtained in step S2 is connected again and is combined into different sequences by S3, samples multiple for correspondence
The sequence of product picks out the SNP site that can be distinguished these samples, as core SNP in conjunction with artificial screening.
Further, software screening method condition is MAF=0.2, hardy weinberg equilibrium p- in the step S2 of the step 5)
value> 10-7。
The present invention also provides the SNP sites to identify and/or distinguish the application in Germplasm Resources on Phaseolus Vulgaris.
A method of identifying and/or distinguish Germplasm Resources on Phaseolus Vulgaris using the SNP site, includes the following steps:
The base of above-mentioned SNP site (is from left to right, from top to bottom from left to right by dyeing by chromosome sequence by SS1
Body serial number just refers to position of the site on each chromosome from top to bottom) it connects, according to the polymorphic of different loci
Property composition represent the sequences of different Bean Varieties, establish Kidney bean information database；
For SS2 by the sequence alignment in the Kidney bean information database established in kind to be measured and step SS1, emphasis is to compare
Information on the site SNP；
SS3 may determine that if the sequence of kind to be measured is consistent with some sequence in database as corresponding to the sequence
Bean Varieties.
The utility model has the advantages that
The present invention provides the one group of SNP site and its screening technique of Kidney bean, and to these sites in germplasm resources on Phaseolus vulgaris identification
Application studied.The big genome coverage rate of SNP marker quantity is high, and parting accuracy easy to operate is high, under various circumstances
Unified standard can be formed, SNP is compared with SSR, and SNP density in full-length genome is high, representativeness is strong, genetic stability is good；SNP
Label is two allele, represents the smallest hereditary variation unit in genome, and data statistics is simple, accurate；The detection of SNP
Method is versatile and flexible, easily realizes automation.
Detailed description of the invention
Distribution (field color more deeply feel show section in Tag quantity more) of Fig. 1 SNP on Kidney bean chromosome.
Fig. 2 adjacent method constructs the systematic evolution tree of 200 Bean Varieties.
Specific embodiment
The screening of embodiment SNP site
1 materials and methods
1.1 test material
200 parts of Kidney bean test materials are from both at home and abroad, wherein 152 parts of materials are quoted from US West's plant introduction station
(Western Regional PI Station), from Mexico, Colombia, Peru, Guatemala, Bolivia etc.
10 countries, domestic germplasm resource bank collect 48 parts, and material type is divided into local varieties, wild varieties and cultivar.
1.2 DNA are extracted and IIB-RAD sequencing
Bean gene group DNA, which is extracted, uses Ezup pillar plant genome DNA extraction agent box (Sangon Biotech)
Extracting, specific method refer to kit specification.Then by 1% agarose and NanoDrop ND2000 (Thermo) to base
Because the quality and concentration of group DNA sample are detected.Simplify genome measurement by Qingdao Ou Yi Biotechnology Co., Ltd
Illumina Hiseq Xten platform is completed.
The analysis of 1.3 sequencing qualities and SNP Genotyping
The label sequencing library of 200 parts of Kidney beans is constructed using IIB-RAD technology, IIBRAD is a kind of simplified gene order-checking
Technology, principle are that genomic DNA is carried out digestion using IIB type restriction endonuclease, are then carried out to endonuclease bamhi
High-flux sequence.200 samples carry out both-end (Pair-end) sequencing in Illumina Hiseq Xten platform, using standard
Type NNN connector builds library.Original reads (minmal sequence unit when sequencing) is filtered (optimization) according to the following conditions, is obtained
Subsequent analysis is used for high quality reads: (1) rejecting the sequence for not containing restriction enzyme (BsaXI) recognition site；(2)
Reject low quality sequence (base of the mass value lower than 30 is more than 15%, is determined as low quality reads)；(3) base containing N is rejected
Sequence.
For there is the label parting for referring to genome, parting is carried out using maximum likelihood method using RADtyping software.For
The accuracy and preciseness for guaranteeing SNP site parting, carry out the filtering of the following conditions: 1) rejecting the smallest allele frequency
The SNP site of rate (MAF) less than 0.01；2) site that SNP parting miss rate is higher than 20% is rejected；3) the same label is rejected
The data of upper SNP site more than two.200 samples obtain 25,561 SNP sites altogether.
1.4 information analysis
It is for statistical analysis using Haploview 4.2, SNP label is selected, is obtained SNP minimum used in identification Kidney bean
Point combination, i.e. core SNP site calculate distance matrix, building cluster point by treebest software (Version:1.9.2)
Analyse chadogram.
2 results and analysis
The distribution of 2.1 SNP sites
Referring to the Genotyping strategy of Fu et al., with Kidney bean be with reference to genome (ftp:// ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/499/845/GCF_000499845.1_PhaVulg1_0/ GCF_000499845.1_PhaVulg1_0_genomic.fna.gz),According to comparison result count sample obtain number of tags and
Depth information simultaneously calculates sequencing data to the coverage of reference genome.The label average number of all samples is 83,497, is put down
Sequencing depth be 29 ×, coverage range 0.38%~0.49%.200 samples obtain 25,561 SNP sites altogether, make
The distribution map of SNP on chromosome is drawn with the mode for drawing window, window size is set as 200Kbp, moves 100Kbp every time,
The SNP number in section is counted, as a result as shown in Figure 1.Be evenly distributed density of the SNP on Kidney bean chromosome is 4.92X10-2
A kb-1
The screening of 2.2 core SNP sites
The SNP for having missing is deleted first from 25 obtained, 561 SNP sites, remaining 3302 SNP sites will be each
After 3302 sites not lacked of sample connect into sequence, 199 different sequences, but P-190 and P-200 two are obtained
A sample cannot distinguish between out.Tag SNP, screening conditions MAF=0.2 are selected using Haploview 4.2, breathes out enlightening Weinberg
Balance p-value > 10-7, 19 sites are obtained, 19 sites of each sample are connected into sequence, obtain 146 sequences.Its
In, the sample for the numbers such as some sequences are 16,17,5,3 corresponding.Continued to select 16 samples with Haploview software
In tag SNP (Tag SNP) pick out 10 sites in conjunction with artificial screening, 16 samples can be separated.For correspondence
The sequence of multiple samples finally uses 46 sites, obtains 199 different sequences in conjunction with artificial screening.In order to by P-190
It is distinguished with two samples of P-200, it is necessary to using the SNP site for having missing, by using NC_023749.1-7722596
Point obtains 200 different sequences, i.e., completes 200 Kidney bean sample area division of labor by 47 SNP sites and make.
The information of 1 47 SNP sites of table
2.3 clustering chadograms
Each individual SNP marker is joined end to end, if lacking corresponding site, is replaced with "-".The sequence of acquisition is adopted
Chadogram is constructed with adjacent method (neighbor-joining method).Pass through treebest software (Version:1.9.2)
Distance matrix is calculated, is obtained cluster analysis system chadogram (as shown in Figure 2).
2 47 SNP sites of embodiment are identifying and/or are distinguishing the application in Germplasm Resources on Phaseolus Vulgaris
The case where this 47 loci polymorphisms that P001 kind obtains after sequencing, is as follows:
The base of SNP1-SNP47 is linked in sequence composition sequence such as from left to right, from top to bottom by chromosome sequence
Shown in lower:
CGTTAAGGCCGGCCTTTTAAGGCCCCAGCCGGAGCCAACTAACCTTGTAGATCTTTCTCT GTCCCTG
GAACCGGAGAGCCGGCGATGGCCAAAG
By the sequence alignment in kind to be measured and the Kidney bean information database of foundation, emphasis is the letter compared on 47 sites
Breath, if consistent with the sequence of P-001 kind, therefore can determine whether that the kind to be measured is P-001 kind in information bank.
Claims (9)
1. one group of SNP site for Germplasm Resources on Phaseolus Vulgaris identification, which is characterized in that the SNP site is as follows:
The site SNP1 is upper 46683rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP2 is upper 1017737th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP3 is upper 1086014th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP4 is upper 1254713rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP5 is upper 1311225th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP6 is upper 2131483rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP7 is upper 3007865th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP8 is upper 3135424th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP9 is upper 3923914th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP10 is upper 4942315th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP11 is upper 5432345th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP12 is upper 6522078th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP13 is upper 6620054th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP14 is upper 7722620th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP15 is upper 12162033rd deoxyribonucleotide of chromosome NC_023749.1；
The site SNP16 is upper 26664238th deoxyribonucleotide of chromosome NC_023749.1；
The site SNP17 is upper 168481st deoxyribonucleotide of chromosome NC_023750.1；
The site SNP18 is upper 890411st deoxyribonucleotide of chromosome NC_023750.1；
The site SNP19 is upper 4491604th deoxyribonucleotide of chromosome NC_023750.1；
The site SNP20 is upper 30328074th deoxyribonucleotide of chromosome NC_023750.1；
The site SNP21 is upper 42337957th deoxyribonucleotide of chromosome NC_023750.1；
The site SNP22 is upper 3674063rd deoxyribonucleotide of chromosome NC_023751.1；
The site SNP23 is upper 28221712nd deoxyribonucleotide of chromosome NC_023751.1；
The site SNP24 is upper 36187449th deoxyribonucleotide of chromosome NC_023751.1；
The site SNP25 is upper 7900898th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP26 is upper 28047209th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP27 is upper 35763840th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP28 is upper 44269374th deoxyribonucleotide of chromosome NC_023752.1；
The site SNP29 is upper 17327453rd deoxyribonucleotide of chromosome NC_023753.1；
The site SNP30 is upper 1206438th deoxyribonucleotide of chromosome NC_023754.1；
The site SNP31 is upper 11184227th deoxyribonucleotide of chromosome NC_023755.1；
The site SNP32 is upper 22706619th deoxyribonucleotide of chromosome NC_023756.1；
The site SNP33 is upper 34249539th deoxyribonucleotide of chromosome NC_023756.1；
The site SNP34 is upper 13974494th deoxyribonucleotide of chromosome NC_023757.1；
The site SNP35 is upper 18532434th deoxyribonucleotide of chromosome NC_023757.1；
The site SNP36 is upper 19472651st deoxyribonucleotide of chromosome NC_023757.1；
The site SNP37 is upper 24331691st deoxyribonucleotide of chromosome NC_023757.1；
The site SNP38 is upper 27358347th deoxyribonucleotide of chromosome NC_023757.1；
The site SNP39 is upper 43130693rd deoxyribonucleotide of chromosome NC_023757.1；
The site SNP40 is upper 8716636th deoxyribonucleotide of chromosome NC_023758.1；
The site SNP41 is upper 8945758th deoxyribonucleotide of chromosome NC_023758.1；
The site SNP42 is upper 21880092nd deoxyribonucleotide of chromosome NC_023758.1；
The site SNP43 is upper 46446342nd deoxyribonucleotide of chromosome NC_023758.1；
The site SNP44 is upper 48062570th deoxyribonucleotide of chromosome NC_023758.1；
The site SNP45 is upper 10896730th deoxyribonucleotide of chromosome NC_023759.1；
The site SNP46 is upper 16082599th deoxyribonucleotide of chromosome NC_023759.1；
The site SNP47 is upper 37515677th deoxyribonucleotide of chromosome NC_023759.1.
2. a kind of screening technique of one group of SNP site for Germplasm Resources on Phaseolus Vulgaris identification, which is characterized in that including walking as follows
It is rapid:
1) genomic DNA is extracted from Kidney bean, using the sequencing library of IIB-RAD technology building Kidney bean, obtains initial data；
2) initial data is filtered optimization, obtains RAD sequencing data；
3) number and sequencing depth that the RAD sequencing data obtained in step 2) is counted to and obtained each individual RAD label, are obtained
Obtain the SNP site data A of sample；
4) the SNP site data A obtained in step 3) is subjected to parting and secondary filter optimization obtains SNP site data B；
5) core SNP is selected in the SNP site data B obtained from step 3), obtains minimum SNP site used in identification Kidney bean
Combination constructs clustering chadogram.
3. the screening technique of one group of SNP site according to claim 2 for Germplasm Resources on Phaseolus Vulgaris identification, feature exist
In the condition of the filtering optimization in the step 2) is as follows:
A does not contain the sequence of restriction enzyme enzyme recognition site；
B rejects low quality sequence, i.e. base of the mass value lower than 30 is more than the 15% of series sum, is determined as low quality
Sequence；
The sequence of c rejecting base containing N.
4. the screening technique of one group of SNP site according to claim 2 for Germplasm Resources on Phaseolus Vulgaris identification, feature exist
In the condition of the filtering optimization in the step 4) is as follows:
1. rejecting SNP site of the smallest gene frequency less than 0.01；
2. rejecting the site that SNP parting miss rate is higher than 20%；
3. rejecting the data of SNP site more than two on the same label.
5. the screening technique of one group of SNP site according to claim 2 for Germplasm Resources on Phaseolus Vulgaris identification, feature exist
In using maximum likelihood method to SNP site progress parting in the step 4).
6. the screening technique of one group of SNP site according to claim 2 for Germplasm Resources on Phaseolus Vulgaris identification, feature exist
In the step of selecting core SNP in the step 5) is as follows:
The SNP site for having missing is deleted in the SNP site data B that S1 is obtained in step 4), can obtain SNP site data
a；
The SNP site data a connection obtained in step S1 is combined into different sequences by S2, using software screening method tag SNP, is obtained
Obtain SNP site data b；
The SNP site data b obtained in step S2 is connected again and is combined into different sequences by S3, samples multiple for correspondence
Sequence, the SNP site that can be distinguished these samples, as core SNP are picked out in conjunction with artificial screening.
7. the screening technique of one group of SNP site according to claim 2 for Germplasm Resources on Phaseolus Vulgaris identification, feature exist
In software screening method condition is MAF=0.2, hardy weinberg equilibrium p-value > 10 in the step S2 of the step 5)-7。
8. the present invention also provides such as described in any item SNP sites of claim 1-7 to identify and/or distinguish germplasm resources on Phaseolus vulgaris money
Application in source.
9. a kind of utilize the side for identifying and/or distinguishing in Germplasm Resources on Phaseolus Vulgaris such as the described in any item SNP sites of claim 1-7
Method, which comprises the steps of:
SS1 is connected the base of above-mentioned SNP site by chromosome sequence from left to right, from top to bottom, according to different loci
Polymorphism composition represent the sequences of different Bean Varieties, establish Kidney bean information database；
For SS2 by the sequence alignment in the Kidney bean information database established in kind to be measured and step SS1, emphasis is to compare SNP
Information on site；
SS3 may determine that if the sequence of kind to be measured is consistent with some sequence in database as dish corresponding to the sequence
Beans kind.
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Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN110910959A (en) * | 2019-11-04 | 2020-03-24 | 中国水稻研究所 | Population genetic evolution map and construction method thereof |
| CN110910959B (en) * | 2019-11-04 | 2022-08-30 | 中国水稻研究所 | Population genetic evolution map and construction method thereof |
| CN113795597A (en) * | 2021-02-08 | 2021-12-14 | 中国农业科学院作物科学研究所 | Soybean SNP typing detection chip and application thereof in molecular breeding and basic research |
| WO2022165853A1 (en) * | 2021-02-08 | 2022-08-11 | 中国农业科学院作物科学研究所 | Soybean snp typing detection chip and use thereof in molecular breeding and basic research |
| CN113795597B (en) * | 2021-02-08 | 2023-11-17 | 中国农业科学院作物科学研究所 | Soybean SNP (Single nucleotide polymorphism) typing detection chip and application thereof in molecular breeding and basic research |
| CN113322341A (en) * | 2021-06-10 | 2021-08-31 | 山东大丰园农业有限公司 | Blueberry variety specific molecular marker locus as well as screening method and application thereof |
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Application publication date: 20190517 |