Mung bean SNP liquid chip, molecular marker combination and application thereof

Abstract

The application discloses a mung bean SNP liquid-phase chip, a molecular marker combination and application thereof, and relates to the technical field of plant molecular genetics and breeding. The SNP molecular marker combination is composed of 20526 SNP molecular markers. A mung bean SNP chip is also provided, which comprises probes and / or primers for detecting the mung bean SNP molecular marker combination. The mung bean SNP chip can quickly and effectively track the genetic material of mung beans, and is favorable to accelerating the breeding process of mung beans with high yield, early maturity, high quality and disease resistance, and improving the efficiency of excellent new variety breeding. The patent technology is the first mung bean breeding chip on the market, has numerous important yield, quality and disease resistance function sites, wide genetic diversity, more uniform coverage of chromosomes, more flexible chip, higher detection rate and better repeatability.

Description

TECHNICAL FIELD

[0001] The application belongs to the technical field of plant molecular genetics and breeding, and particularly relates to a mung bean SNP liquid chip, a molecular marker combination and application thereof. BACKGROUND

[0002] Mung bean (Vigna radiata L.) belongs to the genus Vigna of the family Leguminosae and contains 11 chromosomes. As a functional food raw material, mung bean seeds are rich in protein, various essential amino acids for human body, carbohydrates, dietary fiber and bioactive substances. With the improvement of people's living standards and the demand for healthy diet, the high nutritional value of mung bean has been valued by people, and the demand for mung bean is gradually increasing.

[0003] The demand for mung bean in China is about more than 900,000 tons per year, and the mung bean yield in China is about 600,000 tons, about 33% of which needs to be imported. In scientific research, accelerating the breeding of high-quality, high-yield and early-maturing mung bean varieties, carrying out joint research and improving the adaptability, high yield and quality of mung bean varieties are the main research directions of mung bean breeding. However, the current mung bean molecular breeding research mainly targets a small number of quality trait loci, and there is no effective molecular breeding system for mung bean yield and quality controlled by multiple genes.

[0004] Mung bean is a legume plant originally from Asia and widely planted in temperate and subtropical regions. The countries with large planting areas in Asia include India, China, Thailand and the like, and the planting areas in the United States and Australia are also expanding. Mung bean is rich in nutrients, and the protein content in the seeds is as high as 19.5% to 33.1%, which is significantly higher than that of cereal crops, 2.3 times of wheat flour, 3.0 times of corn flour, 3.2 times of rice and 2.7 times of millet. Mung bean is also a crop with strong stress resistance, and it has a short growth period, a large planting period flexibility, a wide adaptability, is conducive to land use and land reclamation, and has high economic benefits. However, the current mung bean molecular breeding research is still very few, and there is no effective molecular breeding system for yield and quality controlled by multiple genes, and there is no report of mung bean whole genome SNP typing chip further limiting its application in mung bean scientific research and molecular breeding.

[0005] DNA molecular marker technology is a technical method for identifying genetic variation by using the differences of DNA between biological individuals. There are four types of DNA molecular markers at present; the first type mainly includes restriction fragment length polymorphism markers (RFLP), variable number of tandem repeat sequence markers (VNTR), single-strand conformation polymorphism RFLP (SSCP, RFLP) and the like; the second type mainly includes random amplified polymorphic DNA (RAPD), simple sequence repeat DNA marker (SSR), sequencing tag site (STS), expressed sequence tag (EST) and sequenced amplified region (SCAR); the third type mainly includes amplified fragment length polymorphism (AFLP) and cleaved amplified polymorphic sequence (CAPS) markers; and the fourth type is DNA marker based on single nucleotide polymorphism, mainly single nucleotide polymorphism (SNP). Compared with other genetic markers such as morphological markers, biochemical markers and cytological markers, the DNA molecular marker has the following advantages: most of them are co-dominant, and it is very convenient to select recessive traits; the genome variation is rich, and the number of markers is large; and the detection means is simple and rapid. With the development of molecular biology technology, the DNA molecular marker technology has been applied to the construction of genetic linkage map and gene location, genetic breeding, species relationship identification, gene library construction, gene cloning and the like, and is widely used in animals and plants.

[0006] SNP (Single Nucleotide Polymorphism) refers to the polymorphism of DNA sequence formed by the variation of a single nucleotide on a genome. Any nucleotide on a genomic DNA has four possible forms (A, T, G and C), and in general, a site has only two base variations in the species, which is converted into another base by a base conversion (Transition) or transversion (Transversion), and the frequency of conversion is usually higher than that of transversion, so the SNP marker is usually biallelic, and the SNP is widely distributed on the genome. There are two main types of new high-throughput molecular marker technologies based on SNP: one type is high-throughput molecular marker technology based on new generation sequencing technology; and the other type is molecular marker technology based on gene chip technology.

[0007] Based on the SNP genotype, the mung bean can be subjected to genetic diversity analysis, whole genome association analysis, QTL fine mapping, molecular evolution analysis, molecular marker assisted breeding and whole genome selection. The mung bean will play a significant role in the aspects of polymerization breeding and broadening the genetic basis of varieties.

[0008] At present, there is no mung bean whole genome SNP typing chip, and in the molecular breeding era, the related blank limits the application of Chinese mung bean scientific research and molecular breeding. SUMMARY

[0009] Therefore, the main purpose of the present application is to provide a mung bean SNP molecular marker combination, which is composed of 20526 SNP molecular markers, as shown in Table 2 in the embodiment, the position and variation information of the SNP site are represented in the form of chromosome: physical position: reference genotype / variation allele genotype.

[0010] The present application utilizes high-throughput DNA sequencing technology to perform whole genome resequencing on 613 mung bean samples from different countries and regions. The analysis uses Wm82.a2.v1 as the reference genome, uses BWA software for alignment, and uses GATK-3.8 software for variation detection. The raw variation data obtained after analysis of the 613 samples is filtered through the inherent screening strategy process (see Figure 1 ), and a total of 4,048,862 high-quality variation sites are obtained. According to the self-defined chip design principle, 20526 core SNP sites are selected from them.

[0011] The second purpose of the present application is to provide a mung bean SNP chip (green chip No. 1), which comprises probes and / or primers for detecting the above-mentioned mung bean SNP molecular marker combination.

[0012] The green chip No. 1 chip data of the present application is derived from the resequencing results of 613 mung beans, most of which are Chinese core germplasm, have wide representativeness, and have important significance in Chinese mung bean genomics research; the reference genome of the green chip No. 1 is SuLv1.

[0013] Among them, the probe for detecting the above-mentioned mung bean SNP molecular marker combination is a single-stranded DNA synthesized according to the mung bean 20K (a total of 20526) SNP molecular marker.

[0014] The third purpose of the present application is to provide a kit comprising probes and / or primers for detecting the above-mentioned mung bean SNP molecular marker combination.

[0015] The present application also provides the application of the above-mentioned mung bean SNP molecular marker combination or the above-mentioned mung bean SNP chip or the above-mentioned kit in mung bean variety identification.

[0016] The present application also provides the application of the above-mentioned mung bean SNP molecular marker combination or the above-mentioned mung bean SNP chip or the above-mentioned kit in detecting mung bean yellow mosaic disease-resistant breeding materials.

[0017] The application also aims to provide the application of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in the mung bean whole genome association analysis.

[0018] The application also aims to provide the application of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in the molecular marker assisted breeding.

[0019] The application also aims to provide the application of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in the mung bean germplasm resource DNA fingerprint analysis.

[0020] The application also aims to provide the application of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in the mung bean whole genome selection breeding.

[0021] The application also aims to provide the application of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in any one of the following:

[0022] (1) mung bean kinship identification;

[0023] (2) mung bean population structure analysis;

[0024] (3) mung bean genetic diversity analysis;

[0025] (4) mung bean variety authenticity test;

[0026] (5) mung bean excellent cultivar genotype identification.

[0027] The application has at least the following beneficial effects:

[0028] (1) evenly distributed: the average distance is about 23 kb, and the coverage of SNP sites with MAF>0.1 reaches 99.4% in the 60K interval.

[0029] (2) high representation: information comes from the resequencing data of 613 representative mung bean core germplasm in China and internationally.

[0030] (3) strong function: a high proportion of SNPs are Large-effect sites of annotated genes, covering important gene-related sites, domestication selection intervals, and SNP sites specific to wild and cultivated mung bean subgroups.

[0031] (4) good practicability: basically covering important trait-related markers published, highlighting important traits such as flavonoids, amino acids, vitexin, plant height, hundred-grain weight, disease resistance, drought and waterlogging tolerance, etc.

[0032] (5)Support site filling: with super-high density site filling rate.

[0033] (6)Chip upgradeable: can continuously increase the number of significant QTN / QTL sites and closely related sites according to the increased phenotype data and filled genome sequence, and upgrade the chip.

[0034] That is, the scheme of the present application is the first mung bean breeding chip on the market, which has many important yield, quality and disease resistance functional sites, wide genetic diversity, more uniform coverage of chromosomes, more flexible chip, higher detection rate and better repeatability; the provided SNP molecular marker combination for mung bean genotyping, the distribution of the mung bean whole genome chip is uniform, representative, functional and practical, supports site filling; according to the increased phenotype data, the number of closely related sites is filled, the chip is upgraded, has great economic practical value and application prospect; can quickly and effectively track the genetic material of mung bean, which is beneficial to speed up the breeding process of mung bean high yield, early maturity, high quality and disease resistance, and improve the efficiency of excellent new variety breeding. BRIEF DESCRIPTION OF DRAWINGS

[0035] Figure 1 It is a basic flow chart of site screening of the green chip No. 1 chip of the present application; wherein, QTL-quantitative trait locus; GWAS-whole genome association analysis; mGWAS-metabolite whole genome association analysis; MAF-minimum allele frequency; SNP-single nucleotide polymorphism.

[0036] Figure 2 It is a whole genome distribution map of the 20K liquid phase gene chip site of the present application; wherein, 1). More than 19,700 representative variation sites covering the genome are selected; 2). The chip covers more than 300 significant sites related to metabolite traits; 3). The chip covers more than 10 yield trait new sites, such as the significant QTN site of pods per plant shown in the figure; 4). The chip covers part of the functional genes / QTNs reported in the literature.

[0037] Figure 3 It is the SNP site density of the green chip No. 1 chip of the present application; wherein, the number of sites represents the number of single nucleotide polymorphisms.

[0038] Figure 4 It is the MAF distribution of the SNP site of the present application.

[0039] Figure 5 It is the functional site analysis result of the green chip No. 1.

[0040] Figure 6 It is the population structure analysis chart of the green chip No. 1 in 892 MAGIC materials; a) MAGIC population structure analysis, b) MAGIC population structure display chart.

[0041] Figure 7 Manhattan plot for resistance to yellow mosaic disease (GLM) and validation results; a) Manhattan plot for resistance to yellow mosaic disease, b) Validation plot for Chr4-14132960 developed KASP molecular marker.

[0042] Figure 8 Manhattan plot for initial flowering date (GLM).

[0043] Figure 9 Manhattan plot for 100-seed weight (GLM).

[0044] Figure 10 Phenotypes for each trait and prediction. DETAILED DESCRIPTION

[0045] The technical solutions in the embodiments of the present application will be clearly and completely described below. Obviously, the described embodiments are only a part of the embodiments of the present application, rather than all the embodiments. Based on the embodiments in the present application, all the other embodiments obtained by a person of ordinary skill in the art without creative work are within the protection scope of the present application.

[0046] In addition, the technical solutions in each embodiment of the present application can be combined with each other, but it must be based on that a person of ordinary skill in the art can realize the combination, and when the combination of the technical solutions appears contradictory or unachievable, it should be considered that the combination of the technical solutions does not exist and is not within the protection scope of the present application.

[0047] The schemes proposed by the present application will be specifically described below through specific embodiments:

[0048] Example 1 SNP site screening

[0049] The chip site screening process is as shown in Figure 1 .

[0050] (1) Collection of initial data set

[0051] The green core No. 1 SNP marker information is derived from 613 domestic and foreign mung bean germplasm resources (including 414 core germplasm resources, 199 micro-core germplasm resources, covering northeast, Huanghuaihai and southern ecological regions of cultivated varieties, local varieties and wild varieties and foreign germplasm, constituting a natural population with rich genotype and phenotype data) provided by the Economic Crops Institute of Jiangsu Academy of Agricultural Sciences. First, Novaseq platform (Illumina Inc.) sequencing technology is used for whole genome sequencing, and 10X whole genome coverage is obtained for each sample. The reads with low quality and with linker contamination are excluded to obtain clean data. All clean data is mapped to sulv 1 genome by BWA software, PCR repeats are removed, and GATK software is used for variant typing, and then 3,068,512 SNP variation sites are obtained.

[0052] At the same time, the green core No. 1 SNP marker information is also derived from QTL, GWAS, domestication related genes, intraspecific subpopulation difference, excellent traits, terminator, alternative splicing, nonsynonymous mutation loci, and locus type profile 1:

[0053] Table 1 Green core No. 1 SNP marker information is also derived from

[0054]

[0055] (2) Quality control of initial data

[0056] Evaluation: (1) Quality control: sample call rate 90%, site call rate 90%, MAF>0.05, sample heterozygosity rate 20% or less, Hardy-Weinberg equilibrium 0.00001; (2) non-repeated sample; all the above quality controls are completed by Plink software, and finally 80,216 site sets are obtained for subsequent Green Core No. 1 chip selection. Chip site screening: the above data are screened according to the self-defined site screening principle: (1) tiling order 1 = excellent QTL site, GWAS site; (2) tiling order 2 = interspecific and intraspecific subpopulation difference domestication site; (3) tiling order 3 = significant mGWAS site, site significantly associated with metabolites; (4) tiling order 4 = important gene (VIP), terminator / alternative splicing / non-synonymous mutation site. According to the priority of tiling order, the site is further considered comprehensively, and the principle of MAF≥0.01 is retained, the site without polymorphism is deleted, the site with interfering flanking sequence of SNP is deleted, then the sequence is selected by sliding window, in addition, the factors to be considered include: non-A / T, G / C site priority; uniform coverage of whole genome; site evaluation score above 0.4; probe sequence repeatability below 99%; deletion rate below 3%; whether it is single copy; not in transposon, repeat region.

[0057] The variation site set of Green Core No. 1 chip is constructed by the above principles, and finally 20526 molecular markers (green bean 20K) are screened. The distribution of them on the green bean genome is shown in Figures 2-3 , and the MAF value is shown in Figure 4 . It can be seen that the average distance of the molecular markers provided by the application is about 23Kb, and the coverage of SNP sites with MAF>0.1 in 60K interval reaches 99.4%. The information of the 20526 SNP molecular markers is shown in Table 2, that is, the green bean SNP molecular marker combination composed of 20526 SNPs in the application.

[0058] Table 2 Position information of green bean 20K liquid phase gene chip SNP site

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[0094] (3)Detection principle

[0095] There are four bases of plant genomic DNA, which are A, C, G and T. In the detection process of SNP chip, A and T are labeled with DNP (dinitrophenyl), which can bind to anti-DNP antibody labeled with red fluorescence, thereby showing red color; C and G are labeled with biotin, which can bind to streptavidin labeled with green fluorescence, thereby showing green color. When the SNP typing is A / T and G / C, only one color label is needed to be detected by two probes; when the SNP typing is non-A / T and G / C, two color labels are needed to be detected by one probe.

[0096] (4) Detection method

[0097] (1) DNA extraction: DNA extraction kit is used to extract DNA from the green bean sample to be tested; (2) DNA quality inspection: DNA quality is analyzed by agarose gel electrophoresis; the integrity is accurately detected by Agilent 2100. The standard for quality inspection is that the total amount is not less than 2 μg, the sample concentration is less than 50 ng / μl, and there is no impurity; (3) library construction: the qualified sample DNA is randomly broken by using an ultrasonic crusher, and DNA fragments of the required length are recovered by electrophoresis. Adapters are added to the ends to form a library; (4) sequencing library construction: the sample library is amplified and purified by using LMPCR, which is used for subsequent probe hybridization experiment; (5) hybridization capture library construction: 300 ng of the constructed sequencing library is taken, freeze-dried, and then added with green bean 20K SNP target capture probe and hybridization reagent. After denaturation, it is incubated at 60°C for 16 hours to complete the hybridization reaction. The hybridization product is washed with washing solution, and then 5 rounds of PCR are carried out to complete the construction of the hybridization capture library; (6) hybridization capture library quality inspection: the effective concentration of the library is accurately quantified by using qPCR to ensure the quality of the library; (7) sequencing: the library concentration is detected by using Qubit fluorescence quantifier, and the fragment size is detected by agarose gel electrophoresis. After the concentration and fragment size are determined to be qualified, the sequencing library construction is completed. The prepared library is used for high-throughput sequencing by using Huada sequencer; (8) analysis: after obtaining the off-machine data, the sequencing data is aligned with the reference genome by using BWA, and the standard call SNP of the data is carried out by using GATK; thereby the genomic genotyping result of the sample to be tested is obtained.

[0098] Example 2: Capture efficiency of target sites of mung bean 20K liquid gene chip

[0099] A total of 25 test samples were tested, 18 of which were mung bean cultivars, 7 of which were wild species and related species mung bean materials. The mung bean 20K liquid gene chip was designed with an additional 5% target sites based on the pre-evaluation. The actual capture rate was more than 20K target sites, which could normally capture the results. The overall site capture rate was more than 96%, reaching the predetermined design capture efficiency. It can be standardized and popularized for detection. The specific detection rate statistics are shown in Table 3.

[0100] Table 3: Capture data of target sites of mung bean 20K liquid gene chip

[0101] Test sample name Coverage depth coverage_1x Coverage depth coverage_5x Coverage depth coverage_10x SL1 0.999226 0.998888 0.998549393 KPS1 0.999081 0.998356 0.998017504 KPS2 0.985107 0.980223 0.977660655 NM 0.96359 0.954258 0.949180407 G12 0.983947 0.975968 0.973308834 G204 0.978047 0.971423 0.96890866 ASG 0.981722 0.974421 0.97108457 G274 0.97945 0.962913 0.945457183 G327 0.990571 0.975291 0.959818191 JL7 0.984333 0.977274 0.97393743 V2709 0.94918 0.933417 0.926986123 V2817 0.969876 0.961462 0.95899618 NJY 0.975485 0.966829 0.96320294 Xbz 0.975727 0.966153 0.96252599 NAU 0.973986 0.964557 0.959818191 CN60 0.984817 0.97945 0.97746724 G250 0.984333 0.974179 0.97026256 G393 0.983995 0.977371 0.974420966 TC1966 0.878923 0.836903 0.824379866 JP229327 0.816788 0.773367 0.758764083 JP229281 0.828538 0.78149 0.76809632 JP229290 0.831294 0.777719 0.762245539 JP229287 0.837725 0.79295 0.780329771 JP226873 0.799478 0.740003 0.696484696 NI1135 0.668972 0.607272 0.589720033

[0102] Example 3: Analysis of genetic function sites of Green No. 1

[0103] Experimental material: Green No. 1; genotype data source: chip acquisition. Green No. 1 has agronomic trait-related sites and disease trait-related sites, as shown in Table 1. Figure 5 The related sites on the functional genes include reported agronomic trait-related sites including hundred-grain weight, grain length, starch, protein, and pod number per plant, and metabolite flavonoids; and also include stress resistance-related sites such as mung bean yellow mosaic virus disease, salt tolerance, and drought tolerance.

[0104] Example 4: Application of mung bean SNP molecular marker combination in polymorphism and population structure analysis of mung bean breeding materials.

[0105] Using the developed mung bean 20K liquid breeding chip, 892 magic materials of mung bean were detected (8 parent-derived populations), and the target site genotype was extracted. The average detection rate of the sample was 99.10%, and the consistent rate of the same batch of materials was 99.62%, indicating that the liquid chip target site detection rate of the present scheme is high, and the genotyping result is accurate and reliable. ADMIXTURE was used to estimate the ancestry of individuals, and Admixture divided the genotypes into 5 equal parts for cross-validation, and found the best K value from 1 to 12 (a). Figure 6 Using Plink software to calculate the genetic distance matrix and clustering analysis of mung bean breeding materials, a phylogenetic tree diagram was constructed to determine the genetic relationship, evolutionary relationship and composition structure of different materials. Using the present application, 892 mung bean materials from different populations were clustered and analyzed, and it was found that the mung bean breeding materials were divided into 8 subpopulations, which was consistent with the actual grouping, and the analysis results are shown in Figure 6 b, indicating that the 20526 SNP sites screened have high representativeness.

[0106] Example 5: Green Core No. 1 Anti-yellow leaf disease association analysis

[0107] Experimental material: 892 materials magic material population analysis; genotype data source: obtained by Green Core No. 1 chip detection; analysis model: mixed linear model.

[0108] Experimental results: Using mixed linear model (MLM) to analyze the correlation of the test population to yellow leaf disease, the results show that under the P<1x10 -7 level, 1 significant associated site with yellow leaf disease is located on 4 chromosomes Figure 7 a) Near the site Chr4-14132960, there are 10 genes, including EVM0033654, EVM0003495, EVM0024933, EVM0009281, EVM0009509, EVM0029763, EVM0004327, EVM0008202, EVM0009824, EVM0009117 and EVM0030586, etc. Among them, the Arabidopsis thaliana homologous gene AT5G24320 of EVM0003495 is a gene with WD40 repeat domain, which has typical disease resistance gene structure characteristics. EVM0030586 (PR gene) has a pathogenesis-related protein against environmental stress. At the same time, the Chr4-14132960 site can develop KASP molecular markers for the identification of yellow leaf disease-resistant varieties. 76 materials were tested by KASP molecular marker mymv-1, and the accuracy of distinguishing between disease-resistant and disease-susceptible varieties reached 98.61% (b), and Green Core No. 1 can effectively perform GWAS analysis on green bean traits. Figure 7

[0109] Example 6: Green Core No. 1 green bean flowering period association analysis

[0110] Experimental material: 414 green bean materials for flowering period trait association analysis; genotype data source: obtained by Green Core No. 1 chip detection; analysis model: 3VmrMLM mixed linear model.

[0111] Experimental results: Using 3VmrMLM to analyze the correlation of the test population to flowering period, the results show that under the P<1x10 -7 level, 15 significant QTNs are significantly associated with flowering period. Chr3-47757894 (P-=5.21E-10~1.02E-09; LOD=11.30; r 2 =0.95%) is associated with DAF Figure 8 ​), which is near 7 genes including EVM0009174, EVM0010314, VrLFR, EVM0030971, EVM0026674, EVM 0024476 and EVM0028334, wherein VrLFR / EVM0022630 is significantly differentially expressed between different flowering period germplasm.

[0112] Example 7: Association analysis of grain weight of Green No.1

[0113] Experimental materials: 414 materials for grain weight trait association analysis; genotype data source: obtained by Green No.1 chip detection; analysis model: 3VmrMLM mixed linear model.

[0114] Experimental results: using 3VmrMLM to perform association analysis on flowering period traits of the test population, the results show that, under P<1x10 -7 significantly associated with mung bean grain at 19 sites under P<1x10 2 =0.47%~1.14%) Figure 9 ) associated with HSW; DAF associated, which is near 4 genes including VrKIN-14L, EVM0001506, EVM0032287, and EVM0029001, wherein VrKIN-14L / EVM0013458 is significantly differentially expressed between different grain weight germplasm, and the related gene has less research reports.

[0115] Example 8: Application of Green No.1 in GS

[0116] Experimental materials: 892 materials of magic material population analysis; analysis: important phenotypes such as plant height, disease resistance, and 100-seed weight; genotype data source: obtained by Green No.1 chip detection; analysis model: BB, BL, BRR, GB, RF and RKHS model.

[0117] Prediction accuracy verification: 5fold cross-validation and 10fold cross-validation, and comparison of the correlation between predicted GEBV and phenotype. The results show that, the prediction accuracy of RF model constructed based on pedigree relationship is the lowest in all traits, which is below 0.73. The prediction accuracy of BL method is between 0.73 and 0.86, and the prediction effect is better than other methods. It can be seen that, in this experiment, the pedigree relationship between materials cannot improve the prediction accuracy, and the BL prediction effect is better based on the model constructed by genotype data. Taking BL as an example, the prediction accuracy of plant height is the highest, reaching 0.83, and the accuracy of 100-seed weight and disease resistance also reaches above 0.75 (Table 4, Figure 10). These selected marker loci have a significant advantage in prediction accuracy. The machine learning method may not be prominent due to the size of the sample. In summary, the green core No. 1 can be used for molecular breeding analysis and prediction of mung beans.

[0118] Table 4 prediction accuracy verification results

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[0120] It should be noted that in this paper, the term "includes", "contains" or any other variant thereof is intended to cover non-exclusive inclusion, so that the process, method, article or device including a series of elements not only includes those elements, but also includes other elements not explicitly listed or inherent to such process, method, article or device. Without more limitations, the element defined by the statement "includes a" does not exclude the presence of other identical elements in the process, method, article or device including the element.

[0121] The above-mentioned embodiment serial numbers of the application are only for description, not representing the advantages and disadvantages of the embodiments.

[0122] The above embodiments are only used to illustrate the technical solutions of the present application and not limit the present application. Although the present application has been described in detail with reference to the preferred embodiments, it should be understood by those skilled in the art that the technical solutions of the present application can be modified or replaced equivalently without departing from the purpose and scope of the present application, which should be covered in the scope of the claims of the present application.

Claims

1. A mung bean SNP chip, characterized in that, The mung bean SNP chip includes: (1) A probe for detecting mung bean SNP molecular marker combinations; or (2) Probes and primers for detecting mung bean SNP molecular marker combinations; The mung bean SNP molecular marker combination consists of 20,526 SNP molecular markers, as shown in Table 2. The location and variation information of the SNP sites are represented in the form of chromosome: physical location: reference genotype / variant allele. The 20,526 SNP loci are based on Wm82.a2.v1 as the reference genome.

2. A reagent kit, characterized in that, The kit contains: (1) A probe for detecting mung bean SNP molecular marker combinations; or (2) Probes and primers for detecting mung bean SNP molecular marker combinations; The mung bean SNP molecular marker combination consists of 20,526 SNP molecular markers, as shown in Table 2. The location and variation information of the SNP sites are represented in the form of chromosome: physical location: reference genotype / variant allele. The 20,526 SNP loci are based on Wm82.a2.v1 as the reference genome.

3. The application of the mung bean SNP chip as described in claim 1 or the reagent kit as described in claim 2 in the identification of mung bean varieties.

4. The application of the mung bean SNP chip as described in claim 1 or the kit as described in claim 2 in detecting mung bean breeding materials resistant to yellow mosaic virus.

5. The application of the mung bean SNP chip as described in claim 1 or the kit as described in claim 2 in the whole genome association analysis of mung beans.

6. The application of the mung bean SNP chip as described in claim 1 or the kit as described in claim 2 in molecular marker-assisted breeding.

7. The application of the mung bean SNP chip as described in claim 1 or the kit as described in claim 2 in the DNA fingerprinting analysis of mung bean germplasm resources.

8. The application of the mung bean SNP chip as described in claim 1 or the kit as described in claim 2 in whole-genome selection breeding of mung beans.

9. The use of the mung bean SNP chip as described in claim 1 or the reagent kit as described in claim 2 in any of the following: (1) Phylogenetic analysis of mung beans; (2) Analysis of mung bean population structure; (3) Analysis of genetic diversity in mung beans; (4) Verification of the authenticity of mung bean varieties; (5) Identification of the genotype of superior mung bean cultivars.

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