Mung bean SNP (Single Nucleotide Polymorphism) liquid chip, molecular marker combination and application thereof

Abstract

The invention discloses a mung bean SNP (Single Nucleotide Polymorphism) liquid chip, a molecular marker combination and application thereof, and relates to the technical field of plant molecular genetic breeding. The SNP molecular marker combination is composed of 20526 SNP molecular markers; the invention also provides a mung bean SNP chip. The mung bean SNP chip comprises a probe and / or a primer for detecting the mung bean SNP molecular marker combination. The mung bean SNP chip can quickly and effectively track genetic materials of mung beans, is favorable for accelerating the high-yield, early-maturing, high-quality and disease-resistant breeding process of the mung beans, and improves the breeding efficiency of excellent new varieties. The patented technology disclosed by the invention is the first mung bean breeding chip on the market at present, has numerous important yield quality and disease-resistant functional sites, has wide genetic diversity, more uniformly covers chromosomes, is more flexible, and has higher detection rate and better repeatability.

Description

Technical Field

[0001] The invention belongs to the technical field of plant molecular genetic breeding, and in particular relates to a mung bean SNP liquid phase chip, a molecular marker combination and applications thereof. Background Art

[0002] Mung bean (Vigna radiata L.), belongs to the genus Vigna of the Leguminosae family, contains 11 chromosomes. As a functional food raw material, mung bean seeds are rich in protein, multiple essential amino acids, 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 beans has begun to be valued by people, and the demand for mung beans has gradually increased.

[0003] China's demand for mung beans is about 900,000 tons per year, while my country's mung bean production is about 600,000 tons, and about 33% of mung beans need to be imported. In scientific research, accelerating the selection and breeding of high-quality, high-yield, and early-maturing mung bean varieties, carrying out joint research, and improving the adaptability, high yield and high quality of mung bean varieties are the main research directions of mung bean breeding. However, the current research on mung bean molecular breeding mainly targets a few quality trait gene loci, and there is no effective molecular breeding system for complex quantitative traits controlled by multiple genes such as mung bean yield and quality.

[0004] Mung bean is a legume plant native to Asia and is widely cultivated in temperate and subtropical regions. Countries with large planting areas in Asia include India, China, Thailand, etc., and the planting areas in the United States and Australia are also expanding. Mung bean is rich in nutrients, with a protein content of up to 19.5% to 33.1% in the grains, which is significantly higher than cereal crops, 2.3 times that of wheat flour, 3.0 times that of cornmeal, 3.2 times that of rice, and 2.7 times that of millet. Mung bean is also a crop with strong stress resistance. Due to its short growth period, large sowing period flexibility, and wide adaptability; it is conducive to land use and conservation; and it has high economic benefits. However, there are still few studies on molecular breeding of mung beans. There is no effective molecular breeding system for complex quantitative traits controlled by multiple genes such as yield and quality. In addition, there is no report on the whole genome SNP typing chip of mung beans, which further limits its application in mung bean scientific research and molecular breeding.

[0005] DNA molecular marker technology is a technical method that uses the differences in DNA between biological individuals to identify genetic variations. There are currently four types of DNA molecular markers; the first type mainly includes restriction fragment length polymorphism markers (RFLP), variable number tandem repeat sequence markers (VNTR), single-stranded conformation polymorphism RFLP (SSCP, RFLP), etc.; the second type mainly includes random amplified polymorphic DNA (RAPD), simple repeat DNA markers (SSR), sequence tag sites (STS), expressed sequence tags (EST), and sequenced amplified regions (SCAR); the third type is mainly amplified fragment length polymorphism (AFLP), and enzymatic amplified polymorphic sequence (CAPS) markers; the fourth type is DNA markers based on single nucleotide polymorphisms, mainly single nucleotide acid polymorphisms (SNP). Compared with several other genetic markers - morphological markers, biochemical markers, and cytological markers, DNA molecular markers have their advantages: most of them are co-dominant, which is very convenient for selecting recessive traits; the genome variation is rich, the number of markers is large; the detection method is simple and rapid. With the development of molecular biology technology, DNA molecular marker technology has been applied to the construction of genetic linkage maps and gene positioning, genetic breeding, species relationship identification, gene bank construction, gene cloning, etc., 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 in the genome. Any nucleotide in genomic DNA has four possible forms (A, T, G, C). Usually, a certain site has only two base variations in the species, and one base undergoes transitions or transversions to another base. Usually, the frequency of transitions is higher than that of transversions, so SNP markers are usually biallelic genes, and SNPs are widely distributed in the genome. There are two main types of new high-throughput molecular marker technologies based on SNP: one is a high-throughput molecular marker technology based on the next-generation sequencing technology; the other is a molecular marker technology based on gene chip technology.

[0007] Based on SNP genotype, genetic diversity analysis, whole genome association analysis, QTL fine positioning, molecular evolution analysis, molecular marker-assisted breeding, whole genome selection, etc. can be performed on mung bean. It will play a significant role in aggregate breeding and broadening the genetic basis of varieties.

[0008] At present, there is no mung bean whole-genome SNP typing chip available. In the era of molecular breeding, the relevant gap has limited the application of mung bean scientific research and molecular breeding in China. Summary of the invention

[0009] In view of this, the main purpose of the present invention is to provide a mung bean SNP molecular marker combination, which consists of 20526 SNP molecular markers. The 20526 SNP molecular markers are shown in Table 2 in the embodiment, and the position and variation information of the SNP site are expressed in the form of chromosome: physical position: reference genotype / variant allele type.

[0010] The present invention uses 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 GATK-3.8 software for variation detection. The raw variation data of the 613 samples obtained after analysis were analyzed through the inherent screening strategy process (see Figure 1 ) were filtered, and a total of 4,048,862 high-quality variant sites were obtained. According to the custom chip design principles, 20,526 core SNP sites were selected from them.

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

[0012] The data of the Zhonglvxin No. 1 chip of the present invention are derived from the resequencing results of 613 mung beans, most of which are Chinese core germplasms, are widely representative, and are of great significance in the research of mung bean genomics in China; the reference genome of the Zhonglvxin No. 1 chip is SuLv1.

[0013] The probe used to detect the above-mentioned mung bean SNP molecular marker combination is a single-stranded DNA synthesized based on mung bean 20K (a total of 20,526) SNP molecular markers.

[0014] The third object of the present invention is to provide a kit, which comprises probes and / or primers for detecting the above-mentioned mung bean SNP molecular marker combination.

[0015] The present invention also aims to provide the use of the above-mentioned mung bean SNP molecular marker combination or the above-mentioned mung bean SNP chip or the above-mentioned kit in the identification of mung bean varieties.

[0016] The present invention also aims to provide the use of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in detecting mung bean yellow mosaic disease resistance breeding materials.

[0017] The present invention also aims to provide the use of the mung bean SNP molecular marker combination or the mung bean SNP chip or the kit in mung bean genome-wide association analysis.

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

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

[0020] The present invention also aims to provide the use 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 whole genome selection breeding.

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

[0022] (1) Identification of mung bean relatives;

[0023] (2) Analysis of mung bean population structure;

[0024] (3) Analysis of genetic diversity of mung bean;

[0025] (4) Authenticity inspection of mung bean varieties;

[0026] (5) Identification of genotypes of superior mung bean cultivars.

[0027] The beneficial effects of the present invention include at least:

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

[0029] (2) High representativeness: The information comes from the resequencing data of 613 representative mung bean core germplasms from China and internationally.

[0030] (3) Strong functionality: A high proportion of SNPs are large-effect sites of annotated genes, covering important gene-related sites and domestication selection intervals as well as SNP sites unique to wild and cultivated mung bean subpopulations.

[0031] (4) Good practicality: It basically covers the relevant markers of the published important traits, and highlights important traits such as flavonoids, amino acids, vitexin, plant height, 100-grain weight, disease resistance, drought resistance and flood resistance.

[0032] (5) Support site filling: has ultra-high density site filling rate.

[0033] (6) The chip can be upgraded: The number of significant QTN / QTL sites and closely associated sites can be continuously increased and upgraded based on the additional phenotypic data and the filled genome sequence.

[0034] That is, the solution of the present invention is the first mung bean breeding chip currently on the market, which has many important yield quality and disease resistance functional sites, extensive genetic diversity, more even coverage of chromosomes, more flexible chips, higher detection rate and better repeatability; the SNP molecular marker combination that can be used for mung bean genotyping and the mung bean whole genome chip provided are evenly distributed, highly representative, highly functional, and practical, and support site filling; the number of closely associated sites is filled according to the additional phenotypic data, and the chip is upgraded, which has great economic and practical value and application prospects; the genetic material of mung beans can be quickly and effectively tracked, which is conducive to accelerating the breeding process of high-yield, early-maturing, high-quality and disease-resistant mung beans, and improving the efficiency of selecting excellent new varieties. BRIEF DESCRIPTION OF THE DRAWINGS

[0035] Figure 1 This is the basic flow chart of the site screening of the Green Core No. 1 chip of the present invention; wherein, QTL-quantitative trait location; GWAS-genome-wide association analysis; mGWAS-metabolite genome-wide association analysis; MAF-minimum allele frequency; SNP-single nucleotide polymorphism.

[0036] Figure 2 This is the distribution map of the mung bean 20K liquid phase gene chip sites in the whole genome in the present invention; among them, 1). More than 19,700 representative variation sites covering the genome were selected; 2). The chip covers more than 300 significant sites related to metabolite traits; 3). The chip covers more than 10 new sites for yield traits, such as the significant QTN site for the number of pods per plant shown in the figure; 4). The chip covers the functional gene / QTN positioning reported in some literatures.

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

[0038] Figure 4 This is the MAF distribution of the SNP site of the present invention.

[0039] Figure 5 This is the result of functional site analysis of Green Core No. 1.

[0040] Figure 6 This is the group structure analysis diagram of Green Core No. 1 in 892 MAGIC materials; a) MAGIG group structure analysis, b) MAGIC group structure display diagram.

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

[0042] Figure 8 Manhattan plot (GLM) of the flowering date.

[0043] Fig. 9 This is the Manhattan plot (GLM) of 100-grain weight.

[0044] Fig.10 Phenotype and prediction for each trait. DETAILED DESCRIPTION

[0045] The technical solutions in the embodiments of the present invention are described clearly and completely below. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0046] In addition, the technical solutions between the various embodiments of the present invention can be combined with each other, but it must be based on the fact that ordinary technicians in the field can implement it. When the combination of technical solutions is contradictory or cannot be implemented, it should be deemed that such combination of technical solutions does not exist and is not within the scope of protection required by the present invention.

[0047] The solution proposed by the present invention is specifically described below through specific embodiments:

[0048] Example 1 SNP site screening

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

[0050] (1) Collection of initial dataset

[0051] The SNP marker information of Green Core No. 1 comes from 613 domestic and foreign mung bean germplasm resources provided by the Institute of Economic Crops of Jiangsu Academy of Agricultural Sciences (including 414 core germplasm resources and 199 micro-core germplasm resources, covering cultivated varieties, local varieties and wild varieties in the Northeast, Huanghuaihai and Southern ecological zones, as well as foreign germplasm, forming a natural population with rich genotypic and phenotypic data). The whole genome was sequenced using the Novasek platform (Illumina Inc.) sequencing technology, and each sample obtained 10X whole genome coverage. Low-quality reads and reads with adapter contamination were excluded to obtain clean data. All clean data were mapped to the sulv No. 1 genome using BWA software, PCR duplications were removed, and variant typing was performed using GATK software, and a total of 3,068,512 SNP variant sites were obtained.

[0052] At the same time, Green Core No. 1 SNP marker information also comes from sites covering QTL, GWAS, domestication-related genes, intraspecific subpopulation differences, excellent traits, terminators, variable splicing, non-synonymous mutations, etc. The site type overview is shown in Table 1:

[0053] Table 1 Green Core No. 1 SNP marker information source

[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 below 20%, Hardy-Weinberg equilibrium 0.00001; (2) Non-repeated samples; The above quality controls were completed by Plink software, and finally 80,216 sites were obtained for subsequent Green Core No. 1 chip site selection. Chip site screening The above data were screened and evaluated according to the custom site screening principle: (1) tiling order 1 = excellent QTL sites, GWAS sites; (2) tiling order 2 = sites of differential domestication between species and intraspecific subpopulations; (3) tiling order 3 = significant mGWAS sites, sites significantly associated with metabolites; (4) tiling order 4 = important genes (VIP), terminators / variable splicing / non-synonymous mutation sites. The sites were further comprehensively considered according to the priority of the tiling order, the principle of MAF ≥ 0.01 was retained, non-polymorphic sites were deleted, sites with interference from the SNP flanking sequences were deleted, and then the sequences were selected by sliding windows. Other factors to be considered included: priority for non-A / T and G / C sites; uniform coverage of the whole genome; site evaluation score above 0.4; probe sequence repeatability below 99%; deletion rate below 3%; whether it is a single copy; and not in transposon or repeat regions.

[0057] The above principles were used to construct the variable site set of the Green Core No. 1 chip, and ultimately 20,526 molecular markers (Mung Bean 20K) were screened. Their distribution on the Mung Bean genome is shown in the figure below. Figure 2-3 As shown, the MAF value is Figure 4 As shown; it can be seen that the average distance of the molecular markers provided by the present invention is about 23Kb, and the coverage of the SNP sites with MAF>0.1 in the 60K interval reaches 99.4%. The information of the 20526 SNP molecular markers is shown in Table 2 below, that is, the mung bean SNP molecular marker combination composed of 20526 SNP molecules in the present invention.

[0058] Table 2 Location information of SNP sites in mung bean 20K liquid phase gene chip

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[0094] (3) Detection principle

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

[0096] (4) Detection method

[0097] (1) DNA extraction: DNA was extracted from the mung bean samples using a DNA extraction kit; (2) DNA quality inspection: DNA quality was analyzed using agarose gel electrophoresis; and integrity was accurately detected using Agilent 2100. The quality inspection qualified standards are: the total amount is not less than 2μg, the sample concentration is less than 50ng / μl, and there is no impurity. (3) Library construction: Use an ultrasonic crusher to randomly interrupt the qualified sample DNA, electrophoretically recover the DNA fragments of the required length, and add adapters to their ends to form a library; (4) Sequencing library construction: Use LMPCR to amplify the sample library and purify it for subsequent probe hybridization experiments; (5) Hybridization capture library construction: Take 300ng of the constructed sequencing library, freeze-dry it, add mung bean 20K SNP targeted capture probe and hybridization reagent, denature it and incubate it at 60℃ for 16 hours to complete the hybridization reaction; after the hybridization product is washed with washing solution, 5 rounds of PCR are performed to complete the construction of the hybridization capture library; (6) Hybridization capture library quality inspection: Use the qPCR method to accurately quantify the effective concentration of the library to ensure the quality of the library; (7) Sequencing: Use Qubit fluorescence quantification instrument to detect the library concentration, and agarose gel electrophoresis to detect the fragment size. After the concentration and fragment size are qualified, the sequencing library construction is completed. The prepared library is sequenced using a BGI sequencer; (8) Analysis: After obtaining the data, the sequencing data is compared with the reference genome using BWA, and GATK is used to perform standard SNP calls on the data; thereby obtaining the genotyping results of the genome to be tested.

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

[0099] There were 25 test samples, 18 of which were cultivated mung beans, and 7 were wild and closely related mung bean materials. The mung bean 20K liquid phase gene chip was designed based on the pre-evaluation, and 5% more target sites were designed. The actual capture rate was that all target sites exceeding 20K could be captured normally and the results were obtained. The overall site capture rate exceeded 96%, reaching the predetermined design capture efficiency. The detection can be standardized and promoted. The specific detection rate statistics are shown in Table 3.

[0100] Table 3. Data display of target site capture of mung bean 20K liquid phase 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 NJV 0.975485 0.966829 0.96320294 Xgb 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 gene function sites of Green Core No. 1

[0103] Experimental material: Green Core No. 1; Genotype data source: obtained from chip. Green Core No. 1 has agronomic trait-related loci and disease trait-related loci, such as Figure 5 The related loci on the functional genes include the reported agronomic trait related loci including 100-grain weight, grain length, starch, protein, number of pods per plant and metabolite flavonoids; and also include the mung bean yellow mosaic virus disease, salt tolerance and drought tolerance and other stress resistance related loci.

[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 phase breeding chip, 892 magic materials of mung bean were tested (groups from 8 parents), and the target site genotyping was extracted. The average detection rate of the samples was 99.10%, and the repetition consistency rate of the same batch of materials was 99.62%, indicating that the liquid phase chip target site detection rate of this scheme is high, and the typing results are accurate and reliable. ADMIXTURE is used to estimate the ancestral points of individuals. Admixture divides the genotypes into 5 equal-sized parts for cross-validation, and finds the best K value from 1 to 12 ( Figure 6 a). Plink software is then used to calculate the genetic distance matrix and perform cluster analysis on mung bean breeding materials. A phylogenetic tree diagram is constructed to determine the kinship, evolutionary relationship and composition structure of different materials. The present invention is used to perform cluster analysis on 892 mung bean materials from different groups. It is found that the mung bean breeding materials are divided into 8 subgroups, and the effect is consistent with the actual grouping. The analysis results are as follows Figure 6 As shown in b, the 20,526 SNP sites screened out have high representativeness.

[0106] Example 5: Association analysis of resistance of Green Core No. 1 to yellow mosaic disease

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

[0108] Experimental results: Mixed linear model (MLM) was used to analyze the association between the test population and yellow mosaic disease resistance. The results showed that when P < 1 × 10 -7 At the same time, a locus significantly associated with yellow mosaic disease was colocalized on four chromosomes ( Figure 7 a). Near the site Chr4-14132960, there are more than 10 genes, including EVM0033654, EVM0003495, EVM0024933, EVM0009281, EVM0009509, EVM0029763, EVM0004327, EVM0008202, EVM0009824, EVM0009117 and EVM0030586, among which the Arabidopsis homologous gene AT5G24320 of EVM0003495 is a gene with a WD40 repeat domain and has typical disease resistance gene structural characteristics. EVM0030586 (PR gene) has a pathogenesis-related protein that resists environmental stress. At the same time, the Chr4-14132960 site can be used to develop KASP molecular markers for the identification of yellow mosaic-resistant varieties. 76 accessions were tested for markers, and the KASP molecular marker mymv-1 had an accuracy of 98.61% in distinguishing between resistant and susceptible varieties ( Figure 7 b) Green Core No. 1 can effectively conduct GWAS analysis on mung bean traits.

[0109] Example 6: Correlation analysis of the flowering period of Green Core No. 1 mung bean

[0110] Experimental materials: Association analysis of flowering period traits of 414 mung bean materials; Genotype data source: obtained by Green Core No. 1 chip detection; Analysis model: 3VmrMLM mixed linear model.

[0111] Experimental results: 3VmrMLM was used to conduct association analysis on the flowering period traits of the test population. The results showed that when P < 1 × 10 -7 At the same level, there were 15 significant QTN loci significantly associated with flowering time. 2 =0.95%) is associated with DAF ( Figure 8), there are 7 genes near this site, including EVM0009174, EVM0010314, VrLFR, EVM0030971, EVM0026674, EVM 0024476 and EVM0028334, among which VrLFR / EVM0022630 was significantly differentially expressed among germplasms with different flowering periods.

[0112] Example 7: Re-association analysis of Green Core No. 1 mung beans

[0113] Experimental materials: Association analysis of mung bean grain weight traits of 414 samples; Genotype data source: obtained by Green Core No. 1 chip detection; Analysis model: 3VmrMLM mixed linear model.

[0114] Experimental results: 3VmrMLM was used to conduct association analysis on the flowering period traits of the test population. The results showed that when P < 1 × 10 -7 At the same level, there were 19 significant QTN loci significantly associated with mung bean grains. 2 =0.47%~1.14%))( Fig. 9 ) is associated with HSW; DAF is associated with, there are 4 genes near this site, including VrKIN-14L, EVM0001506, EVM0032287, and EVM0029001, among which VrKIN-14L / EVM0013458 is significantly differentially expressed among germplasms with different grain weights, and there are few reports on related genes.

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

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

[0117] Prediction accuracy verification: 5-fold cross-validation and 10-fold cross-validation were used to compare the correlation between predicted GEBV and phenotype. The results showed that the RF model constructed based on pedigree relationships had the lowest prediction accuracy among all traits, all below 0.73. The prediction accuracy of the BL method was between 0.73 and 0.86, and the prediction effect was 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 of the model constructed based on genotype data is better. Taking BL as an example, the prediction accuracy of plant height was the highest, reaching 0.83, and the accuracy of 100-grain weight and disease resistance also reached above 0.75 (Table 4, Fig.10). These selected marker loci have a significant advantage in prediction accuracy. The machine learning method may not be effective due to the problem of sample size. In summary, Green Core No. 1 can be used for molecular breeding analysis and prediction of mung beans.

[0118] Table 4 Prediction accuracy verification results

[0119]

[0120] It should be noted that, in this article, the terms "include", "comprises" or any other variations thereof are intended to cover non-exclusive inclusion, so that a process, method, article or device including a series of elements includes not only those elements, but also other elements not explicitly listed, or also includes elements inherent to such process, method, article or device. In the absence of further restrictions, an element defined by the sentence "comprises a ..." does not exclude the existence of other identical elements in the process, method, article or device including the element.

[0121] The serial numbers of the above embodiments of the present invention are only for description and do not represent the advantages or disadvantages of the embodiments.

[0122] The above embodiments are only used to illustrate the technical solutions of the present invention rather than to limit it. Although the present invention has been described in detail with reference to the preferred embodiments, those skilled in the art should understand that the technical solutions of the present invention can be modified or replaced by equivalents without departing from the purpose and scope of the technical solutions of the present invention, which should be included in the scope of the claims of the present invention.

Claims

1. A mung bean SNP molecular marker combination, characterized in that: The SNP molecular marker combination consists of 20,526 SNP molecular markers, and the 20,526 SNP molecular markers are shown in Table 2. The position and variation information of the SNP site are expressed in the form of chromosome: physical position: reference genotype / variant allele type.

2. A mung bean SNP chip, characterized in that: The mung bean SNP chip comprises probes and / or primers for detecting the mung bean SNP molecular marker combination according to claim 1.

3. A kit, characterized in that: The kit comprises probes and / or primers for detecting the mung bean SNP molecular marker combination according to claim 1.

4. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in mung bean variety identification.

5. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in detecting mung bean yellow mosaic disease resistance breeding materials.

6. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in mung bean genome-wide association analysis.

7. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in molecular marker-assisted breeding.

8. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in DNA fingerprint analysis of mung bean germplasm resources.

9. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in mung bean whole genome selection breeding.

10. Use of the mung bean SNP molecular marker combination according to claim 1, the mung bean SNP chip according to claim 2, or the kit according to claim 3 in any of the following: (1) Identification of mung bean relatives; (2) Analysis of the structure of mung bean population; (3) Analysis of genetic diversity of mung bean; (4) Authenticity inspection of mung bean varieties; (5) Identification of genotypes of superior mung bean cultivars.

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