Soybean SNP molecular marker combination, chip and application thereof

Abstract

The invention discloses a soybean SNP molecular marker combination, a chip and application thereof, and relates to the field of soybean molecular genetic breeding. The SNP molecular marker combination developed by the invention is uniformly distributed on 20 chromosomes of a soybean whole genome, and the accuracy of related research application such as gene positioning can be improved. The SNP molecular marker combination provided by the invention is rich in information amount and has important value in variety identification, correlation analysis and molecular marker-assisted breeding. On the basis, detection products such as SNP typing chips, kits and the like which are high in capture rate, high in density and high in polymorphism and are uniformly distributed in a genome can be developed.

Description

Technical Field

[0001] The present invention relates to the field of soybean molecular genetic breeding, and in particular to a soybean SNP molecular marker combination, a chip and applications thereof. Background Art

[0002] Traditional morphological markers have limited distinguishing capabilities and are greatly affected by the environment. They also have disadvantages such as large identification workload, long cycle, and seasonal restrictions. Molecular markers based on DNA polymorphism have become a powerful tool for analyzing biological genetic diversity. These molecular markers have the advantages of being unaffected by the environment, having a large number of markers to choose from, and being able to perform high-throughput testing and analysis. They have become an important means of analyzing crop kinship, identifying seed purity, and detecting the authenticity of varieties.

[0003] Single-nucleotide polymorphism (SNP) refers to the polymorphism of DNA sequence caused by the variation of a single nucleotide at the genomic level. Compared with SSR markers, SNP markers have more advantages: first, the number of SNP sites is more abundant and their distribution on the genome is more even; second, since SNP does not use DNA length differences as a detection method, it gets rid of the bottleneck limitation of gel electrophoresis and is easy to achieve high-throughput and automated analysis; third, SNP sites usually have only two alleles, which makes it easy to integrate data between platforms.

[0004] Soybean originated in China and is the main source of plant protein and fat for humans. It is one of the main crops in my country. Among the germplasm resources in stock, many have only recorded phenotypic traits and lack in-depth genetic identification. The huge number of varieties has increased the difficulty of soybean variety management. Soybean genetic resource analysis, variety identification and functional genomics research rely heavily on the development of high-density molecular markers. With the completion of soybean whole genome sequencing and the development of resequencing technology, the development of SNP sites has made important progress in soybeans. Through resequencing of wild soybeans and cultivated soybeans, tens of millions of SNP sites can be screened from the soybean genome. However, due to limitations such as computing resources and chip throughput, blindly increasing density will not only not improve accuracy, but will lead to rising costs. Therefore, it is urgent to develop a SNP typing chip with high capture rate, high density, high polymorphism, and uniform distribution in the genome.

[0005] In view of this, the present invention is proposed. Summary of the invention

[0006] The purpose of the present invention is to provide a soybean SNP molecular marker combination, a chip and its application to solve the above technical problems.

[0007] The present invention is achieved in that:

[0008] Glossary:

[0009] SNP (Single Nucleotide Polymorphism): Single nucleotide polymorphism refers to the DNA sequence polymorphism caused by a single nucleotide variation at the genome level.

[0010] Bi-allelic SNP: A biallelic SNP site refers to a gene with only two alleles at one SNP site.

[0011] MAF (Minor Allele Frequency): Minimum allele frequency (minor allele frequency), usually refers to the frequency of uncommon alleles at a certain site in a specific population.

[0012] SNP site detection rate: refers to the ratio of samples with a certain SNP site successfully detected to all samples, generally required to be ≥90%, and will be adjusted according to the target data and the number of target sites. When analyzing SNP genotypes, the minimum depth is generally ≥10X, that is, the target site is covered by at least 10 reads.

[0013] In a first aspect, the present invention provides a soybean SNP molecular marker combination, which includes 35196 SNP molecular markers, and the information of the 35196 SNP molecular markers is as follows:

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[0106] Among them, 1 to 20 on the left side of the site number indicates the chromosome number where the site is located, the middle value indicates the position of the site on the chromosome of the reference genome, the base type in the site number indicates the SNP base type of the site in the reference genome, and the version number of the whole genome sequence of the reference genome is: Glycine_max_v4.0.

[0107] The present invention analyzed 2040 soybean resequencing samples and obtained a total of 43,377,445 SNP sites. By filtering biallelic SNP sites, sequencing depth ≥10, MAF ≥0.01, genome single copy regions and retaining one effective marker every 5kb, 42,450 high-quality SNP marker combinations were finally obtained. The 42,450 high-quality SNP marker combinations were subsequently evaluated for probe design, and a total of 35,196 sites passed the evaluation.

[0108] After testing, the above-mentioned SNP molecular marker combination has a site detection rate of more than 96% for 20 soybean samples when the resequencing data volume is 2Gb. The SNP molecular marker combination developed by the present invention is evenly distributed on the 20 chromosomes of the soybean genome, which can improve the accuracy of related research applications such as gene positioning. The SNP molecular marker combination provided by the present invention is rich in information and has important value in variety identification, association analysis and molecular marker-assisted breeding. Based on this, a SNP typing chip, kit and other detection products with high capture rate, high density, high polymorphism and uniform distribution in the genome can be developed.

[0109] In a second aspect, the present invention provides a soybean whole genome SNP detection product, which includes: a nucleotide sequence for detecting the above-mentioned soybean SNP molecular marker combination.

[0110] In a preferred embodiment of the present invention, the detection product is selected from a chip, a reagent or a kit.

[0111] The chip can also be called a suspension array or a liquid array, which includes a carrier and nucleic acid molecules (such as primers and / or probes) bound to the surface of the carrier.

[0112] The aforementioned carrier can be made of a variety of materials and forms, for example, it can be preferably selected from containers with a flat bottom. A more typical preferred example is a multi-well plate widely used in biochemical detection, a microplate, a microfluidic-based device (such as a microfluidic chip), a container similar to a watch glass, etc., and is not limited thereto.

[0113] The microfluidic chip is a PDMS chip or a metal droplet generator selected from a T-type chip, a flow focusing chip or a coaxial flow chip, or a PMMA microfluidic chip.

[0114] The soybean whole genome SNP detection product can further realize the detection of soybean whole genome SNP with the help of high-throughput sequencing or imaging detection methods, but is not limited to this.

[0115] In a preferred embodiment of the present invention, the nucleotide sequence is a primer sequence and / or a probe sequence.

[0116] Furthermore, the kit may also include instructions for use, detection reagents, etc. Typical detection reagents include at least one of detection antibodies or ligands labeled with fluorescent dyes, detection antibodies or ligands labeled with biotin, avidin-fluorescent protein (preferably phycoerythrin) conjugates, avidin-horseradish peroxidase complexes, chemiluminescent reagents (such as luminol, luminol derivatives, acridinium esters, luciferase, and oxidants such as hydrogen peroxide, etc.), and are not limited thereto.

[0117] In an optional embodiment, the fluorescent dyes include but are not limited to fluorescein dyes and their derivatives (for example, including but not limited to fluorescein isothiocyanate (FITC), hydroxyfluorescein (FAM), tetrachlorofluorescein (TET), etc. or their analogs), rhodamine dyes and their derivatives (for example, including but not limited to red rhodamine (RBITC), tetramethylrhodamine (TAMRA), rhodamine B (TRITC), etc. or their analogs), Cy series dyes and their derivatives (for example, including but not limited to Cy2, Cy3, Cy3B, Cy3.5, Cy3.7, Cy3.8, Cy3.9, Cy3.10, Cy3.11, Cy3.12, Cy3.13, Cy3.14, Cy3.15, Cy3.16, Cy3.17, Cy3.18, Cy3.19, Cy3.20, Cy3.31, Cy3.32, Cy3.33, Cy3.34, Cy3.35, Cy3.36, Cy3.37, Cy3.38, Cy3.39, Cy3.40, Cy3.41, Cy3.42, Cy3.43, Cy3.44, Cy3.45, Cy3.46, Cy3.47, Cy3.48, Cy3.49, Cy3.50, Cy3.51, Cy3.52, Cy3.53, Cy3.54, Cy3.55, Cy3.56, Cy3.57, Cy3.58, Cy3.59, Cy3.59, Cy3.60, Cy3.61, Cy3.62, Cy3.63, Cy3.77, Cy3.78, Cy3.79, Cy3. 5, Cy5.5, Cy3, etc. or their analogs), Alexa series dyes and their derivatives (for example, including but not limited to AlexaFluor350, 405, 430, 488, 532, 546, 555, 568, 594, 610, 33, 647, 680, 700, 750, etc. or their analogs) and protein dyes and their derivatives (for example, including but not limited to phycoerythrin (PE), phycocyanin (PC), allophycocyanin (APC), pre-chlorophyll protein (preCP), etc.).

[0118] Furthermore, the kit may also include at least one of a buffer solution, a detection reagent, a diluent, and a washing solution, but is not limited thereto.

[0119] In a third aspect, the present invention provides the use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination or the above-mentioned soybean whole genome SNP detection product in soybean genotyping.

[0120] In a preferred embodiment of the present invention, genotyping is performed on soybean germplasm resources or genetic populations.

[0121] In a fourth aspect, the present invention provides the use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination or the above-mentioned soybean whole genome SNP detection product in soybean whole genome association analysis.

[0122] In a fifth aspect, the present invention provides the use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination or the above-mentioned soybean whole genome SNP detection product in soybean cluster analysis and kinship identification.

[0123] In the sixth aspect, the present invention provides the application of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination or the above-mentioned soybean whole genome SNP detection product in establishing soybean germplasm resources or variety DNA fingerprint map, soybean genetic diversity analysis or soybean molecular marker assisted breeding.

[0124] In a seventh aspect, the present invention provides the use of at least one soybean SNP molecular marker in a soybean SNP molecular marker combination in the preparation of a soybean SNP site detection product, wherein the detection product is selected from a chip, a reagent or a kit.

[0125] In an eighth aspect, the present invention provides a method for genotyping soybean germplasm resources or genetic populations, comprising the following steps: designing detection primers and / or probes based on at least one soybean SNP molecular marker in the above-mentioned soybean SNP molecular marker combination, performing PCR amplification on the test soybean sample DNA based on the detection primers and / or probes or using the above-mentioned soybean whole genome SNP detection product; and detecting the PCR amplification products.

[0126] In a preferred embodiment of the present invention, a DNA library of the soybean sample to be tested is first constructed, and then the probe and the DNA library are mixed and incubated; after incubation, the library of DNA hybridization products is captured; and then the captured DNA hybridization library is sequenced.

[0127] For example, the probe and DNA library are mixed and incubated at 65°C-66°C for 2-3 hours.

[0128] In a preferred embodiment of the present invention, library capture includes: incubating DNA hybridization products with magnetic beads, then performing library amplification on the combination of magnetic beads and DNA hybridization products; and processing the library amplification products to obtain a DNA hybridization library.

[0129] The processing of the library amplification product includes hot washing the combination of magnetic beads and DNA hybridization products at 65°C, and then washing the magnetic beads at room temperature with magnetic bead washing solution. The washed magnetic beads are resuspended in water.

[0130] Furthermore, after the captured DNA hybridization library is sequenced, the sequencing data is also subjected to FastQC (www.bioinformatics.babraham.ac.uk / project) quality control.

[0131] In a ninth aspect, the present invention provides a method for constructing a DNA fingerprint of soybean germplasm resources or varieties, comprising the following steps:

[0132] Based on at least one soybean SNP molecular marker in the above-mentioned soybean SNP molecular marker combination, detection primers and / or probes are respectively designed, and the genotypes of the above-mentioned SNP molecular markers are detected based on the detection primers and / or probes or by using the above-mentioned soybean whole genome SNP detection product. The genotypes of the SNP molecular markers of each soybean germplasm resource or variety are arranged in combination according to the order of site numbers to form a specific sequence combination, and the specific sequence combination is the DNA fingerprint map of the soybean germplasm resource or variety.

[0133] In an optional embodiment, when constructing a DNA fingerprint of soybean germplasm resources or varieties, the above 35,196 SNP molecular markers are optimized, screened or classified, and a part or all of the SNP molecular markers are selected for the fingerprint design of wild or cultivated soybeans. Thus, a more accurate and concise fingerprint or a more accurate and detailed fingerprint can be constructed, which can be adjusted by those skilled in the art as needed.

[0134] In an optional embodiment, the method for constructing a DNA fingerprint map of soybean germplasm resources or varieties includes the following steps: S1. Collecting soybean varieties, tissues or DNA samples; S2. Using the chip product of the present invention to perform a whole genome scan analysis on 35,196 soybean SNP molecular markers of the above samples; S3 analyzing the genetic differences between soybean samples based on the genotyping results; S4. Using competitive allele-specific PCR (KASP) technology to verify the accuracy of some SNP markers; S5. Constructing high-density fingerprint maps of different varieties.

[0135] The present invention has the following beneficial effects:

[0136] The SNP molecular marker combination developed by the present invention is evenly distributed on the 20 chromosomes of the soybean genome, and has the advantages of high accuracy, rich variation, and simple operation. The developed molecular markers are not affected by environmental factors and can directly reflect the differences in soybean gene levels. Therefore, they can be widely used in soybean genome-wide association analysis, genetic map construction, soybean population typing and identification, and soybean resource protection. After sample testing and verification, the inventors found that the site detection rate of the above-mentioned SNP molecular marker combination for soybean sample data volume is about 2Gb when the site detection rate is above 96%, indicating that the SNP molecular marker combination provided by the present invention has a large amount of useful information and has a large utilization value. In addition, the SNP molecular marker combination developed by the present invention is evenly distributed on the 20 chromosomes of the soybean genome, which can improve the accuracy of related research applications. Based on this, a SNP typing chip, kit and other detection products with high capture rate, high density, high polymorphism, and uniform distribution in the genome can be developed. BRIEF DESCRIPTION OF THE DRAWINGS

[0137] In order to more clearly illustrate the technical solutions of the embodiments of the present invention, the drawings required for use in the embodiments are briefly introduced below. It should be understood that the following drawings only show certain embodiments of the present invention and therefore should not be regarded as limiting the scope. For ordinary technicians in this field, other related drawings can be obtained based on these drawings without creative work.

[0138] Figure 1 It is a diagram of the identification and screening process of SNP markers;

[0139] Figure 2 This is a graph of designed probes and coverage statistics;

[0140] Figure 3 This is the statistical table of site detection rates of 20 samples;

[0141] Figure 4 This is a diagram showing the distribution of the number of SNP markers on different chromosomes;

[0142] Figure 5 It is a uniform distribution diagram of SNP markers on different chromosomes;

[0143] Figure 6 This is the MAF distribution statistical result diagram;

[0144] Figure 7 This is a diagram showing the distribution of SNP markers in the gene structure. DETAILED DESCRIPTION

[0145] References to embodiments of the present invention will now be provided in detail, one or more examples of which are described below. Each example is provided as an explanation rather than a limitation of the present invention. In fact, it will be apparent to those skilled in the art that various modifications and variations may be made to the present invention without departing from the scope or spirit of the present invention. For example, a feature illustrated or described as part of one embodiment may be used in another embodiment to produce a further embodiment.

[0146] In order to make the purpose, technical scheme and advantages of the embodiments of the present invention clearer, the technical scheme in the embodiments of the present invention will be described clearly and completely below. If the specific conditions are not specified in the embodiments, they are carried out according to conventional conditions or conditions recommended by the manufacturer. If the manufacturer of the reagents or instruments used is not specified, they are all conventional products that can be purchased commercially.

[0147] The features and performance of the present invention are further described in detail below in conjunction with the embodiments.

[0148] Example 1

[0149] This example provides a method for developing and screening a soybean 35K SNP molecular marker combination.

[0150] (1) A total of 43,377,445 SNP sites were obtained by analyzing 2040 soybean resequencing samples. By filtering biallelic SNP sites, sequencing depth ≥10, MAF ≥0.01, single-copy regions of the genome, and retaining one effective marker every 5 kb, 42,450 high-quality SNP marker combinations were finally obtained. The identification and screening process of SNP markers was referred to Figure 1 shown.

[0151] (2) Chip site evaluation

[0152] Through the above selection process, 42,450 background sites were finally obtained for subsequent probe design evaluation. Among them, 35,196 sites passed the evaluation, corresponding to 63,352 probes for subsequent test analysis ( Figure 2 ).

[0153] Experimental Example 1

[0154] Twenty random soybean samples were tested using the following methods: library construction, hybridization capture, library quality inspection, and sequencing analysis.

[0155] 1. Construction of library.

[0156] The DNA library was constructed according to the GenoBaits library construction kit.

[0157] 2. Library hybridization capture

[0158] The genotype of the target sample at 35K SNP sites was determined using a liquid phase gene chip.

[0159] (1) DNA hybridization: Take 500 ng of the constructed sample genomic DNA sequencing library, add 5 μL GenoBaits Block I and 2 μL GenoBaits Block II, place on an Eppendorf Concentrator plus vacuum concentrator, and evaporate to dry powder at ≤70°C. Add 8.5 μL GenoBaits 2×Hyb Buffer, 2.7 μL GenoBaits Hyb Buffer Enhancer, and 2.8 μL Nuclease-Free Water to the dry powder tube, mix with a pipette, and place on an ABI 9700 PCR instrument for incubation at 95°C for 10 min. Then take out the PCR tube and add 3 μL of the synthesized probe (the concentration of the probe is 60 ng / μL), vortex and mix, and place on an ABI 9700 PCR instrument for incubation at 65°C for 2 hours to complete the probe hybridization reaction.

[0160] (2) DNA capture

[0161] Add 100μL GenoBaits DNA Probe Beads to the reaction system after hybridization in the previous step, pipette up and down 10 times, and incubate at 65℃ for 45 minutes in the ABI 9700PCR instrument to allow the magnetic beads to bind to the probe. Use 100μL GenoBaits Wash Buffer I and 150μL GenoBaits Wash Buffer II to heat wash the magnetic beads after binding to the probe at 65℃, and then use 100μL GenoBaits Wash Buffer I, 150μL GenoBaits Wash Buffer II and 150μL GenoBaits Wash Buffer III to wash the magnetic beads at room temperature. Resuspend the washed beads with 20μL Nuclease-Free Water.

[0162] Take 13 μL of resuspended DNA (with magnetic beads) and add it to a new 0.2 mL PCR tube, then add 15 μL GenoBaits PCR Master Mix and 2 μL GenoBaits Primer Mix to configure the post-PCR system, and use ABI9700 PCR instrument to amplify the library. The amplification program is: pre-denaturation at 95°C for 5 min, denaturation at 95°C for 30 s, annealing at 60°C for 30 s, and extension at 72°C for 30 s; repeat steps 2 to 4 for a total of 15 cycles; extend at 72°C for 5 min.

[0163] Add 45 μL BeckmenAMPure XP Beads (Beackman) to the post-PCR product and pipette up and down to mix evenly, then place the 0.2 mL PCR tube on a magnetic stand until the solution is clear, discard the supernatant and wash the magnetic beads twice with 75% ethanol, and elute the library DNA with Tris-HCl at pH 8.0 to complete the hybridization capture of the probe.

[0164] (3) DNA hybridization capture library quality inspection

[0165] The DNA concentration of the library was measured by Qubit Fluorometric Quantitation (Thermo Fisher), and then agarose gel electrophoresis was used to detect whether the fragment size of the library DNA was between 300 and 400 bp.

[0166] (4) DNA hybridization capture library sequencing

[0167] The constructed DNA library was sequenced by Shijiazhuang Boredy Biotechnology Co., Ltd.

[0168] (5) Genotype data analysis

[0169] Sequencing data

[0170] After FastQC (www.bioinformatics.babraham.ac.uk / project) quality control, the data were aligned to the reference genome using BWA software (v0.7.17), and SNPs were identified using GATK software. The site test results were referred to Figure 3 Show. Figure 3 The results show that in 20 soybean populations, the site detection rate of the SNP molecular marker provided by the present invention exceeds 96%, indicating that the SNP molecular marker combination provided by the present invention has a large amount of useful information and has great utilization value.

[0171] Figure 4 This is a diagram showing the distribution of 35,196 SNP markers on different chromosomes. The statistical results of the number of target sites on different chromosomes: the horizontal axis is the chromosome ID; the left example Count is the number of sites / segments; the right example Length is the chromosome length (in bp). The results show that the SNP sites are evenly distributed on the 20 chromosomes.

[0172] Figure 5 The uniform distribution of SNP markers on different chromosomes shows 20 soybean chromosomes, and the drawing unit length in the figure is 1,000,000bp.

[0173] Figure 6 This is the MAF distribution statistical result diagram. Figure 6 The SNP combination provided by the present invention has a large amount of available information, and the number of markers greater than 0.1 accounts for 67%. The MAF numerical statistics of the core sites in the segment, the larger the MAF value of the target site, the better the polymorphism of the site. The horizontal axis MAF is the different ranges of MAF values, and the vertical axis Count is the number of core sites within the MAF range.

[0174] Figure 7 The distribution of SNP markers in gene structure shows that the most SNPs are found in intergenic sequences, followed by introns, upstream and downstream of genes, CDS regions, and UTR regions. The horizontal axis is the gene structure type, and the vertical axis is the number of target sites under this type.

[0175] The present invention screened out 35,196 sites that met the evaluation requirements and their corresponding 63,352 probes for subsequent testing and analysis. When the data volume of 20 samples used in the test was 2Gb, the site detection rate was between 96.3% and 97.6%.

[0176] The above description is only a preferred embodiment of the present invention and is not intended to limit the present invention. For those skilled in the art, the present invention may have various modifications and variations. Any modification, equivalent replacement, improvement, etc. made within the spirit and principle of the present invention shall be included in the protection scope of the present invention.

Claims

1. A soybean SNP molecular marker combination, characterized in that: It includes 35196 SNP molecular markers, and the information of 35196 SNP molecular markers is as follows: Among them, 1 to 20 on the left side of the site number indicates the chromosome number where the site is located, the middle value indicates the position of the site on the chromosome of the reference genome, the base type in the site number indicates the SNP base type of the site in the reference genome, and the version number of the whole genome sequence of the reference genome is: Glycine_max_v4.

0.

2. A soybean whole genome SNP detection product, characterized in that: It includes: Used to detect the nucleotide sequence of the soybean SNP molecular marker combination described in claim 1.

3. The soybean whole genome SNP detection product according to claim 2, characterized in that: The detection product is selected from a chip, a reagent or a kit; Preferably, the nucleotide sequence is a primer sequence and / or a probe sequence.

4. Use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination according to claim 1 or the soybean whole genome SNP detection product according to any one of claims 2 to 3 in soybean genotyping; Preferably, the soybean germplasm resources or genetic populations are genotyped.

5. Use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination according to claim 1 or the soybean whole genome SNP detection product according to any one of claims 2 to 3 in soybean whole genome association analysis.

6. Use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination according to claim 1 or the soybean whole genome SNP detection product according to any one of claims 2 to 3 in soybean cluster analysis and kinship identification.

7. Use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination as described in claim 1 or the soybean whole genome SNP detection product as described in any one of claims 2-3 in establishing soybean germplasm resources or variety DNA fingerprints, soybean genetic diversity analysis or soybean molecular marker-assisted breeding.

8. Use of at least one soybean SNP molecular marker in the soybean SNP molecular marker combination according to claim 1 in preparing a soybean SNP site detection product, characterized in that: The detection product is selected from a chip, a reagent or a kit.

9. A method for genotyping soybean germplasm resources or genetic populations, characterized in that: The method comprises the following steps: designing detection primers and / or probes based on at least one soybean SNP molecular marker in the soybean SNP molecular marker combination according to claim 1, performing PCR amplification on the soybean sample DNA to be tested based on the detection primers and / or probes or using the soybean whole genome SNP detection product according to any one of claims 2-3; and detecting the PCR amplification product; Preferably, the amplified product is subjected to fluorescence scanning, and the fluorescence signal is read and analyzed to obtain the genotyping result of the tested soybean sample DNA at the SNP site; Preferably, a DNA library of the soybean sample to be tested is first constructed, and then the probe is mixed with the DNA library and incubated; after incubation, the library of DNA hybridization products is captured; and then the captured DNA hybridization library is sequenced; Preferably, the library capture comprises: incubating the DNA hybridization product with magnetic beads, and then performing library amplification on the combination of the magnetic beads and the DNA hybridization product; and processing the library amplification product to obtain a DNA hybridization library.

10. A method for constructing a DNA fingerprint of soybean germplasm resources or varieties, characterized in that: The steps include: Design detection primers and / or probes based on at least one soybean SNP molecular marker in the soybean SNP molecular marker combination according to claim 1, respectively, and use the detection primers and / or probes or the soybean whole genome SNP detection product according to any one of claims 2-3 to perform genotyping for soybean germplasm resources or varieties; detect the genotypes of the SNP molecular markers described in claim 1, and arrange the genotypes of each soybean germplasm resource or variety at the SNP molecular markers in order of site numbers to form a specific sequence combination, which is a DNA fingerprint of the soybean germplasm resources or varieties.

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