A SNP related to soybean salt tolerance and yield traits, a molecular marker and application thereof

Abstract

The application belongs to the technical field of molecular genetics and breeding, and particularly relates to a SNP related to salt tolerance and yield traits of soybean, a molecular marker and application thereof. The SNP is located at 10009293 bp of chromosome 17 of Wm82.a2.v1.0 of the soybean genome, and the polymorphism is A / T, which is denoted as Chr17_10009293. The haplotype HapA is closely related to salt tolerance and yield traits of soybean, can significantly regulate salt tolerance of soybean seedlings, and thus improves yield of mature soybean, and can greatly improve the efficiency and accuracy of breeding of high-yield salt-tolerant soybean. The application provides strong technical support for breeding of salt-tolerant soybean varieties, and the molecular marker has far-reaching significance for research on plant salt tolerance traits, and has wide application prospect and high application value in soybean salt-tolerant molecular breeding.

Description

Technical Field

[0001] This invention belongs to the field of molecular genetic breeding technology, specifically relating to a SNP, molecular marker and its application related to soybean salt tolerance and yield traits. Background Technology

[0002] Soybeans Glycine max Soybean is a major oilseed crop globally, rich in high-quality vegetable oil and protein, but it is generally sensitive to salt. With increasing scarcity of arable land resources and the worsening problem of soil salinization, salt stress has become one of the major abiotic stress factors limiting soybean production. Salt stress severely affects soybean germination, seedling growth, root development, and yield formation, leading to reduced germination rate, inhibited taproot growth, and decreased biomass, ultimately resulting in a significant reduction in grain weight per plant and total yield. Therefore, improving soybean salt tolerance is an urgent problem to be solved in soybean breeding.

[0003] Traditional soybean salt-tolerance breeding relies primarily on field phenotypic screening, requiring multi-year, multi-location identification under salt stress conditions. This approach is limited by its long cycle, high cost, susceptibility to environmental influences, and low selection efficiency. However, the rapid development of high-throughput sequencing technology and the reduction in sequencing costs enable the rapid detection of higher quality and more numerous variations, generating massive amounts of genotypic data. This provides a solid foundation for uncovering significantly relevant SNPs using genome-wide association studies (GWAS) and haplotype analysis. Kompetitive allele-specific PCR (KASP) is a method for precise SNP genotyping based on primer terminal base specific matching. It features high throughput, low cost, and high accuracy, making it the mainstream SNP genotyping technology internationally. It is particularly suitable for detection scenarios with large sample sizes and few loci, and has been widely applied in molecular breeding of crops such as soybean, rice, and wheat.

[0004] High-throughput genome-wide association analysis (GWAS) was used to discover functional sites for soybean salt tolerance, and specific KASP molecular markers were developed for screening salt-tolerant plants based on superior haplotypes. This is of great significance for reducing the workload of soybean breeding and accelerating the process of molecular breeding for soybean salt tolerance. Summary of the Invention

[0005] To address the shortcomings of the existing technology, the purpose of this invention is to provide a SNP, molecular marker, and its application related to soybean salt tolerance and yield traits.

[0006] To achieve the above objectives, the present invention adopts the following technical solution: In a first aspect, the present invention provides a SNP associated with salt tolerance and yield traits in soybeans, wherein the SNP is located at 10009293 bp on chromosome 17 of soybean genome Wm82.a2.v1.0, and has a polymorphism of A / T, and is denoted as Chr17_10009293.

[0007] Furthermore, the SNP is located at the 420th base of the sequence shown in SEQ ID NO:1.

[0008] The A base variation corresponding to the above SNP is significantly positively correlated with the salt tolerance of the plant under salt stress conditions, and is defined as a "superior allele" or "favorable allele"; while the T base allele variation at this locus corresponds to the unfavorable phenotype of lower salt tolerance.

[0009] Furthermore, the indicators for salt tolerance are the main root length, fresh weight, dry weight, and single-plant grain weight of soybeans under salt stress.

[0010] This invention also provides a gene for high-yield, salt-tolerant soybeans. GmERS1 The haplotype is located at position 10004935_10010961 bp on chromosome 17 of soybean genome Wm82.a2.v1.0, where an A-to-T substitution occurs at 10,009,293 bp. The haplotype with A at this site is the superior haplotype of GmERS1, and the promoter nucleotide sequence of the superior haplotype is shown in SEQ ID NO:1. The haplotype with T at this site is the non-superior haplotype of GmERS1, and the promoter nucleotide sequence of the non-superior haplotype is shown in SEQ ID NO:2.

[0011] Haplotype analysis using SNPs present in target genes, and the development of specific KASP molecular markers for screening salt-tolerant plants based on superior haplotypes, is of great significance for reducing the workload of soybean breeding and accelerating the process of high-yield and salt-tolerant molecular breeding of soybeans.

[0012] A second aspect of the present invention provides a KASP primer set for detecting the SNP described in the first aspect, comprising an upstream primer F1 with a nucleotide sequence as shown in SEQ ID NO:3, an upstream primer F2 with a nucleotide sequence as shown in SEQ ID NO:4, and a downstream primer R with a nucleotide sequence as shown in SEQ ID NO:5.

[0013] This invention uses 186 randomly selected soybean germplasm resources as research materials. KASP markers were developed targeting the SNP sites described in the first aspect, resulting in upstream primer F1 (nucleotide sequence shown in SEQ ID NO:3), upstream primer F2 (nucleotide sequence shown in SEQ ID NO:4), and downstream primer R (nucleotide sequence shown in SEQ ID NO:5). The KASP-marked primers were used to amplify and genotype the 186 soybean materials on a Pherastar microplate reader. The results showed that the developed KASP markers can directly and specifically distinguish and detect SNP sites with an accuracy of up to 100%. These KASP markers have good application value and can be used for pre-selection of soybean salt tolerance traits and molecular-assisted breeding.

[0014] A third aspect of the invention provides a reagent or kit comprising the KASP primer set described in the second aspect.

[0015] A fourth aspect of the invention provides the use of the SNP described in the first aspect, the KASP primer set described in the second aspect, or the reagent or kit described in the third aspect in any of the following: (1) Identify the salt tolerance traits of soybeans during germination; (2) Screening for salt-tolerant soybean varieties or lines during the germination period; (3) Breeding of salt-tolerant soybeans; (4) Breeding of high-yield, salt-tolerant soybeans; (5) Develop salt-tolerant soybean varieties; (6) Develop high-yield, salt-tolerant soybean varieties; (6) Identification or auxiliary identification of high-yielding salt-tolerant soybean varieties; (7) Marker-assisted breeding of soybeans; (8) Improve salt-tolerant soybean germplasm resources.

[0016] In a fifth aspect, the present invention provides a method for identifying or assisting in the identification of salt-tolerant or high-yielding salt-tolerant soybeans, the method comprising detecting the genotype of the SNP site Chr17_10009293 of the soybean to be tested, and determining the salt tolerance of the soybean based on the genotype; wherein the SNP site Chr17_10009293 is located at 10009293 bp on chromosome 17 of the soybean genome Wm82.a2.v1.0.

[0017] Furthermore, the soybeans tested with genotype AA were high salt-tolerant soybean varieties, while the soybeans tested with genotype TT were low salt-tolerant soybean varieties.

[0018] In a sixth aspect, the present invention provides a method for breeding salt-tolerant or high-yielding salt-tolerant soybeans, the method comprising detecting the genotype of the soybean SNP site Chr17_10009293 and selecting soybeans with the AA genotype for breeding; wherein the SNP site Chr17_10009293 is located at 10009293 bp on chromosome 17 of the soybean genome Wm82.a2.v1.0.

[0019] A seventh aspect of the present invention provides the application of the method described in the fifth or sixth aspect in soybean breeding.

[0020] Furthermore, breeding methods include transgenic, hybridization, backcrossing, self-pollination, or asexual reproduction.

[0021] Compared with the prior art, the technical solution of the present invention has the following beneficial effects: This invention provides a single-nucleotide polymorphism (SNP) associated with salt tolerance and yield traits in soybean, located at 10009293 bp on chromosome 17 of the soybean genome Wm82.a2.v1.0, with an A / T polymorphism, denoted as Chr17_10009293. The A base variation shows a significant positive correlation with plant salt tolerance under salt stress conditions. Under salt stress, haplotype HapA exhibits higher taproot length, fresh weight, dry weight, and grain weight per plant than haplotype HapT. Furthermore, the KASP marker developed based on superior haplotype information in this invention can directly and specifically distinguish and detect this SNP site with an accuracy of up to 100%. This KASP marker has significant application value, enabling pre-selection of soybean salt tolerance traits and molecular-assisted breeding. Attached Figure Description

[0022] Figure 1 for GmERS1 A schematic diagram of the results of different haplotype analyses.

[0023] Figure 2 for GmERS1 The activity of different haplotype promoters.

[0024] Figure 3 for GmERS1 Germination of soybean germplasm resources of Hap “A” and Hap “T” under water treatment and 150 mM salt treatment conditions.

[0025] Figure 4 for GmERS1 The emergence rate, plant height, and single-plant grain weight of soybean germplasm resources of Hap "A" and Hap "T" in saline-alkali land were compared.

[0026] Figure 5 The results of KASP genotyping for the SNP locus Chr17_10009293 in germplasm resources. Detailed Implementation

[0027] It should be noted that the following detailed descriptions are exemplary and intended to provide further illustration of the invention. Unless otherwise specified, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains.

[0028] It should be noted that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the exemplary embodiments of the present invention. As used herein, the singular form is intended to include the plural form as well, unless the context clearly indicates otherwise. Furthermore, it should be understood that when the terms "comprising" and / or "including" are used in this specification, they indicate the presence of features, steps, operations, and / or combinations thereof.

[0029] This invention utilizes conventional techniques and methods from the fields of genetic engineering and molecular biology. Those skilled in the art can employ other conventional techniques, methods, and reagents based on the embodiments provided in this invention, without being limited to the specific embodiments of this invention.

[0030] To enable those skilled in the art to better understand the technical solution of the present invention, the technical solution of the present invention will be described in detail below with reference to specific embodiments.

[0031] Unless otherwise specified, all materials, reagents, strains, plasmids, enzymes, kits, etc. used in the following examples were obtained commercially.

[0032] Example 1 GmERS1 haplotypes in soybeans The soybean sources used included 562 representative soybean germplasm resources, which are preserved in the low-temperature germplasm bank of Professor Xiang Fengning's research group at the College of Life Sciences, Qingdao Campus, Shandong University. Some of these varieties are shown in Table 1. Whole-genome resequencing was performed at a depth of 10X. Using the William 82 (Glyma.Wm82.a2.v1.0) genome as a reference sequence, SNP differential sites were summarized based on sequencing data and alignment results. According to the selection criteria of missing rate ≤10% and minor allele frequency (MAF) ≥5%, a total of 5,600,946 high-density SNP molecular markers covering the entire genome were finally obtained. Based on the physical location of the target genes on the chromosome, genotype data of the target regions were generated and analyzed using the Haps Format module in Haploview 4.2 software. GmERS1 Haplotypes in soybean germplasm resources, such as Figure 1 As shown.

[0033] Table 1. SNPs for identifying salt-tolerant soybean plants, soybean GmERS1 The haplotypes used in some soybean varieties

[0034] Example 2 GmERS1 Activity analysis of different haplotype promoters For testing GmERS1 The transcriptional activity of different haplotype variants of the promoter was investigated by cloning the GmERS1-HapA promoter from HapA material and the GmERS1-HapT promoter from HapT material.

[0035] GmERS1-HapA promoter sequence: gatgcagagaactacgaaaacttcaaaggaagagatttgaaagggaaaattcagatgaaagagaattatatgattttgggaagatagagcctcggcttcaggaa ccctaaacgcgatgttagcctaataataacgaccgtggaggcggctgggatgaaatctccccgtccacgtgtcaacgcattggagcatcttgttcgagtggctgg attgtgctgtctaatgtagactatggttaaatcttgctaatccttttaaccatggttcggttaggtttggtggagctgcggaatggaataaaatattgcaaaaat gccgacgactagttttttcttttaaagatcgctatgtttcaaaagaagctaaaaagtccgtgcttaaagttgaatttataacttgtataagtttgtttttttttt a

[0036] GmERS1-HapT promoter sequence: gatgcagagaactacgaaaacttcaaaggaagagatttgaaagggaaaattcagatgaaagagaattatatgattttgggaagatagagcctcggcttcaggaaccctaaacgcgatgttagcctaataataacgaccgtggaggcggctgggatgaaatctccccgtccacgtgtcaacgcattggagcatcttgttcgagtggctggattgtgctgtctaatgtagactatggttaaatcttgctaatccttttaaccatggttcggttaggtttggtggagctgcggaatggaataaaatattgcaaaaatgccgacgactagttttttcttttaaagatcgctatgtttcaaaagaagctaaaaagtccgtgcttaaagttgaatttataacttgtataagtttgtttttttttt t

[0037] The aforementioned 2,000 bp promoter fragments were cloned into the pGreenII0800-LUC vector to drive the expression of the firefly luciferase (LUC) reporter gene; the Renilla luciferase (REN) gene, driven by the cauliflower mosaic virus (CaMV) 35S promoter in the same vector backbone, was used as an internal control to correct for differences in transformation efficiency. In Nicotiana benthamiana (… Nicotiana benthamiana Transient co-expression was performed in leaves. Leaves were treated with 0 mM (Mock) or 150 mM NaCl. The fluorescence activities of LUC and REN were measured using the Vazyme Dual-Luciferase Reporter Gene Detection Kit on a SpectraMax i3x multi-functional microplate reader, and the ratio of LUC activity to REN activity (LUC / REN) was used as an indicator of transcriptional activation capacity. Data are expressed as mean ± standard deviation (mean ± SD), n=6. All experiments were performed in at least three independent biological replicates.

[0038] like Figure 2 As shown, the HapA haplotype promoter exhibits significantly stronger transcriptional activation activity, especially under 150 mM NaCl treatment, thus identifying this SNP as a functional variant site leading to phenotypic differences.

[0039] Example 3 GmERS1 Compared to Hap T, Hap “A” can improve soybean salt tolerance and yield per plant. GmERS1 Hap “A” and Hap “T” refer to the genotype of the SNP site Chr17_10009293 being AA or TT, respectively.

[0040] 1. Identification and phenotypic analysis of salt tolerance in soybean varieties with different haplotypes during germination. Plump and uniformly sized soybean seeds were selected and surface-sterilized using chlorine fumigation. The specific procedure was as follows: seeds were placed in a desiccator, and 100 mL of sodium hypochlorite solution (effective chlorine concentration 4%-6%) was placed at the bottom of the container. Then, 5 mL of concentrated hydrochloric acid was slowly added, and the desiccator lid was immediately sealed to allow the reaction to produce chlorine gas. The seeds were fumigated in a sealed chlorine environment for 16 hours, and then dried in a clean bench under sterile air for 30 minutes to completely remove residual chlorine. The sterilized seeds were then placed in 9 cm diameter petri dishes lined with two layers of sterile filter paper, with 10 seeds evenly distributed per dish. Three petri dishes were used for each genotype as biological replicates. The treatment group received 5 mL of 150 mM NaCl solution to fully saturate the filter paper, while the control group received an equal volume of sterile distilled water. The petri dishes were placed in an artificial climate incubator with a culture temperature of 25℃, a photoperiod of 16 h light / 8 h dark, and a light intensity of 200 μmol·m⁻¹. -2 ·s -1 Seeds were cultured continuously for 7 days, with the appropriate solution replenished every 2 days to keep the filter paper moist. Seed germination was observed and recorded daily, with the radicle breaking through the seed coat by 2 mm as the germination standard, and the germination rate was calculated. Each treatment was performed in at least 3 independent replicates.

[0041] Table 2. Soybean varieties used to identify haplotype germination rates of soybean GmERS1.

[0042] like Figure 3 As shown, on days 2, 4 and 6 after treatment with 150 mM NaCl, the germination rate of soybean varieties carrying GmERS1-HapA was significantly higher than that of soybean varieties carrying GmERS1-HapT.

[0043] 2. GmERS1 The emergence rate, plant height, and single-plant grain weight of soybean germplasm resources of Hap "A" and Hap "T" in saline-alkali land. Field salt tolerance assessments were conducted in 2022 and 2024 on naturally saline-alkali plots in the Agricultural High-tech Zone of Dongying City, Shandong Province. Before sowing, soil samples from the 0-20 cm topsoil layer were collected using a five-point sampling method. After natural air drying, the samples were sieved through a 1 mm sieve and extracted at a soil-to-water ratio of 1:5. The conductivity of the extract was measured using a conductivity meter, and the total salt content of the soil was calculated using the oven-drying method (drying at 105℃ to constant weight). In salt-stressed areas, the total salt content of the soil was 0.2-0.3 g / 100 g dry soil. Each treatment plot used a randomized block design, with three rows planted per plot, each row 1.5 m long, with a row spacing of 0.5 m and a plant spacing of 0.05 m, and three replicates. Field management followed local conventional cultivation practices. Plant height was assessed at maturity (R8 stage); at maturity, each plot was harvested and threshed individually, and the grain weight per plant was measured. One-way ANOVA was performed on the data using SPSS 26.0 software, and Duncan's method was used for multiple comparisons. The significance level was set at P<<0.05.

[0044] like Figure 4 As shown in the field trial, the results of the agronomic traits test at maturity showed that the plant height and single-plant grain weight of soybean germplasm carrying GmERS1-HapA were significantly higher than those of GmERS1-HapT, indicating that GmERS1-HapA can effectively improve the salt tolerance and yield performance of soybeans in saline-alkali soil.

[0045] Example 4 Soybeans GmERS1 Excellent haplotype KASP marker development 1. GmERS1 (Hap “A”) and GmERS1 (Hap "T") marker development, germplasm resource DNA extraction, and genotyping detection.

[0046] The test materials consisted of 184 soybean germplasm resources.

[0047] Table 3 Soybean varieties used in the development of the superior haplotype KASP marker for GmERS1.

[0048] (1) Design primer sequences The upstream primer F1 is 5'-FAM-TCCTAAAATAAAAACTTACATAAATCAAAAAA-3' (SEQ ID NO:3); The upstream primer F2 is 5'-HEX-CCTAAAATAAAAACTTACATAAATCAAAAAT-3' (SEQ ID NO:4); The downstream primer R is 5'-CCGTGCTTAAAGTTGAATTTATAACTTGTA-3' (SEQ ID NO:5).

[0049] (2) Extraction of DNA from soybean leaves (CTAB method) Fresh, tender soybean material was weighed, and fresh, tender soybean tissue samples were selected for the experiment. These samples were quickly placed into EP centrifuge tubes pre-cooled with liquid nitrogen, and the samples were rapidly frozen and fixed using liquid nitrogen. After freezing, the frozen samples were thoroughly ground using a tissue homogenizer until they were pulverized into a fine powder. Once the liquid nitrogen in the centrifuge tubes had completely evaporated, 1 mL of preheated cetyltrimethylammonium bromide (CTAB) lysis buffer was immediately added. After thorough mixing by vortexing, the samples were placed in a 65 ℃ constant temperature oven for lysis for 30–60 min. After lysis, the samples were centrifuged at 12000 rpm for 15 min. After centrifugation, 800 μl of the supernatant was accurately aspirated and transferred to a brand new 1.5 mL EP centrifuge tube. Add 200 μl of chloroform reagent to the collected supernatant, shake vigorously for 15 s to ensure thorough mixing of the reagent and sample solution, centrifuge again at 12000 rpm for 10 min, and then transfer 600 μL of supernatant to a new 1.5 mL EP tube. Add an equal volume of isopropanol to the obtained supernatant, gently invert and mix for 15 s, then incubate the sample at -20℃ for 10 min to complete DNA precipitation and enrichment. After alcohol precipitation, centrifuge at 8000 rpm for 10 min, discard the supernatant waste in the tube, and retain the white DNA precipitate at the bottom of the tube. Then add 1 mL of 75% ethanol solution to the precipitate for rinsing to remove impurities. To thoroughly remove residual impurities and salts, this rinsing step is repeated twice. After rinsing, place the opened EP tubes in a laminar flow hood to air dry for 5-10 minutes until the ethanol has completely evaporated. Then, add 200 μL of sterile ultrapure water (ddH2O) and mix thoroughly at 65 °C to completely dissolve the DNA precipitate. Take 1 μL of the dissolved DNA stock solution and use a micro spectrophotometer to determine the nucleic acid concentration and OD of the sample. 260 / OD 280 Purity ratio; simultaneously, take another 2 μL DNA sample and detect DNA integrity and overall sample quality by agarose gel electrophoresis. Soybean genomic DNA samples that pass the tests are stored at -20℃ and can be used for subsequent experiments.

[0050] (3) KASP marker genotyping detection PCR amplification was performed using genomic DNA from germplasm resources as templates. A 1 μL micro-reaction system was constructed using a Meridian automated liquid handling workstation. 1536-well plates were sealed using a Kube heat sealer or a Fusion laser sealer to ensure no cross-contamination during water-bath PCR. Immediately after sealing, the plates were centrifuged at 2000 rpm for 1 minute using a Megafuge 1.0 plate centrifuge to concentrate the reaction solution at the bottom of the wells and remove air bubbles. The sealed, centrifuged plates were then placed in a Hydrocycler water-bath PCR instrument for thermal cycling amplification. After the PCR reaction, the plates were removed, the bottom and outer walls were dried, and the plates were allowed to equilibrate at room temperature for 10 minutes before being read for fluorescence signals using a Pherastar multi-functional microplate reader. Excitation and detection wavelengths were set according to the characteristics of the FAM and HEX fluorescent groups, and Standard Rox reference fluorescence was collected for data normalization. The raw fluorescence data output from Pherastar was imported using SNPviewer software provided by LGC Genomics. Scatter clustering was plotted with FAM fluorescence intensity as the X-axis and HEX fluorescence intensity as the Y-axis. Based on the differences in fluorescence signals, the samples were divided into three genotype groups: homozygous genotype T (strong FAM signal, weak HEX signal) near the X-axis, homozygous genotype A (strong HEX signal, weak FAM signal) near the Y-axis, and heterozygous genotype located in the diagonal region (both fluorescence signals are strong).

[0051] The results are as follows Figure 5 As shown, the typing accuracy of both genotypes was 100%, which is consistent with the resequencing results, indicating that the KASP marker has good application value and can be safely used for molecular marker-assisted breeding of soybean salt tolerance.

[0052] The PCR reaction system used in the above experiment was as follows: 0.500 μL of 2×KASP Master mix, 0.014 μL of 72×Assay mix, and 0.486 μL of sterile ultrapure water, for a total volume of 1.000 μL. The specific procedure consisted of three steps: the first step was pre-denaturation at 94℃ for 15 minutes, repeated once; the second step included denaturation and annealing extension, with denaturation at 94℃ for 20 seconds and annealing extension starting at 61℃, decreasing by 0.6℃ per cycle for 60 seconds, for a total of 10 cycles; the third step also included denaturation and annealing extension, with denaturation at 94℃ for 20 seconds and annealing extension at 55℃ for 60 seconds, for a total of 26 cycles.

[0053] Finally, it should be noted that the above description is merely a preferred embodiment of the present invention and is not intended to limit the present invention. Although the present invention has been described in detail with reference to the foregoing embodiments, those skilled in the art can still modify the technical solutions described in the foregoing embodiments or make equivalent substitutions for some of them. Any modifications, equivalent substitutions, improvements, etc., made within the spirit and principles of the present invention should be included within the protection scope of the present invention.

Claims

1. A SNP related to soybean salt tolerance and yield traits, characterized in that, The SNP is located at 10009293 bp on chromosome 17 of soybean genome Wm82.a2.v1.0, with a polymorphism of A / T, and is denoted as Chr17_10009293.

2. The SNP as described in claim 1, characterized in that, The indicators for salt tolerance are the main root length, fresh weight, dry weight, and single-plant grain weight of soybeans under salt stress.

3. The KASP primer set for detecting the SNP of any one of claims 1-2, characterized in that, It includes upstream primer F1 with nucleotide sequence as shown in SEQ ID NO:3, upstream primer F2 with nucleotide sequence as shown in SEQ ID NO:4, and downstream primer R with nucleotide sequence as shown in SEQ ID NO:

5.

4. A reagent or kit, characterized in that, Includes the KASP primer set as described in claim 3.

5. The use of the SNP of claim 1, the KASP primer set of claim 3, or the reagent or kit of claim 3 in any of the following: (1) Identify the salt tolerance traits of soybeans during germination; (2) Screening for salt-tolerant soybean varieties or lines during the germination period; (3) Breeding of salt-tolerant soybeans; (4) Breeding of high-yield, salt-tolerant soybeans; (5) Develop salt-tolerant soybean varieties; (6) Develop high-yield, salt-tolerant soybean varieties; (6) Identification or auxiliary identification of high-yielding salt-tolerant soybean varieties; (7) Marker-assisted breeding of soybeans; (8) Improve salt-tolerant soybean germplasm resources.

6. A method for identifying or assisting in the identification of salt-tolerant or high-yielding salt-tolerant soybeans, characterized in that, The method includes detecting the genotype of the SNP site Chr17_10009293 in the soybean to be tested, and determining the salt tolerance of the soybean based on the genotype; the SNP site Chr17_10009293 is located at 10009293 bp on chromosome 17 of the soybean genome Wm82.a2.v1.

0.

7. The method as described in claim 5, characterized in that, Soybeans with genotype AA are high salt-tolerant soybean varieties, while soybeans with genotype TT are low salt-tolerant soybean varieties.

8. A method for cultivating salt-tolerant or high-yielding salt-tolerant soybeans, characterized in that, The method includes detecting the genotype of the soybean SNP site Chr17_10009293, and selecting soybeans with the AA genotype for breeding; the SNP site Chr17_10009293 is located at 10009293 bp on chromosome 17 of the soybean genome Wm82.a2.v1.

0.

9. The application of the method according to claim 6 or claim 8 in soybean breeding.

10. The application as described in claim 9, characterized in that, Breeding methods include transgenic, hybridization, backcrossing, self-pollination, or asexual reproduction.

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