CN-122012786-A - SNP locus related to soybean hundred-grain weight and application thereof

Abstract

The invention discloses a soybean hundred-grain weight related SNP locus and application thereof, wherein the SNP locus is positioned at a physical position 39283583 bp of a 11 th chromosome of a soybean genome, and comprises two allele types, namely a G type and an A type, and soybeans with different genotypes have different hundred-grain weight character phenotypes. The application of the SNP locus in soybean breeding, in the preparation of soybean breeding products, in the identification or auxiliary identification of soybean hundred-grain weight characters, in the preparation of soybean hundred-grain weight character identification or auxiliary identification products, and in the screening or breeding of soybean single plants or strains or varieties according to the soybean hundred-grain weight characters. The invention lays a foundation for cloning the soybean hundred-grain weight related genes and provides a practical molecular tool for high-yield soybean breeding.

Inventors

• YAN LONG
• LIU LUPING
• LIU ZHI
• LIU BINGQIANG
• CHEN QIANG
• SHI XIAOLEI
• MENG QINGMIN
• YANG CHUNYAN
• YANG QING
• WU XINTONG
• ZHANG MENGCHEN
• Suo Wenying

Assignees

• 河北省农林科学院粮油作物研究所

Dates

Publication Date

20260512

Application Date

20260310

Claims (10)

1. 1. A SNP locus related to the hundred-grain weight of soybean is characterized in that the SNP locus is positioned at a physical position 39283583 bp of chromosome 11 of soybean genome, the locus comprises two allele types, namely G type and A type, and soybeans with different genotypes have different hundred-grain weight character phenotypes.
2. 2. The SNP locus according to claim 1, wherein the application is any one of the following: (1) The SNP locus is applied to soybean breeding; (2) The SNP locus is applied to the preparation of products in soybean breeding; (3) The SNP locus is applied to identification or auxiliary identification of soybean hundred grain weight characters; (4) The SNP locus is applied to the preparation of products for identifying or assisting in identifying the soybean hundred-grain weight characteristics; (5) The SNP locus is applied to screening or breeding soybean single plants or strains or products of strains or varieties according to the soybean hundred-grain weight character.
3. 3. A method for identifying or assisting in identifying soybean hundred-grain weight characters is characterized in that the specific genotype based on the SNP locus as set forth in claim 1 is used for identifying or assisting in identifying soybean hundred-grain weight characters, and the hundred-grain weight of type A genetic soybean is higher than or candidate higher than that of type G genetic soybean.
4. 4. The method for identifying or assisting in identifying soybean hundred-grain weight characters according to claim 3, wherein the method for detecting whether the genotype of SNP locus in soybean genome is G type or A type is that PCR amplification is carried out on the soybean genome DNA to be detected by using a specific KASP marker, and the genotype of the soybean to be detected is determined after fluorescent scanning.
5. 5. The method for identifying or assisting in identifying soybean hundred-grain weight traits according to claim 4, wherein the specific KASP marker comprises a downstream primer R shown in SEQ ID NO. 1, and upstream primers Chr17-KASP-FAM and Chr17-KASP-VIC shown in SEQ ID NO. 2 and 3.
6. 6. The method for identifying or assisting in identifying soybean hundred grain weight characters according to claim 5, wherein the specific KASP marker in claim 5 is used for carrying out PCR amplification on soybean genome DNA to be detected to obtain a PCR product, fluorescent signals are converted into analyzable values, and a fluorescent scanning result is subjected to graphical display, wherein if FAM fluorescence is carried out, the genotype of SNP loci in the soybean genome to be detected is G type, if VIC fluorescence is carried out, the genotype of SNP loci in the soybean genome to be detected is A type.
7. 7. A specific KASP-labeled primer combination is characterized by comprising a downstream primer R shown in SEQ ID NO. 1 and upstream primers Chur 17-KASP-FAM and Chur 17-KASP-VIC shown in SEQ ID NO. 2 and 3 for detecting the SNP locus as set forth in claim 1.
8. 8. A reagent or a kit for identifying or assisting in identifying soybean hundred-grain weight characters is characterized in that the reagent or the kit is used for detecting SNP locus genotypes according to claim 1 and at least comprises a specific KASP marking primer combination according to claim 7.
9. 9. Use of the method of any one of claims 3-6, the specific KASP tagged primer combination of claim 7, the reagent or kit of claim 8 in any one of the following (1) - (6): (1) Application of identifying or assisting in identifying soybean hundred-grain weight related characters; (2) The application in preparing products for identifying or assisting in identifying the soybean hundred-grain weight related characters; (3) Screening or assisting in screening high-hundred-grain great soybean varieties; (4) Application of soybean hundred grain weight related character breeding or auxiliary breeding; (5) The application of the soybean hundred-grain weight related character breeding or auxiliary breeding products is prepared; (6) The application in identifying or assisting in identifying soybean yield.
10. 10. A soybean breeding method, characterized in that the genotype of the SNP locus of claim 1 in soybean genome is detected first, and homozygous soybean with the SNP locus A is selected as parent for breeding.

Description

SNP locus related to soybean hundred-grain weight and application thereof Technical Field The invention relates to the technical field of molecular biology, in particular to a SNP locus related to soybean hundred-grain weight and application thereof. Background Soybeans are important commercial crops, being the major source of human vegetable oils and vegetable proteins. With the continued growth of the global population and the increasing level of living, the global demand for soybean is steadily increasing. Thus, increasing soybean yield remains a key goal in soybean breeding. Seed weight is a key component affecting soybean yield, and significantly affects the appearance and overall quality of seeds. Thus, identification of Quantitative Trait Loci (QTLs) and functional genes associated with grain weight is critical for genetic improvement of soybean yield potential. In soybean, more than 300 QTL sites associated with grain weight have been identified by linkage analysis and whole genome association analysis. However, the confidence intervals for many QTLs are large due to the low density of genetic map markers early used for QTL localization, and population size. Furthermore, differences in genetic background make many QTLs more difficult to apply in molecular assisted breeding. Fine localization is an important way to narrow QTL intervals and discover functional genes. In addition, several hundred-grain weight related functional genes have been identified by methods such as GWAS analysis, transcriptome analysis, and the like. GmSWEET10a/b seed size control by regulating the transport of sucrose from the seed coat to the cotyledons, gmSW17 encodes a ubiquitin-specific protease that interacts with GmSGF and GmENY2 to form a deubiquitin enzyme module. The module influences the H2Bub level, negatively regulates GmDP-E2F-1 expression, thereby inhibiting G1-to-S conversion and influencing seed size. GmJAZ3 regulates the expression of the GmCKXs gene by interacting with GmRR a/GmMYC2a, and participates in regulating the size and grain weight of seeds. In addition, gmPP C-1, gmCYP78A72, gmKIX-1, gmST05 and other genes are also involved in regulating the grain weight of soybean seeds. However, the number of QTLs and the functional genes identified that have been finely localized is relatively limited compared to the number of QTLs. Therefore, the novel soybean hundred-grain weight related SNP locus which is high in phenotype interpretation rate and stability and is suitable for the multi-ecological-area germplasm is mined, and the method has important significance in promoting the cultivation of high-yield and high-quality soybean varieties and improving the soybean industry competitiveness. Disclosure of Invention The invention aims to provide an SNP locus related to soybean hundred-grain weight and application thereof. In order to solve the technical problems, the technical scheme adopted by the invention is as follows. A SNP locus related to the hundred grain weight of soybean, the SNP locus is positioned at physical position 39283583 bp of chromosome 11 of soybean genome, the reference genome is wm82.a2v1, the locus comprises two allele types, namely G type and A type, and soybeans with different genotypes have different hundred grain weight character phenotypes. Specifically, the sequence of the upstream and downstream of the SNP is shown as follows (corresponding to SEQ ID NO.4 in the sequence Listing): TCTGCGTTGTGATGTCACTGGGAAGATTCTTATGAAGTGCTTTCTTTCTGGAATGCCTGATTTAAAGTTGGGTCTGAATGACAAGATTGGTCTTGAGAAAGAAGCACAACTTAAGTCCCGTCCTRCTAAAAGGTAGCCTTCTGTTGCACTCATTTCCCCTTTTGGCCACCAATGTTTTTTTTTTTTCCTTTAAATATTGTCATTTCAAACTTTAGTCTTTATGCTCTTCTGTTATGTTAGCATTGATA; Wherein r= [ G/a ]. The invention also includes the use of the SNP locus according to claim 1, wherein the use is any one of the following: (1) The SNP locus is applied to soybean breeding; (2) The SNP locus is applied to the preparation of products in soybean breeding; (3) The SNP locus is applied to identification or auxiliary identification of soybean hundred grain weight characters; (4) The SNP locus is applied to the preparation of products for identifying or assisting in identifying the soybean hundred-grain weight characteristics; (5) The SNP locus is applied to screening or breeding soybean single plants or strains or products of strains or varieties according to the soybean hundred-grain weight character. The invention also comprises a method for identifying or assisting in identifying soybean hundred-grain weight characters, wherein the specific genotype based on the SNP locus is used for identifying or assisting in identifying soybean hundred-grain weight characters, and the hundred-grain weight of the type A gene soybean is higher than or the candidate is higher than that of the type G gene soybean. As a preferable technical scheme of the invention, the method for detecting whether the genotype of the SNP locus in the soybean genome is G type or A ty