Dissection of genetic characteristics of storability via GWAS and haplotype analysis of candidate genes in soybean

ZHU Yixin; LI Chongyang; WANG Jun; LI Minmin; GENG Yating; GAO Huawei; LIU Like

doi:10.19728/j.issn1672-6634.2025030004

Abstract：The storability of soybean seeds is a crucial factor in determining the germination potential(GP)and germination rate(GR)of stored seeds,which are of great significance for agricultural production and food processing.In this study,the GP and GR of 879 soybean germplasms stored under natural conditions for 3.5 years were measured.Through a genome-wide association study(GWAS),58 significantly associ-ated SNPs were found,among which one SNP was associated with GP and 57 SNPs were related to GR.These significant SNPs were distributed either independently or in clusters on ten different chromosomes.The SNP clusters on chromosomes 2,9,and 10 were identified as three QTLs related to GR.Five known QTLs that overlapped with these three QTLs were considered co-located QTLs,and two genes,namely Glyma.02g170500 and Glyma.09g182900,were identified as candidate genes.The results of haplotype analysis showed that 11 tag SNPs located in the non-coding region of Glyma.02g170500 could be divided into 4 blocks,with GP and GR differing significantly between different haplotypes in all blocks except the block 2.A total of 38 tag SNPs were found for Glyma.09g182900,forming 840 haplotypes.Due to the small number of accessions for each haplotype,further analysis was not conducted.The haplotype with significantly higher GP and GR than the other haplotypes contained more accessions from the Huang-Huai region than from other regions,and more landraces than improved cultivars.The results of this study will provide a theoretical basis and technical support for the subsequent breeding of soybean varieties with high storability and the elucidation of the genetic mechanism of soybean seed storability.