Cold Tolerance SNPs and Candidate Gene Mining in the Soybean Germination Stage Based on Genome-Wide Association Analysis

Abstract Low temperature is a key factor affecting the geographical distribution, growth, development, and yield of soybeans. Exposing soybean seeds to low-temperature stress during the germination stage can lead to a substantial reduction in productivity. At present, there is limited information on the genetic mechanisms associated with cold tolerance during the soybean germination stage. In this study, we assessed the germination phenotype of a population of 260 soybean accessions under low-temperature stress (3°C). Using a mixed linear model, we performed a genome-wide association analysis (GWAS) of 30,799 single nucleotide polymorphism (SNP) markers and identified a total of 71 SNPs associated with cold tolerance. SNP (BARC_2.01 Chr18_53718636_A_G) was associated with two traits: (1) the ratio of germination potential under low-temperature stress to germination potential under normal conditions (CT-GP) and (2) the germination potential at 3°C. Within the linked genetic region of this marker, there were six genes, including Glyma.18g250900 and Glyma.18g251400, which exhibited differential expression levels in two groups of materials with different cold tolerances. These two genes had 4 and 3 haplotypes, respectively. Soybean germplasms harboring Glyma.18g250900-Hap3, Glyma.18g251400-Hap2, and Glyma.18g251400-Hap3 exhibited strong cold tolerance during the germination stage. Glyma.18g250900 and Glyma.18g251400 were predicted to be potential candidate genes involved in the response of soybean germination to low-temperature stress. The SNPs and candidate genes identified in this study have important implications for marker-assisted selection and gene editing in cold-tolerant soybean breeding and provide a valuable reference for understanding the underlying genetic mechanisms of cold tolerance in soybean germination.