Genome-wide association study reveals the genetic basis of cold tolerance in soybean

Soybean [Glycine max (L.) Merr.] is an important seed crop with agricultural sustainability that can be used to meet the growing demand for plant-based oil and protein worldwide. Expanding the cultivation of soybean to high-latitude regions could be an effective strategy for enhancing soybean production. Low temperatures in these regions can inhibit seed germination during the planting season. Despite their importance, many cold tolerance-related genes in soybean remain unidentified. Here, we carried out a genome-wide association study (GWAS) in a diverse soybean population with large variations in cold tolerance-related germination traits. The analyses led to the identification of a total of 46 single-nucleotide polymorphisms (SNPs) that were significantly associated with cold tolerance-related traits. We identified a new locus on chromosome 18, qCold-18–3, that was associated with both the low-temperature germination rate and potential. Furthermore, Abscisic Acid-Deficient4 (GmABA4) was prioritized as the most promising candidate gene. In addition, GmABA4 was strongly induced in a cold-tolerant accession by cold stress during germination, and it contains cis-acting elements associated with low temperature in its promoter region. Haplotype analysis revealed that the accessions harboring Hap3 of GmABA4 were more tolerant to low temperature than those harboring the other haplotypes. In this study, a new cold tolerance-related candidate gene, GmABA4, was identified through GWAS, and further study could advance our understanding of the underlying genetic mechanisms and facilitate the breeding of soybean with improved cold tolerance.