Genome wide association mapping of soybean elite germplasm for spring-season adaptation by using high-density SNP array

Soybean (Glycine max L.) is a globally important crop and a major source of edible oil and plant-based protein; however, spring-season cultivation exposes soybean to elevated temperatures during critical reproductive stages, adversely affecting yield and seed quality. A panel of 100 advanced soybean accessions was screened across two variable planting dates of the spring season for two consecutive growing years, 2020 and 2021. Phenotypic data of six yield-related traits, i.e., plant height (PH), number of pods per plant (Pods), number of seeds per plant (Seeds), 100-seed weight (HSW), yield per plant (YPP), and days to maturity (DM) were collected. A genome-wide association study (GWAS) was conducted using the Fixed and Random Model Circulating Probability Unification (Farm-CPU) method by using 42,449 high-quality single-nucleotide polymorphisms (SNPs) from the SoySNP50K array. A total of 77 significant marker trait associations (MTAs) were identified. The highest number of MTAs is linked with plant height, and the lowest number of MTAs is linked with yield per plant. Genome-wide means of major allele frequency (MAF), genetic diversity (GD), and polymorphic information content (PIC) were 0.78, 0.28, and 0.28, respectively. Population structure and phylogenetic tree analysis were used to divide the whole population into two distinct groups. Furthermore, seven SNPs, i.e., ss715582919, ss715588087, ss715588504, ss715592876, ss715599604, ss715599732, and ss715599766, were associated with multiple traits across planting dates. Various clusters of significant SNPs were marked on chromosomes Gm08, Gm10, Gm17, Gm02, Gm12, Gm15, and Gm16 associated with various yield traits. Candidate gene analysis identified genes related to thermotolerance (HSP90, HSFA2), flowering time (FT2a), pod number (NAC29), and carbohydrate transport (SWEET15) within flanking regions of key SNPs. A comprehensive insight into the genetic architecture of soybean yield under spring-season conditions is a prerequisite for the development of climate-resilient soybean genotypes. These findings will contribute to devising future breeding strategies in soybean.