Genome-Wide Association Analysis for Submergence Tolerance at the Early Vegetative and Germination Stages in Wild Soybean ( Glycine soja )

Cultivated soybean is an important legume crop that is generally sensitive to flooding stress, including submergence and waterlogging treatments. Wild soybeans, the ancestor of cultivated soybeans, have been potential genetic resources for resistance to abiotic or biotic stresses. The present study aimed to evaluate 163 wild soybean accessions for foliar damages at the early vegetative stage and 105 accessions for germination rates, normal seedling rates, and electrical conductivity at the germination stage under submergence stress. In addition, a genome-wide association study (GWAS) was conducted to identify genomic regions associated with phenotypic measurements at these two growth stages by using MLM and FarmCPU models with publicly available genotypic data. The phenotypic evaluation revealed six and three accessions were tolerant to submergence at the early vegetative and germination stages, respectively. Notably, only one wild soybean accession showed a tolerance reaction to submergence at two stages. Through GWAS analysis, 16 and 20 SNPs across different chromosomes were determined for the submergence-related traits at the early vegetative and germination stages, respectively. Based on the linkage disequilibrium block on the detected genomic regions, ten and four putative genes were identified at the early vegetative and germination stages, respectively. Of these genes, certain genes may be related to submergence stress in wild soybeans. Further studies should be performed to validate the function of these putative genes in the responses of wild soybeans to submergence stress.