Stable pleiotropic loci and candidate genes for fresh pod- and seed-related characteristics across multiple environments in soybean (Glycine max)

Soybean provides irreplaceable protein and oil. Pods and seeds are essential soybean harvested organs. To illustrate the genetic basis of pod- and seed-related traits, a natural population was assessed for eight related traits under four environments. In all, 15 associated SNPs were identified across multiple environments or controlling various traits, and 11 were verified through BLUP. Two SNPs on chromosome 15 were associated with six traits across multiple environments. Two SNPs on chromosome 2 were also associated with six traits under multiple environments. Significant phenotype differences between favourable and unfavourable alleles/haplotypes under four environments were detected. Significant association of pod length SNP and large-pod phenotype (pod length >= 4.5 cm) was detected. The genetic basis of elite germplasms was analysed, and 'Chuxiu' possessed all of the 15 favourable alleles with best phenotype. Some candidate genes participating in cell wall structural remodelling, gibberellin and ethylene pathways were selected with different expressions in pod developmental stages. These results provided novel insights into genetic basis and molecular markers/candidate genes for soybean fresh pod and seed genetic improvement.