Genome-wide association studies (GWAS) reveal candidate genes for plant height and number of primary branches in soybean [Glycine max (L.) Merrill]

Plant height and the number primary branches are important traits having bearing on yield. Understanding genetic control of these traits would help in the development of improved soybean genotypes suitable for water-stress and normal conditions. In this study, 63 diverse soybean accessions were genotyped with 2, 84, 923 single nucleotide polymorphism (SNP) markers, and phenotyping was done under optimal and moisture-stress conditions in two locations viz., New Delhi and Dharwad. Significant variation was observed among the genotypes for the traits in both the locations. Interaction of the genotypes with locations and the situations was also found to be significant. The population structure and genetic diversity analysis indicated existence of four sub-sets of population among the genotypes. GWAS conducted through Mixed Linear Model identified several Quantitative Trait Nucleotides(QTNs) associated with plant height and branches/plant. Genes associated with the identified QTNs and their functions have also been identified. Two novel QTNs for number of branches/plant were mapped on Chromosomes 3 and 16. The identified QTNs and the genes would facilitate designing of gene-specific markers which would pave the way for development of soybean genotypes with optimum height, branches and yield.