SSR allele scoring and statistical analysis

The fragment size of amplified DNA products was determined by comparing with 50 bp DNA ladder (Thermo scientific, USA). The SSR bands scored in soybean accessions were used for genetic diversity analysis. Major allele frequency, gene diversity, polymorphic information content (PIC) and heterozygosity for each SSR locus were calculated using Power Marker 3.25 and a phylogenetic tree was constructed using neighbour-joining method (Liu and Muse 2005). Population structure was inferred by using the model-based program, STRUCTURE 2.3.4 (Pritchard et al. 2000). For each K, three replications were run where each run was implemented over a burn-in period of 50,000 steps and 100,000 Monte Carlo Markov Chain replicates. The membership of each genotype was run for K = 1–20 by taking admixture model and correlated allele frequency into account. The final population was determined by applying the second-order statistics (ΔK) developed by Evanno et al. (2005) using ‘Structure harvester’ software (Earl and vonHoldt 2012). Venn diagram analysis was performed to identify common accessions between clusters and populations using online software Venny 2.1 (Oliveros 2007).