Assessment of phenotypic and molecular diversity in soybean [Glycine max (L.) Merr.] germplasm using morpho-biochemical attributes and SSR markers

Soybean is a high-nutritional crop that provides a sustainable source of dietary protein and edible oil for human consumption and animal diet. In this investigation, we evaluated 56 test entries and three commercial checks for yield and quality characters for two consecutive seasons (2017–2018), whereas molecular diversity among the tested genotypes was also estimated through simple sequence repeat (SSR). Results revealed significant variation among tested entries for all measured traits. The principal component analysis (PCA) resulted in three significant components, which accounted for 72.05% of the total variation. The first two PCs were mainly characterized by seed yield plant−1, 100-seed weight, plant height, number of filled pods and oil content, whereas the essential genotypes that contributed significantly to the phenotypic variability were K-D, Jhunghwang and 24598. The genotypic (rg) and phenotypic (rp) correlation of seed yield with protein and oil contents were non-significant, whereas a negative association was found between protein content and oil content. Out of 30 SSR-loci, 28 were polymorphic and detected a total of 65 alleles with average value of 2.32 alleles per locus. The polymorphic information contents (PIC) ranged from 0.12 to 0.58 with an average of 0.37, indicating a moderate level of genetic diversity exhibited by the assessed germplasm. In addition, structural analysis and principal coordinate analysis delineated two major sub-populations, representing two diverse gene pools in soybean collection. The neighbor-joining tree inferred five clusters based on their genetic resemblance and geographic origin. Thus, the use of substantial genetic diversity confirmed in the present study will enable soybean breeders to select diverse parents to develop high-yielding varieties with improved quality traits.