Genetic diversity and population structure of soybean ( Glycine max (L.) Merril) germplasm

Soybean ( Glycine max (L.) Merril) is a significant legume crop for oil and protein. However, its yield in Africa is less than half the global average resulting in low production, which is inadequate for satisfying the continent’s needs. To address this disparity in productivity, it is crucial to develop new high-yielding cultivars by utilizing the genetic diversity of existing germplasms. Consequently, the genetic diversity and population structure of various soybean accessions were evaluated in this study. In pursuit of this objective, a collection of 147 soybean accessions was genotyped via the Diversity Array Technology Sequencing method. This method enables high-throughput analysis of single-nucleotide polymorphisms (SNPs), resulting in the identification of 7,083 high-quality SNPs distributed throughout the soybean genome. The average values observed for polymorphism information content (PIC), minor allele frequency, expected heterozygosity and observed heterozygosity were 0.277, 0.254, 0.344, and 0.110, respectively. The soybean genotypes were categorized into four groups on the basis of model-based population structure, principal component analysis, and discriminant analysis of the principal component. Alternatively, hierarchical clustering was used to organize the accessions into three distinct clusters. Analysis of molecular variance indicated that the genetic variance within the populations exceeded the variance among them. The insights gained from this study will assist breeders in selecting parental lines for genetic recombination. Overall, this study provides valuable information regarding soybean genetic diversity and lays the groundwork for conservation and genetic enhancement initiatives.