Genetic diversity and population structure of Ugandan soybean (Glycine max (L.) germplasm based on DArTseq

Abstract

Soybean (Glycine max (L.) is an important oil crop with production below the real need in Africa. To increase the production, substantial upgrading must be accomplished by enlarging the genetic potential of new cultivars that relays on the parents' genetic diversity. We aimed to assess the genetic diversity and the population structure of soybean accessions, therefore, evaluate soybean value in terms of use for breeding purposes. To accomplish this, a set of 282 soybean accessions were genotyped using the Diversity Array Technology Sequencing with a high throughput of the Single-nucleotide polymorphisms (SNPs). A total of 6,935 high-quality SNPs were identified across the whole soybean genome. The mean value of genetic diversity, major alleles frequency, minor alleles frequency, expected heterozygosity, and the polymorphism information content was respectively estimated at 0.35, 0.77, 0.22, 0.33, and 0.29. The analysis of molecular variance reveals that the variance among the populations is lower than the variance within the populations. The soybean accessions could be classified into two groups based on the model-based population structure and the principal coordinate analysis or into three groups based on the discriminant analysis of the principal component and the Neighbor-joining tree. The information provided in this study will be helpful for breeders.