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.

DArTSNPbased genetic diversity analyses in cassava (Manihot esculenta) genotypes sourced from different regions revealed high level of diversity within population

“…Genetic diversity and population structure assessment of 155 cassava genotypes were performed using 5,247 single nucleotide polymorphism markers by [33]. As a result, a total genetic variation of 66.0% within and 34.0% between sub-populations were quoted.…”

“…These authors also reported five sub-populations in the population admixture analyses and three clusters in the cluster analysis that suggests the existence of high genetic diversity in the study germplasm. [33] conducted genomic analysis of 164 cassava collections from different cassava growing areas of Burkina Faso using selective 36 SNPs marker based on positions of the markers on the genome and reported average minor allele frequency, expected and observed heterozygosity and PIC of 0.06, 0.46, 0.58 and 0.36, respectively. On the other hand, [4] assessed 87 cassava accessions with filtered 10808 SNPs and 10521 SilicoDArT markers and reported informativeness of the markers with average PIC of 0.36 for SilicoDArT and 0.28 for SNP, marker, respectively.…”