DArTSeq SNP-based markers revealed high genetic diversity and structured population in Ethiopian cowpea [Vigna unguiculata (L.) Walp] germplasms

Abstract

Cowpea [Vigna unguiculata (L.) Walp] is one of the important climate-resilient legume crops for food and nutrition security in sub-Saharan Africa. Ethiopia is believed to harbor high cowpea genetic diversity, but this has not yet been efficiently characterized and exploited in breeding. The objective of this study was to evaluate the extent and pattern of genetic diversity in 357 cowpea accestions comprising landraces (87%), breeding lines (11%) and released varieties (2%), using single nucleotide polymorphism markers. The overall gene diversity and heterozygosity were 0.28 and 0.12, respectively. The genetic diversity indices indicated substantial diversity in Ethiopian cowpea landraces. Analysis of molecular variance showed that most of the variation was within in the population (46%) and 44% between individuals, with only 10% of the variation being among populations. Model-based ancestry analysis, the phylogenetic tree, discriminant analysis of principal components and principal coordinate analysis classified the 357 genotypes into three well-differentiated genetic populations. Genotypes from the same region grouped into different clusters, while others from different regions fell into the same cluster. This indicates that differences in regions of origin may not be the main driver determining the genetic diversity in cowpea in Ethiopia. Therefore, differences in sources of origin, as currently distributed in Ethiopia, should not necessarily be used as indices of genetic diversity. Choice of parental lines should rather be based on a systematic assessment of genetic diversity in a specific population. The study also suggested 94 accesstions as core collection which retained 100% of the genetic diversity from the entire collection. This core set represents 26% of the entire collection pinpointing a wide distribution of the diversity within the ethiopian landraces. The outcome of this study provided new insights into the genetic diversity and population structure in Ethiopian cowpea genetic resources for designing effective collection and conservation strategies for efficient utilization in breeding.

Genetic Diversity, Population Structure and Relationship of Ethiopian Barley (Hordeum vulgare L.) Landraces as reveled by Simple Sequence Repeat (SSR) Markers

“…STRUCTURE, UPGMA clustering, and Discriminant analysis of principal component (DAPC) or PCoA; consistently recovered the same seven groups. The consistency of grouping using these methods has also been observed in earlier studies on different crop species (Tascioglu et al, 2016;Ya et al, 2017;Ketema et al, 2020). The differentiation of the population into different subpopulations by fastSTRUCTURE is based on frequencies of relatedness of the genotypes to each of the subpopulations as hypothesized (Nielsen et al, 2014;Chao et al, 2010).…”

“…Bar plots were generated with average results of runs for the most probable K value, using DISTRUCT v.1.1 (Rosenberg, 2004). As suggested in Ketema et al (2020) genotype was considered to belong to a group if its membership coe cient was > 0.70. Genotypes with membership coe cient less than 0.70 at each assigned K were regarded as admixed.…”

Development of a core set of single nucleotide polymorphism markers for genetic diversity analysis and cultivar fingerprinting in cowpea

“…Assessment of genetic diversity in crop germplasm is essential for successful crop improvement (Varshney et al, 2007). In cowpea, the genetic diversity of different germplasm collections in Ghana, China, the United States, Korea, and Ethiopia has been evaluated using different SNP markers (Egbadzor et al, 2014; Ketema et al, 2020; Muňoz‐Amatriaín et al, 2017; Seo et al, 2020; Xu et al, 2017). Most studies aimed to evaluate the extent and pattern of genetic diversity in their own research collections and developed core collections as subsets.…”

DArT-seq based SNP analysis of diversity, population structure and linkage disequilibrium among 274 cowpea (Vigna unguiculata L. Walp.) accessions

“…However, this may require more high-density genome wide markers [33].Differences were observed between the DAPC and Structure analysis in the size of the subgroups which can be attributed to the presence of admixed individuals in the population. Thirty-one (31) accessions were in admixture when the cut-off value of coe cient ancestry was set at 0.52, and this number could increase with higher thresholds, a factor that leads to discrepancies in the results of these analyses [34,35].…”