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

• Published in: PloS one 2020-10, Vol.15 (10), p.e0239122-e0239122
• Main Authors: Ketema, Selamawit, Tesfaye, Bizuayehu, Keneni, Gemechu, Amsalu Fenta, Berhanu, Assefa, Ermias, Greliche, Nicolas, Machuka, Eunice, Yao, Nasser, Chiang, Tzen-Yuh
• Format: Article
• Language: English
• Subjects: Agricultural research; Biology and Life Sciences; Breeding; Cereals; Collection; Collections; Computer and Information Sciences; Conservation; Cowpea; Cowpeas; Current distribution; Deoxyribonucleic acid; Discriminant analysis; Distribution; Diversity indices; DNA; Domestication; Ecology and Environmental Sciences; Engineering and Technology; Gene polymorphism; Genetic aspects; Genetic diversity; Genetic resources; Genotypes; Germplasm; Heterozygosity; Horticulture; Identification and classification; Legumes; Livestock; Markers; Nucleotides; Nutrition; People and Places; Phylogeny; Polymorphism; Population; Population genetics; Population structure; Population studies; Populations; Regions; Resource conservation; Single-nucleotide polymorphism; Variance analysis; Vigna unguiculata
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0239122

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.