Diversity, population structure, and linkage disequilibrium among cowpea accessions

Abstract

Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop.However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor-joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUC-TURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005-0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48-0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for

Genetic Diversity and Association Analysis for Carotenoid Content among Sprouts of Cowpea (Vigna unguiculata L. Walp)

“…The discovery of markers associated with this trait can help in fast tracking, selection, and breeding of cowpea varieties with high carotenoid content in the sprouts. The results showed that the 125 accessions can be distributed into three groups, which corroborates our previous findings in the population of origin of the accessions [ 31 ]. Although the presence of population structure within the germplasm is a positive indication of genetic potential for improvement, it can be a confounding factor in testing the associations between markers and phenotypic variation [ 56 , 57 ].…”

“…The genomic data used in this study consisted of 3,120 SNPs markers ( Table S3 ), previously reported among a diversity panel of cowpea [ 31 ], which includes the 125 accessions used in the present study. The genetic diversity parameters of the germplasm were estimated in GenAlex [ 78 ].…”

“…Cowpea is an important grain legume on which millions of people depend for their daily nutrients needs in the tropics [ 24 , 25 , 26 ]. It is a model grain legume for genomic studies [ 27 ] because of its relatively small (~640.6 Mb) diploid (2 n = 2 x = 22 Chromosomes) genome [ 28 ], and a large portion of the cowpea germplasm is conserved and easily accessible for research at IITA and USDA GRIN gene banks [ 27 , 29 , 30 , 31 ]. Low carotenoid profiles are found in cowpea, dominated (70%) by lutein [ 32 ].…”

“…Sprouts of grain legume or pulses have been shown to increase carotenoid content and overall antioxidant profiles, as well as to minimize the anti-nutritional factors of the dry grains [ 12 , 49 , 50 , 51 ]. Recently, we assembled and genotyped a cowpea germplasm collection using the diversity array technology (DArT) sequencing [ 31 ]. Here, we assessed the variation of carotenoids, including lutein, zeaxanthin, and β-carotene contents, among sprouts of a set of accessions from the germplasm collection and identified quantitative trait loci (QTLs) associated with carotenoid biosynthesis to boost carotenoid biofortification in cowpea.…”

Genetic diversity and population structure of Uganda’s yam (Dioscorea spp.) genetic resource based on DArTseq

“…The 4,957 high-quality selected SNPs were polymorphic as observed in previous SNP-based genetic diversity studies in Dioscorea alata [3] and Dioscorea rotundata [28]. Similar polymorphism values have also been reported in several important food crops such as oilseed crop (0.21) [46], soybean (0.28) [47], rice (0.31) [48], maize (0.19) [49], cowpea (0.24) [50], common bean (0.25) [51] and chickpea (0.32) [52]. This study also demonstrated the possibility of using the selected DArTseq-SNP markers for genomic investigations in yams, which may serve as a foundation for future breeding efforts in Uganda and conservation initiatives in the country.…”