Abstract
The International Institute of Tropical Agriculture maintains the world’s largest collection of cowpea germplasm of over 15,000 accessions. A sub-set of 298 lines from the loosely composed mini core collection of 370 landraces were genotyped based on genotyping by sequencing (GBS). Ward’s minimum variance hierarchical cluster analysis, model-based ancestry analysis and discriminant analysis of principal component (DAPC) were carried out on this sub-set. Three clusters were identified by the different clustering methods. Principal component analysis further supported the three clusters especially when accessions are scattered along the axes of the first two principal components. The first two principal components explained a total of 22.30% of the variation. Cluster one comprises 115 accessions from the largest number of countries and has the highest gene diversity, heterozygosity and polymorphic information content (PIC) values. Cluster two is made up of 102 accessions, 90 percent of which are from West and Central Africa. Analysis of molecular variance shows that the most variation is among accessions and lowest among clusters. No cluster is made exclusively of accessions from a single country. Based on SNP markers, the sub set of cowpea mini core germplasm collection used in this study encompasses the diversity in the crop.
Highlights
Cowpea is one of the important grain legume crops in sub-Saharan Africa (SSA) where it contributes to food and nutritional security, fodder for livestock, soil fertility following N fixation as well as income for farmers and food vendors
GBS is increasingly being used in both genetic diversity analyses of cultivated and wild crop relatives[17,18], development of genetic linkage maps[19], genomic selection and genome wide association studies[20,21] GBS was used to study genetic diversity among 768 cowpea germplasm lines and the results indicated that the route of the migration of cowpea germplasm to different parts of the globe could be traced to the two candidate original areas of West and East Africa[7]
The world’s largest cowpea germplasm collection maintained at the International Institute of Tropical Agriculture (IITA) headquarters in Ibadan Nigeria has more than 15,000 landraces and over 2,000 wild relatives
Summary
Cowpea is one of the important grain legume crops in sub-Saharan Africa (SSA) where it contributes to food and nutritional security, fodder for livestock, soil fertility following N fixation as well as income for farmers and food vendors. GBS is increasingly being used in both genetic diversity analyses of cultivated and wild crop relatives[17,18], development of genetic linkage maps[19], genomic selection and genome wide association studies[20,21] GBS was used to study genetic diversity among 768 cowpea germplasm lines and the results indicated that the route of the migration of cowpea germplasm to different parts of the globe could be traced to the two candidate original areas of West and East Africa[7] Despite their usefulness in studying genetic diversity in crop species, different types of molecular markers are not informative. The high throughput genome complexity reducing procedures such as GBS have advantages over the conventional and allele specific SNP markers as they enable simultaneous discovery and genotyping of genome wide SNP markers within a shorter time and at lower cost
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