Abstract
White yam (Dioscorearotundata Poir.) is one of the most important tuber crops in West Africa, where it is indigenous and represents the largest repository of biodiversity through several years of domestication, production, consumption, and trade. In this study, the genotyping-by-sequencing (GBS) approach was used to sequence 814 genotypes consisting of genebank landraces, breeding lines, and market varieties to understand the level of genetic diversity and pattern of the population structure among them. The genetic diversity among different genotypes was assessed using three complementary clustering methods, the model-based admixture, discriminant analysis of principal components (DAPC), and phylogenetic tree. ADMIXTURE analysis revealed an optimum number of four groups that matched with the number of clusters obtained through phylogenetic tree. Clustering results obtained from ADMIXTURE analysis were further validated using DAPC-based clustering. Analysis of molecular variance (AMOVA) revealed high genetic diversity (96%) within each genetic group. A network analysis was further carried out to depict the genetic relationships among the three genetic groups (breeding lines, genebank landraces, and market varieties) used in the study. This study showed that the use of advanced sequencing techniques such as GBS coupled with statistical analysis is a robust method for assessing genetic diversity and population structure in a complex crop such as white yam.
Highlights
White yam or white guinea yam (Dioscorea roundata Poir.) is one of the most important staple tuber crops of West Africa [1], which is strongly associated with the food security, income, and social culture of >300 million people of this region, having a net value internationally of ≈$15 billion [2]
A total of 814 genotypes were used in this study that included 473 genebank landraces selected from the revised yam core collection [36], 314 breeding lines, and 27 popular market varieties or landraces collected from different markets across Nigeria and Ghana (Table S1)
The present study dissected the genetic relationships between different genetic groups of white yam/white guinea yam (D. rotundata) so that diverse genetic materials are utilized in the yam breeding program to introgress gene(s) of interest for its improvement
Summary
White yam or white guinea yam (Dioscorea roundata Poir.) is one of the most important staple tuber crops of West Africa [1], which is strongly associated with the food security, income, and social culture of >300 million people of this region, having a net value internationally of ≈$15 billion [2]. It belongs to the section Enantiophyllum and Dioscoreaceae family consisting of approximately 600 species distributed in the tropical and subtropical regions of the world [3]. White yam domestication took advantage of a huge reservoir of diversity in this region as a result of years of large production, consumption, and trade [5,6,7,8]
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