Genotyping-by-Sequencing to Unlock Genetic Diversity and Population Structure in White Yam (<i>Dioscorea rotundata</i> Poir.)

• Main Authors: Ranjana Bhattacharjee, Paterne Agre, Guillaume Bauchet, David De Koeyer, Antonio Lopez-Montes, P. Lava Kumar, Michael Abberton, Patrick Adebola, Asrat Asfaw, Robert Asiedu
• Format: Article
• Language: English
• Published: MDPI AG 2020-09-01
• Series: Agronomy
• Subjects: white yam; West Africa; SNP markers; genetic diversity; population structure
• Online Access: https://www.mdpi.com/2073-4395/10/9/1437

White yam (<i>Dioscorea</i><i>rotundata</i> 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.