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.

https://dx.doi.org/10.3390/agronomy10091437

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Ranjana Bhattacharjeehttps://orcid.org/0000-0002-5184-5930

Paterne AGREhttps://orcid.org/0000-0003-1231-2530

David De Koeyerhttps://orcid.org/0000-0001-8064-6538

Antonio Jose Lopez-Monteshttps://orcid.org/0000-0001-5801-2475

P. Lava Kumarhttps://orcid.org/0000-0003-4388-6510

Michael Abbertonhttps://orcid.org/0000-0003-2555-9591

Patrick Adebolahttps://orcid.org/0000-0002-5155-6194

Asrat Asfawhttps://orcid.org/0000-0002-4859-0631

Robert Asieduhttps://orcid.org/0000-0001-8943-2376

https://dx.doi.org/10.3390/agronomy10091437

Biotech and Plant Breeding

Agronomy; Biodiversity; Food Security; Genetic Improvement; Plant Breeding; Plant Genetic Resources; Plant Production; Yam

Yams; Dioscorea Rotundata; Food Security; Genetics; population structure; Single Nucleotide Polymorphism; genetic variation

Africa; West and Central Africa

Benin (Dahomey); Cameroon; Cote d’Ivoire (Ivory Coast); Ghana; Nigeria; Togo

Headquarters and Western Africa Hub

Agronomy