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    Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.)

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    Journal Article (2.707Mb)
    Date
    2020
    Author
    Bhattacharjee, R.
    Agre, A.P.
    Bauchet, G.
    De Koeyer, D.
    Lopez-Montes, A.
    Kumar, P.L.
    Abberton, M.
    Adebola, P.O.
    Asfaw, A.
    Asiedu, R.
    Type
    Journal Article
    Review Status
    Peer Review
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    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
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/6998
    IITA Authors ORCID
    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
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.3390/agronomy10091437
    Research Themes
    Biotech and Plant Breeding
    IITA Subjects
    Agronomy; Biodiversity; Food Security; Genetic Improvement; Plant Breeding; Plant Genetic Resources; Plant Production; Yam
    Agrovoc Terms
    Yams; Dioscorea Rotundata; Food Security; Genetics; population structure; Single Nucleotide Polymorphism; genetic variation
    Regions
    Africa; West and Central Africa
    Countries
    Benin (Dahomey); Cameroon; Cote d’Ivoire (Ivory Coast); Ghana; Nigeria; Togo
    Hubs
    Headquarters and Western Africa Hub
    Journals
    Agronomy
    Collections
    • Journal and Journal Articles4836
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