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    Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers

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    Journal Article (5.778Mb)
    Date
    2020
    Author
    Darkwa, K.
    Agre, P.
    Olasanmi, B.
    Iseki, K.
    Matsumoto, R.
    Powell, A.
    Bauchet, G.,
    De Koeyer, D.
    Muranaka, S.
    Adebola, P.
    Asiedu, R.
    Terauchi, R.
    Asfaw, A.
    Type
    Journal Article
    Review Status
    Peer Review
    Target Audience
    Scientists
    Metadata
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    Abstract/Description
    Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.
    https://dx.doi.org/10.1038/s41598-020-69925-9
    Multi standard citation
    Permanent link to this item
    https://hdl.handle.net/20.500.12478/6987
    IITA Authors ORCID
    Paterne AGREhttps://orcid.org/0000-0003-1231-2530
    Ryo Matsumotohttps://orcid.org/0000-0002-0106-6728
    David De Koeyerhttps://orcid.org/0000-0001-8064-6538
    Patrick Adebolahttps://orcid.org/0000-0002-5155-6194
    Robert Asieduhttps://orcid.org/0000-0001-8943-2376
    Asrat Asfawhttps://orcid.org/0000-0002-4859-0631
    Digital Object Identifier (DOI)
    https://dx.doi.org/10.1038/s41598-020-69925-9
    Research Themes
    Biotech and Plant Breeding
    IITA Subjects
    Agronomy; Genetic Improvement; Plant Breeding; Plant Genetic Resources; Plant Production; Yam
    Agrovoc Terms
    Genetic Improvement; Yams; Dioscorea Rotundata; Genetic Markers; West Africa; Guinea Yam; Morphology
    Regions
    Africa; West Africa
    Countries
    Benin (Dahomey); Cote d’Ivoire (Ivory Coast); Ghana; Nigeria; Togo
    Hubs
    Headquarters and Western Africa Hub
    Journals
    Scientific Reports
    Collections
    • Journal and Journal Articles4475
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