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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

dc.contributor.authorDarkwa, K.
dc.contributor.authorAgre, P.
dc.contributor.authorOlasanmi, B.
dc.contributor.authorIseki, K.
dc.contributor.authorMatsumoto, R.
dc.contributor.authorPowell, A.
dc.contributor.authorBauchet, G.,
dc.contributor.authorDe Koeyer, D.
dc.contributor.authorMuranaka, S.
dc.contributor.authorAdebola, P.
dc.contributor.authorAsiedu, R.
dc.contributor.authorTerauchi, R.
dc.contributor.authorAsfaw, A.
dc.date.accessioned2020-11-06T14:29:33Z
dc.date.available2020-11-06T14:29:33Z
dc.date.issued2020
dc.identifier.citationDarkwa, K., Agre, P., Olasanmi, B., Iseki, K., Matsumoto, R., Powell, A., ... & Asfaw, A. (2020). Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers. Scientific Reports, 10(1), 1-14.
dc.identifier.issn2045-2322
dc.identifier.urihttps://hdl.handle.net/20.500.12478/6987
dc.description.abstractUnderstanding 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.
dc.description.sponsorshipBill & Melinda Gates Foundation
dc.format.extent1-14
dc.language.isoen
dc.subjectGenetic Improvement
dc.subjectYams
dc.subjectDioscorea Rotundata
dc.subjectGenetic Markers
dc.subjectWest Africa
dc.subjectGuinea Yam
dc.subjectMorphology
dc.titleComparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers
dc.typeJournal Article
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationUniversity of Ibadan
cg.contributor.affiliationJapan International Research Center for Agricultural Sciences
cg.contributor.affiliationBoyce Thompson Institute, USA
cg.contributor.affiliationIwate Biotechnology Research Center, Japan
cg.contributor.affiliationAgriculture and Agri-Food Canada
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryBenin (Dahomey)
cg.coverage.countryCote d’Ivoire (Ivory Coast)
cg.coverage.countryGhana
cg.coverage.countryNigeria
cg.coverage.countryTogo
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidDARKWA:2020a
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Genetic Resources
cg.iitasubjectPlant Production
cg.iitasubjectYam
cg.journalScientific Reports
cg.notesOpen Access Journal; Published online: 06 Aug 2020
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://dx.doi.org/10.1038/s41598-020-69925-9
cg.iitaauthor.identifierPaterne AGRE: 0000-0003-1231-2530
cg.iitaauthor.identifierRyo Matsumoto: 0000-0002-0106-6728
cg.iitaauthor.identifierDavid De Koeyer: 0000-0001-8064-6538
cg.iitaauthor.identifierPatrick Adebola: 0000-0002-5155-6194
cg.iitaauthor.identifierRobert Asiedu: 0000-0001-8943-2376
cg.iitaauthor.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.futureupdate.requiredNo


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