Next generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of guinea yams

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cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationInternational Institute of Tropical Agricultureen
cg.contributor.affiliationNational University of Irelanden
cg.contributor.affiliationCornell Universityen
cg.coverage.countryNigeria
cg.coverage.iso3166-alpha2NG
cg.coverage.regionAfrica
cg.coverage.regionWestern Africa
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1007/s00122-014-2339-2en
cg.isijournalISI Journalen
cg.issn0040-5752en
cg.issue8en
cg.journalTheoritical and Applied Geneticsen
cg.reviewStatusPeer Reviewen
cg.subject.iitaYAMen
cg.volume127en
dc.contributor.authorGirma, G.en
dc.contributor.authorHyma, K.E.en
dc.contributor.authorAsiedu, Roberten
dc.contributor.authorMitchell, S.E.en
dc.contributor.authorGedil, Melaku Aen
dc.contributor.authorSpillane, Charlesen
dc.date.accessioned2016-07-11T08:41:34Zen
dc.date.available2016-07-11T08:41:34Zen
dc.identifier.urihttps://hdl.handle.net/10568/76052
dc.titleNext generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of guinea yamsen
dcterms.abstractKey message Genotyping by sequencing (GBS) is used to understand the origin and domestication of guinea yams, including the contribution of wild relatives and polyploidy events to the cultivated guinea yams. Abstract Patterns of genetic diversity within and between two cultivated guinea yams (Dioscorea rotundata and D. cayenensis) and five wild relatives (D. praehensilis, D. mangenotiana, D. abyssinica, D. togoensis and D. burkilliana) were investigated using next-generation sequencing (genotyping by sequencing, GBS). Additionally, the two cultivated species were assessed for intra-specific morphological and ploidy variation. In guinea yams, ploidy level is correlated with species identity. Using flow cytometry a single ploidy level was inferred across D. cayenensis (3x, N = 21), D. praehensilis (2x, N = 7), and D. mangenotiana (3x, N = 5) accessions, whereas both diploid and triploid (or aneuploid) accessions were present in D. rotundata (N = 11 and N = 32, respectively). Multi-dimensional scaling and maximum parsimony analyses of 2,215 SNPs revealed that wild guinea yam populations form discrete genetic groupings according to species. D. togoensis and D. burkilliana were most distant from the two cultivated yam species, whereas D. abyssinica, D. mangenotiana, and D. praehensilis were closest to cultivated yams. In contrast, cultivated species were genetically less clearly defined at the intra-specific level. While D. cayenensis formed a single genetic group, D. rotundata comprised three separate groups consisting of; (1) a set of diploid individuals genetically similar to D. praehensilis, (2) a set of diploid individuals genetically similar to D. cayenensis, and (3) a set of triploid individuals. The current study demonstrates the utility of GBS for assessing yam genomic diversity. Combined with morphological and biological data, GBS provides a powerful tool for testing hypotheses regarding the evolution, domestication and breeding of guinea yams.en
dcterms.accessRightsLimited Access
dcterms.available2014-07-01
dcterms.bibliographicCitationGirma, G., Hyma, K.E., Asiedu, R., Mitchell, S.E., Gedil, M. & Spillane, C. (2014). Next-generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of guinea yams. Theoretical and Applied Genetics, 127(8), 1783-1794.en
dcterms.extentp. 1783-1794en
dcterms.issued2014-08
dcterms.languageen
dcterms.licenseCopyrighted; all rights reserved
dcterms.publisherSpringeren
dcterms.subjectdioscorea rotundataen
dcterms.subjectguinea yamen
dcterms.typeJournal Article

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