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Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata L.)

dc.contributor.authorSharif, B.M.
dc.contributor.authorBurgarella, C.
dc.contributor.authorCormier, F.
dc.contributor.authorMournet, P.
dc.contributor.authorCausse, S.
dc.contributor.authorVan, K.N.
dc.contributor.authorKaoh, J.
dc.contributor.authorRajaonah, M.T.
dc.contributor.authorLakshan, S.R.
dc.contributor.authorWaki, J.
dc.contributor.authorBhattacharjee, R.
dc.contributor.authorGueye, B.
dc.contributor.authorPachakkil, B.
dc.contributor.authorArnau, G.
dc.contributor.authorChaïr, H.
dc.date.accessioned2022-01-11T11:36:53Z
dc.date.available2022-01-11T11:36:53Z
dc.date.issued2020-11-02
dc.identifier.citationSharif, B.M., Burgarella, C., Cormier, F., Mournet, P., Causse, S., Van, K.N., ... & Chair, H. (2020). Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata L.). Annals of Botany, 126(6), 1029-1038.
dc.identifier.issn0305-7364
dc.identifier.urihttps://hdl.handle.net/20.500.12478/7307
dc.description.abstractBackground and Aims Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample. Methods We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach. Key Results Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region. Conclusions Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.
dc.description.sponsorshipCGIAR Research Program on Roots, Tubers and Bananas
dc.description.sponsorshipAgropolis Foundation
dc.format.extent1029-1038
dc.language.isoen
dc.subjectPropagation
dc.subjectDemography
dc.subjectGeographical Distribution
dc.subjectPolyploidy
dc.subjectGenomics
dc.subjectYams
dc.subjectDioscorea Alata
dc.titleGenome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata L.)
dc.typeJournal Article
cg.contributor.crpGenebanks
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationUniversity of Vienna
cg.contributor.affiliationUniversité de Montpellier
cg.contributor.affiliationPlant Resources Center, Vietnam
cg.contributor.affiliationVanuatu Agricultural Research and Technical Centre
cg.contributor.affiliationKew Madagascar Conservation Centre
cg.contributor.affiliationField Crops Research and Development Institute, Sri Lanka
cg.contributor.affiliationNational Agricultural Research Institute, Papua New Guinea
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationTokyo University of Agriculture
cg.coverage.regionAfrica
cg.coverage.regionAsia
cg.coverage.regionCaribbean
cg.coverage.countryBenin (Dahomey)
cg.coverage.countryBurkina Faso (Upper Volta)
cg.coverage.countryCote d’Ivoire (Ivory Coast)
cg.coverage.countryCuba
cg.coverage.countryDominican Republic
cg.coverage.countryEquatorial Guinea
cg.coverage.countryGhana
cg.coverage.countryHaiti
cg.coverage.countryIndia
cg.coverage.countryJamaica
cg.coverage.countryJapan
cg.coverage.countryMadagascar
cg.coverage.countryNigeria
cg.coverage.countryPapua New Guinea
cg.coverage.countryRepublic of the Congo
cg.coverage.countrySaint Lucia
cg.coverage.countrySaint Vincent and the Grenadines
cg.coverage.countrySierra Leone
cg.coverage.countrySri Lanka
cg.coverage.countryTogo
cg.coverage.countryVanuatu
cg.coverage.countryVietnam
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidSHARIF:2020
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectBioscience
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Production
cg.iitasubjectYam
cg.journalAnnals of Botany
cg.notesOpen Access Article; Published online: 27 Jun 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/10.1093/aob/mcaa122
cg.iitaauthor.identifierRanjana Bhattacharjee: 0000-0002-5184-5930
cg.iitaauthor.identifierBadara GUEYE: 0000-0003-3157-8772
cg.futureupdate.requiredNo
cg.identifier.volume126


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