Show simple item record

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

dc.contributor.authorBhattacharjee, R.
dc.contributor.authorAgre, A.P.
dc.contributor.authorBauchet, G.
dc.contributor.authorDe Koeyer, D.
dc.contributor.authorLopez-Montes, A.
dc.contributor.authorKumar, P.L.
dc.contributor.authorAbberton, M.
dc.contributor.authorAdebola, P.O.
dc.contributor.authorAsfaw, A.
dc.contributor.authorAsiedu, R.
dc.date.accessioned2020-11-19T11:14:54Z
dc.date.available2020-11-19T11:14:54Z
dc.date.issued2020
dc.identifier.citationBhattacharjee, R., Agre, P., Bauchet, G., De Koeyer, D., Lopez-Montes, A., Kumar, P., ... & Asiedu, R. (2020). Genotyping-by-sequencing to unlock genetic diversity and population structure in white yam (Dioscorea rotundata Poir.). Agronomy, 10(9), 1437: 1-16.
dc.identifier.issn0002-1962
dc.identifier.urihttps://hdl.handle.net/20.500.12478/6998
dc.description.abstractWhite 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.
dc.description.sponsorshipCGIAR Coordinated Research Project on Roots, Tubers and Bananas
dc.format.extent1-16
dc.language.isoen
dc.subjectYams
dc.subjectDioscorea Rotundata
dc.subjectFood Security
dc.subjectGenetics
dc.subjectpopulation structure
dc.subjectSingle Nucleotide Polymorphism
dc.subjectgenetic variation
dc.titleGenotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.)
dc.typeJournal Article
cg.contributor.crpGenebanks
cg.contributor.crpMaize
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationCornell University
cg.contributor.affiliationAgriculture and Agri-Food Canada
cg.contributor.affiliationInternational Trade Center, Ghana
cg.coverage.regionAfrica
cg.coverage.regionWest and Central Africa
cg.coverage.countryBenin (Dahomey)
cg.coverage.countryCameroon
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.bibtexciteidBHATTACHARJEE:2020
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectBiodiversity
cg.iitasubjectFood Security
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Genetic Resources
cg.iitasubjectPlant Production
cg.iitasubjectYam
cg.journalAgronomy
cg.notesOpen Access Journal; Published online: 22 Sept 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/10.3390/agronomy10091437
cg.iitaauthor.identifierRanjana Bhattacharjee: 0000-0002-5184-5930
cg.iitaauthor.identifierPaterne AGRE: 0000-0003-1231-2530
cg.iitaauthor.identifierDavid De Koeyer: 0000-0001-8064-6538
cg.iitaauthor.identifierAntonio Jose Lopez-Montes: 0000-0001-5801-2475
cg.iitaauthor.identifierP. Lava Kumar: 0000-0003-4388-6510
cg.iitaauthor.identifierMichael Abberton: 0000-0003-2555-9591
cg.iitaauthor.identifierPatrick Adebola: 0000-0002-5155-6194
cg.iitaauthor.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.iitaauthor.identifierRobert Asiedu: 0000-0001-8943-2376
cg.futureupdate.requiredNo


Files in this item

Thumbnail
Name:
U20ArtBhatttacharjeeGenotyping ...
Size:
2.707Mb
Format:
PDF
Description:
Journal Article
View/Open

This item appears in the following Collection(s)

Show simple item record