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

Simple item page
cg.authorship.typesCGIAR and developing country institute
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationCornell University
cg.contributor.affiliationAgriculture and Agri-Food Canada
cg.contributor.affiliationInternational Trade Centre, Ghana
cg.contributor.crpGenebanks
cg.contributor.crpMaize
cg.contributor.crpRoots, Tubers and Bananas
cg.coverage.countryBenin
cg.coverage.countryCameroon
cg.coverage.countryCôte d'Ivoire
cg.coverage.countryGhana
cg.coverage.countryNigeria
cg.coverage.countryTogo
cg.coverage.iso3166-alpha2BJ
cg.coverage.iso3166-alpha2CM
cg.coverage.iso3166-alpha2CI
cg.coverage.iso3166-alpha2GH
cg.coverage.iso3166-alpha2NG
cg.coverage.iso3166-alpha2TG
cg.coverage.regionAfrica
cg.coverage.regionWest and Central Africa
cg.coverage.regionWestern Africa
cg.coverage.regionMiddle Africa
cg.creator.identifierRanjana Bhattacharjee: 0000-0002-5184-5930
cg.creator.identifierPaterne AGRE: 0000-0003-1231-2530
cg.creator.identifierDavid De Koeyer: 0000-0001-8064-6538
cg.creator.identifierAntonio Jose Lopez-Montes: 0000-0001-5801-2475
cg.creator.identifierP. Lava Kumar: 0000-0003-4388-6510
cg.creator.identifierMichael Abberton: 0000-0003-2555-9591
cg.creator.identifierPatrick Adebola: 0000-0002-5155-6194
cg.creator.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.creator.identifierRobert Asiedu: 0000-0001-8943-2376
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.3390/agronomy10091437
cg.identifier.iitathemeBIOTECH & PLANT BREEDING
cg.isijournalISI Journal
cg.issn0002-1962
cg.issue9
cg.journalAgronomy
cg.reviewStatusPeer Review
cg.subject.iitaAGRONOMY
cg.subject.iitaFOOD SECURITY
cg.subject.iitaGENETIC IMPROVEMENT
cg.subject.iitaPLANT BREEDING
cg.subject.iitaPLANT GENETIC RESOURCES
cg.subject.iitaPLANT PRODUCTION
cg.subject.iitaYAM
cg.volume10
dc.contributor.authorBhattacharjee, Ranjana
dc.contributor.authorAgre, A.P.
dc.contributor.authorBauchet, Guillaume J.
dc.contributor.authorKoeyer, D. de
dc.contributor.authorLópez Montes, Antonio José
dc.contributor.authorKumar, P. Lava
dc.contributor.authorAbberton, Michael T.
dc.contributor.authorAdebola, P.O.
dc.contributor.authorAsfaw, A.
dc.contributor.authorAsiedu, R.
dc.date.accessioned2020-11-19T11:12:41Zen
dc.date.available2020-11-19T11:12:41Zen
dc.identifier.urihttps://hdl.handle.net/10568/110236
dc.titleGenotyping-by-sequencing to unlock genetic diversity and population structure in white yam (dioscorea rotundata poir.)en
dcterms.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.en
dcterms.accessRightsOpen Access
dcterms.audienceScientists
dcterms.available2020-09-22
dcterms.bibliographicCitationBhattacharjee, 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.en
dcterms.extent1-16
dcterms.issued2020
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherMDPI
dcterms.subjectyamsen
dcterms.subjectdioscorea rotundataen
dcterms.subjectfood securityen
dcterms.subjectgeneticsen
dcterms.subjectsingle nucleotide polymorphismen
dcterms.subjectgenetic variationen
dcterms.subjectpopulation structureen
dcterms.typeJournal Article

Files

Original bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
U20ArtBhatttacharjeeGenotypingInthomDev.pdf
Size:
2.71 MB
Format:
Adobe Portable Document Format
Description:
Journal Article
Download

License bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
1.75 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

IITA Journal Articles
RTB Journal Articles