Training population optimization for prediction of cassava brown streak disease resistance in west African clones

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cg.authorship.typesCGIAR and developing country instituteen
cg.contributor.affiliationNational Crops Resources Research Institute, Ugandaen
cg.contributor.affiliationCornell Universityen
cg.contributor.affiliationInternational Institute of Tropical Agricultureen
cg.contributor.affiliationUnited States Department of Agricultureen
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.donorBill & Melinda Gates Foundationen
cg.contributor.donorDepartment for International Development, United Kingdomen
cg.coverage.countryTanzania
cg.coverage.countryUganda
cg.coverage.iso3166-alpha2TZ
cg.coverage.iso3166-alpha2UG
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierIsmail Rabbi: 0000-0001-9966-2941
cg.creator.identifierPeter Kulakow: 0000-0002-7574-2645
cg.creator.identifierJean-Luc Jannink: 0000-0003-4849-628X
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1534/g3.118.200710en
cg.identifier.iitathemeBIOTECH & PLANT BREEDING
cg.isijournalISI Journalen
cg.issn2160-1836en
cg.issue12en
cg.journalG3: Genes, Genomes, Geneticsen
cg.reviewStatusPeer Reviewen
cg.subject.iitaCASSAVAen
cg.subject.iitaGENETIC IMPROVEMENTen
cg.subject.iitaPLANT BREEDINGen
cg.subject.iitaPLANT GENETIC RESOURCESen
cg.volume8en
dc.contributor.authorOzimati, A.en
dc.contributor.authorKawuki, R.S.en
dc.contributor.authorEsuma, W.en
dc.contributor.authorKayondo, I.S.en
dc.contributor.authorWolfe, M.en
dc.contributor.authorLozano, R.en
dc.contributor.authorRabbi, Ismail Y.en
dc.contributor.authorKulakow, Peter A.en
dc.contributor.authorJannink, Jean-Lucen
dc.date.accessioned2019-01-21T14:36:35Zen
dc.date.available2019-01-21T14:36:35Zen
dc.identifier.urihttps://hdl.handle.net/10568/99125
dc.titleTraining population optimization for prediction of cassava brown streak disease resistance in west African clonesen
dcterms.abstractCassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector (Bemisia tabaci) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined. Using phenotypic and genotypic data (genotyping-by-sequencing), followed by imputation to whole genome sequence (WGS) for 922 clones from National Crops Resources Research Institute, Namulonge, Uganda as a training population (TP), we predicted CBSD symptoms for 35 genotyped W. African clones, evaluated in Uganda. The highest prediction accuracy (r = 0.44) was observed for cassava brown streak disease severity scored at three months (CBSD3s) in the W. African clones using WGS-imputed markers. Optimized TPs gave higher prediction accuracies for CBSD3s and CBSD6s than random TPs of the same size. Inclusion of CBSD QTL chromosome markers as kernels, increased prediction accuracies for CBSD3s and CBSD6s. Similarly, WGS imputation of markers increased prediction accuracies for CBSD3s and for cassava brown streak disease root severity (CBSDRs), but not for CBSD6s. Based on these results we recommend TP optimization, inclusion of CBSD QTL markers in genomic prediction models, and the use of high-density (WGS-imputed) markers for CBSD predictions across population.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2018-12-01
dcterms.bibliographicCitationOzimati, A., Kawuki, R., Esuma, W., Kayondo, I.S., Wolfe, M., Lozano, R., ... & Jannink, J.L. (2018). Training population optimization for prediction of cassava brown streak disease resistance in west African clones. G3: Genes, Genomes, Genetics, 8(12), 3903-3913.en
dcterms.extent3903-3913en
dcterms.issued2018-12-10
dcterms.languageen
dcterms.licenseCopyrighted; all rights reserved
dcterms.publisherOxford University Pressen
dcterms.subjectcassavaen
dcterms.subjectgenomicsen
dcterms.subjectplant diseasesen
dcterms.subjectugandaen
dcterms.subjecttanzaniaen
dcterms.subjectgeneticsen
dcterms.typeJournal Article

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