Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

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cg.authorship.typesCGIAR and developing country instituteen
cg.contributor.affiliationInternational Institute of Tropical Agricultureen
cg.contributor.affiliationSierra Leone Agricultural Research Instituteen
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.donorBill & Melinda Gates Foundationen
cg.coverage.countryNigeria
cg.coverage.iso3166-alpha2NG
cg.coverage.regionAfrica
cg.coverage.regionWestern Africa
cg.creator.identifierPaterne AGRE: 0000-0003-1231-2530
cg.creator.identifierRobert Asiedu: 0000-0001-8943-2376
cg.creator.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12870-021-03314-wen
cg.identifier.iitathemeBIOTECH & PLANT BREEDING
cg.isijournalISI Journalen
cg.issn1471-2229en
cg.issue1: 552en
cg.journalBMC Plant Biologyen
cg.reviewStatusPeer Reviewen
cg.subject.iitaAGRONOMYen
cg.subject.iitaFOOD SECURITYen
cg.subject.iitaPLANT BREEDINGen
cg.subject.iitaPLANT PRODUCTIONen
cg.subject.iitaYAMen
cg.subject.impactAreaNutrition, health and food security
cg.subject.sdgSDG 2 - Zero hungeren
cg.volume21en
dc.contributor.authorAgre, A.P.en
dc.contributor.authorNorman, P.E.en
dc.contributor.authorAsiedu, R.en
dc.contributor.authorAsfaw, A.en
dc.date.accessioned2022-01-25T11:43:27Zen
dc.date.available2022-01-25T11:43:27Zen
dc.identifier.urihttps://hdl.handle.net/10568/117738
dc.titleIdentification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scanen
dcterms.abstractBackground Improvement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This study assessed quantitative trait nucleotides (QTNs) and the underlying candidate genes related to tuber yield per plant (TYP) and yam mosaic virus (YMV) tolerance in a panel of 406 white Guinea yam (Dioscorea rotundata) breeding lines using a genome-wide association study (GWAS). Results Population structure analysis using 5,581 SNPs differentiated the 406 genotypes into seven distinct sub-groups based delta K. Marker-trait association (MTA) analysis using the multi-locus linear model (mrMLM) identified seventeen QTN regions significant for TYP and five for YMV with various effects. The seveteen QTNs were detected on nine chromosomes, while the five QTNs were identified on five chromosomes. We identified variants responsible for predicting higher yield and low virus severity scores in the breeding panel through the marker-effect prediction. Gene annotation for the significant SNP loci identified several essential putative genes associated with the growth and development of tuber yield and those that code for tolerance to mosaic virus. Conclusion Application of different multi-locus models of GWAS identified 22 QTNs. Our results provide valuable insight for marker validation and deployment for tuber yield and mosaic virus tolerance in white yam breeding. The information on SNP variants and genes from the present study would fast-track the application of genomics-informed selection decisions in breeding white Guinea yam for rapid introgression of the targeted traits through markers validation.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2021-11-22
dcterms.bibliographicCitationAgre, A.P., Norman, P.E., Asiedu, R. & Asfaw, A. (2021). Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan. BMC Plant Biology, 21(1), 1-16.en
dcterms.extent1-16en
dcterms.issued2021-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectgenetic diversityen
dcterms.subjectpopulation structureen
dcterms.subjectyamsen
dcterms.subjectvarietiesen
dcterms.subjectnigeriaen
dcterms.subjectquantitative trait locien
dcterms.typeJournal Article

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