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Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content

dc.contributor.authorIge, A.D.
dc.contributor.authorOlasanmi, B.
dc.contributor.authorBauchet, G.J.
dc.contributor.authorKayondo, S.I.
dc.contributor.authorMbanjo, E.
dc.contributor.authorUwugiaren, R.
dc.contributor.authorMotomura-Wages, S.
dc.contributor.authorNorton, J.
dc.contributor.authorEgesi, C.
dc.contributor.authorParkes, E.
dc.contributor.authorKulakow, P.
dc.contributor.authorCeballos, H.
dc.contributor.authorDieng, I.
dc.contributor.authorRabbi, I.Y.
dc.date.accessioned2022-12-14T07:18:59Z
dc.date.available2022-12-14T07:18:59Z
dc.date.issued2022
dc.identifier.citationIge, A.D., Olasanmi, B., Bauchet, G.J., Kayondo, S.I., Mbanjo, E., Uwugiaren, R., ... & Rabbi, I.Y. (2022). Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content. Frontiers in Plant Science, 13 : 1016170,1-17.
dc.identifier.issn1664-462X
dc.identifier.urihttps://hdl.handle.net/20.500.12478/7973
dc.description.abstractProvitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers’ performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers’ effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.
dc.description.sponsorshipUKs Foreign, Commonwealth & Development Office
dc.description.sponsorshipBill & Melinda Gates Foundation
dc.format.extent1-17
dc.language.isoen
dc.subjectCassava
dc.subjectManihot Esculenta
dc.subjectProvitamins
dc.subjectDry Matter Content
dc.subjectMarker-Assisted Selection
dc.titleValidation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content
dc.typeJournal Article
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationUniversity of Ibadan
cg.contributor.affiliationBoyce Thompson Institute
cg.contributor.affiliationWashington State University
cg.contributor.affiliationUniversity of Hawaii at Manoa
cg.contributor.affiliationCornell University
cg.contributor.affiliationAlliance of Bioversity International and CIAT
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryNigeria
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidIGE:2022
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectCassava
cg.iitasubjectFood Security
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Production
cg.journalFrontiers in Plant Science
cg.notesOpen Access Article; Published online: 12 Oct 2022
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://dx.doi.org/10.3389/fpls.2022.1016170
cg.iitaauthor.identifierKayondo Siraj Ismail: 0000-0002-3212-5727
cg.iitaauthor.identifierEdwige Gaby Nkouaya Mbanjo: 0000-0002-9982-1137
cg.iitaauthor.identifierChiedozie Egesi: 0000-0002-9063-2727
cg.iitaauthor.identifierE J Parkes: 0000-0003-4063-1483
cg.iitaauthor.identifierPeter Kulakow: 0000-0002-7574-2645
cg.iitaauthor.identifierIsmail Rabbi: 0000-0001-9966-2941
cg.futureupdate.requiredNo
cg.identifier.volume13


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