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Conversion and validation of uniplex SNP markers for selection of resistance to Cassava Mosaic Disease in Cassava breeding programs

dc.contributor.authorIge, A.D.
dc.contributor.authorOlasanmi, B.
dc.contributor.authorMbanjo, E.
dc.contributor.authorKayondo, S.I.
dc.contributor.authorParkes, E.
dc.contributor.authorKulakow, P.
dc.contributor.authorEgesi, C.
dc.contributor.authorBauchet, G.J.
dc.contributor.authorNg, E.
dc.contributor.authorLopez-Lavalle, L. A.
dc.contributor.authorCeballos, H.
dc.contributor.authorRabbi, I.Y.
dc.date.accessioned2022-09-20T13:46:34Z
dc.date.available2022-09-20T13:46:34Z
dc.date.issued2021
dc.identifier.citationIge, A.D., Olasanmi, B., Nkouaya Mbanjo, E.G., Kayondo, I.S., Parkes, E.Y., Kulakow, P., ... & Rabbi, I.Y. (2021). Conversion and validation of uniplex SNP markers for selection of resistance to Cassava Mosaic Disease in Cassava breeding programs. Agronomy, 11(3): 420, 1-17.
dc.identifier.issn2073-4395
dc.identifier.urihttps://hdl.handle.net/20.500.12478/7780
dc.description.abstractCassava mosaic disease (CMD) is a major viral disease adversely affecting cassava production in Africa and Asia. Genomic regions conferring resistance to the disease have been mapped in African cassava germplasm through biparental quantitative trait loci (QTL) mapping and genome-wide association studies. To facilitate the utilization of these markers in breeding pipelines to support selections, proof-of-concept technical and biological validation research was carried out using independent pre-breeding and breeding populations. Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) assays were designed from three single nucleotide polymorphism (SNP) markers linked to a major resistance locus on chromosome 12 (S12_7926132, S12_7926163) and a minor locus on chromosome 14 (S14_4626854). The designed assays were robust and easy to score with >99% genotype call rate. The overall predictive accuracy (proportion of true positives and true negatives) of the markers (S12_7926132 and S14_4626854) was 0.80 and 0.78 in the pre-breeding and breeding population, respectively. On average, genotypes that carried at least one copy of the resistant allele at the major CMD2 locus had a significantly higher yield advantage. Nevertheless, variation was observed in prediction accuracies for the major locus (S12_7926132) among sub-families from the two populations, suggesting the need for context-specific utilization, for example, by screening for co-segregation of favorable SNP alleles with resistance in the parents being used for crosses. Availability of these validated SNP markers on the uniplex KASP genotyping platform represents an important step in translational genetics toward marker-assisted selection to accelerate introgression of favorable resistant alleles in breeding populations.
dc.description.sponsorshipUK’s Foreign, Commonwealth and Development Office
dc.description.sponsorshipBill & Melinda Gates Foundation
dc.format.extent1-17
dc.language.isoen
dc.subjectCassava
dc.subjectAfrican Cassava Mosaic Virus
dc.subjectMarker Assisted Selection
dc.subjectPCR
dc.subjectPlant Diseases
dc.subjectNigeria
dc.titleConversion and validation of uniplex SNP markers for selection of resistance to Cassava Mosaic Disease in Cassava breeding programs
dc.typeJournal Article
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationUniversity of Ibadan
cg.contributor.affiliationCornell University
cg.contributor.affiliationInternational Maize and Wheat Improvement Center
cg.contributor.affiliationThe Alliance of Bioversity International and the International Center for Tropical Agriculture
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:2021
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectCassava
cg.iitasubjectFood Security
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Diseases
cg.iitasubjectPlant Production
cg.journalAgronomy
cg.notesOpen Access journal; Published online: 25 Feb 2021
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/agronomy11030420
cg.iitaauthor.identifierKayondo Siraj Ismail: 0000-0002-3212-5727
cg.iitaauthor.identifierE J Parkes: 0000-0003-4063-1483
cg.iitaauthor.identifierPeter Kulakow: 0000-0002-7574-2645
cg.iitaauthor.identifierChiedozie Egesi: 0000-0002-9063-2727
cg.iitaauthor.identifierEng Hwa Ng: 0000-0003-0493-6212
cg.iitaauthor.identifierLuis Augusto Becerra Lopez-Lavalle: 0000-0003-3520-2270
cg.iitaauthor.identifierHernan Ceballos: 0000-0002-8744-7918
cg.iitaauthor.identifierIsmail Rabbi: 0000-0001-9966-2941
cg.futureupdate.requiredNo
cg.identifier.issue3
cg.identifier.volume11
cg.contributor.acknowledgementsThe authors gratefully acknowledge the technical support provided by the staff of the Cassava Breeding Program at the International Institute of Tropical Agriculture, Ibadan, Nigeria during the study. We also thank Excellence-in-Breeding Platform of the CGIAR for supporting the conversion of the trait-linked markers to allele-specific PCR assays. We thank the two anonymous Reviewers and the Editor for constructive comments which helped to improve the manuscript.


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