Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population

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dc.creatorMbanjo, Edwige Gaby Nkouaya
dc.creatorOgungbesan, Adebukola
dc.creatorAgbona, Afolabi
dc.creatorAkpotuzor, Patrick
dc.creatorToyinbo, Seyi
dc.creatorIluebbey, Peter
dc.creatorRabbi, Ismail Yusuf
dc.creatorPeteti, Prasad
dc.creatorWages, Sharon A.
dc.creatorNorton, Joanna
dc.creatorZhang, Xiaofei
dc.creatorBohorquez-Chaux, Adriana
dc.creatorMushoriwa, Hapson
dc.creatorEgesi, Chiedozie
dc.creatorKulakow, Peter
dc.creatorParkes, Elizabeth
dc.date2024
dc.date2024-09-23T14:18:04Z
dc.date2024-09-23T14:18:04Z
dc.date.accessioned2026-06-27T15:59:55Z
dc.descriptionA validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future.
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/152344
dc.identifier.urihttp://hdl.handle.net/123456789/119615
dc.languageen
dc.publisherMDPI
dc.rightsOpen Access
dc.sourceMbanjo, E.G.N.; Ogungbesan, A.; Agbona, A.; Akpotuzor, P.; Toyinbo, S.; Iluebbey, P.; Rabbi, I.Y.; Peteti, P.; Wages, S.A.; Norton, J.; Zhang, X.; Bohorquez-Chaux, A.; Mushoriwa, H.; Egesi, C.; Kulakow, P.; Parkes, E. (2024) Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population. Plants 13(16): 2328. ISSN: 2223-7747
dc.subjectcassava
dc.subjectbiofortification
dc.subjectbreeding
dc.subjectgenetic markers
dc.subjectpopulation structure
dc.subjectselection criteria
dc.titleValidation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population
dc.typeJournal Article

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Instituto Internacional de Agricultura Tropical (IITA)