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Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.)

dc.contributor.authorAgre, A.P.
dc.contributor.authorClark, L.V.
dc.contributor.authorGarcia-Oliveira, A.L.
dc.contributor.authorBohar, R.
dc.contributor.authorAdebola, P.O.
dc.contributor.authorAsiedu, R.
dc.contributor.authorTerauchi, R.
dc.contributor.authorAsfaw, A.
dc.date.accessioned2024-01-09T12:53:38Z
dc.date.available2024-01-09T12:53:38Z
dc.date.issued2023
dc.identifier.citationAgre, A.P., Clark, L.V., Garcia‐Oliveira, A.L., Bohar, R., Adebola, P.O., Asiedu, R., ... & Asfaw, A. (2023). Identification of diagnostic KASP‐SNP markers for routine breeding activities in yam (Dioscorea spp.). Plant Genome, e20419, 1-11.
dc.identifier.issn1940-3372
dc.identifier.urihttps://hdl.handle.net/20.500.12478/8370
dc.description.abstractMaintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.
dc.description.sponsorshipBill & Melinda Gates Foundation
dc.format.extent1-11
dc.language.isoen
dc.subjectYams
dc.subjectBreeding
dc.subjectSingle Nucleotide Polymorphism
dc.subjectGenetic Markers
dc.titleIdentification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.)
dc.typeJournal Article
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationUniversity of Illinois at Urbana-Champaign
cg.contributor.affiliationInternational Maize and Wheat Improvement Center
cg.contributor.affiliationCCS Haryana Agricultural University
cg.contributor.affiliationKyoto University
cg.contributor.affiliationIwate Biotechnology Research Center
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryNigeria
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidAGRE:2023b
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectAgronomy
cg.iitasubjectFood Security
cg.iitasubjectGenetic Improvement
cg.iitasubjectPlant Breeding
cg.journalPlant Genome
cg.notesOpen Access Journal
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://doi.org/10.1002/tpg2.20419
cg.iitaauthor.identifierPaterne AGRE: 0000-0003-1231-2530
cg.iitaauthor.identifierGarcia-Oliveira AL: 0000-0001-8561-4172
cg.iitaauthor.identifierPatrick Adebola: 0000-0002-5155-6194
cg.iitaauthor.identifierRobert Asiedu: 0000-0001-8943-2376
cg.iitaauthor.identifierAsrat Asfaw: 0000-0002-4859-0631
cg.futureupdate.requiredNo
cg.identifier.issuee20419


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