Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationAfrica Rice Centeren
cg.contributor.affiliationUnited States Department of Agricultureen
cg.contributor.affiliationUniversité Nationale des Sciences, Technologies, Ingénierie et Mathématiques, Beninen
cg.contributor.affiliationKenya Agricultural and Livestock Research Organizationen
cg.contributor.affiliationGenetic Resources Research Institute, Kenyaen
cg.contributor.crpGenebanks
cg.contributor.donorGlobal Crop Diversity Trusten
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1038/s41598-021-97689-3en
cg.isijournalISI Journalen
cg.issn2045-2322en
cg.issue1en
cg.journalScientific Reportsen
cg.reviewStatusPeer Reviewen
cg.volume11en
dc.contributor.authorGouda, A.C.en
dc.contributor.authorWarburton, Marilyn L.en
dc.contributor.authorDjedatin, G.L.en
dc.contributor.authorKpeki, S.B.en
dc.contributor.authorWambugu, P.W.en
dc.contributor.authorGnikoua, K.en
dc.contributor.authorNdjiondjop, M.N.en
dc.date.accessioned2022-05-13T12:19:58Zen
dc.date.available2022-05-13T12:19:58Zen
dc.identifier.urihttps://hdl.handle.net/10568/119538
dc.titleDevelopment and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) speciesen
dcterms.abstractMorphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology (“DArTseq”). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies’ diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2021-09-20
dcterms.bibliographicCitationGouda, A.C. Warburton, M.L. Djedatin, G.L. Kpeki, S.B. Wambugu, P.W. Gnikoua, K. Ndjiondjop, M.N.Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species.Scientific Reports.Volume 11 : 18617.en
dcterms.extent18617en
dcterms.issued2021-09-20
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectplant sciencesen
dcterms.subjectriceen
dcterms.subjectoryzaen
dcterms.subjectmolecular biologyen
dcterms.typeJournal Article

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