Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) 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.affiliationUniversity of Albertaen
cg.contributor.affiliationUniversity of Arizonaen
cg.contributor.affiliationKenya Agricultural and Livestock Research Organizationen
cg.contributor.crpGenebanks
cg.contributor.donorFederal Ministry for Economic Cooperation and Development, Germanyen
cg.coverage.countryCôte d'Ivoire
cg.coverage.iso3166-alpha2CI
cg.coverage.regionAfrica
cg.coverage.regionWestern Africa
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1007/s11032-018-0885-zen
cg.isijournalISI Journalen
cg.issn1572-9788en
cg.issue11en
cg.journalMolecular Breedingen
cg.reviewStatusPeer Reviewen
cg.volume38en
dc.contributor.authorNdjiondjop, M.N.en
dc.contributor.authorSemagn, K.en
dc.contributor.authorZhang, J.en
dc.contributor.authorGouda, A.C.en
dc.contributor.authorKpeki, S.B.en
dc.contributor.authorGoungoulou, Alphonse J.en
dc.contributor.authorWambugu, P.en
dc.contributor.authorDramé, K.N.en
dc.contributor.authorBimpong, I.K.en
dc.contributor.authorZhao, D.en
dc.date.accessioned2019-05-25T11:07:43Zen
dc.date.available2019-05-25T11:07:43Zen
dc.identifier.urihttps://hdl.handle.net/10568/101382
dc.titleDevelopment of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) speciesen
dcterms.abstractSpecies misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.en
dcterms.accessRightsOpen Access
dcterms.available2018-10-24
dcterms.bibliographicCitationNdjiondjop, M.N., Semagn, K., Zhang, J., Gouda, A.C., Kpeki, S.B., Goungoulou, A., Wambugu, P., Dramé, K.N., Bimpong, I.K., Zhao, D. 2018. Development of species diagnostic SNP markers for quality control genotyping in four rice (Oryza L.) species. Molecular Breeding 38: 131.en
dcterms.issued2018-11
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectgermplasm collectionsen
dcterms.subjectoryza glaberrimaen
dcterms.subjectgene banksen
dcterms.subjectriceen
dcterms.typeJournal Article

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