Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

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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.affiliationFoundation for Research and Technology-Hellasen
cg.contributor.crpGenebanks
cg.contributor.donorGlobal Crop Diversity Trusten
cg.contributor.donorFederal Ministry for Economic Cooperation and Development, Germanyen
cg.coverage.iso3166-alpha2CI
cg.coverage.regionAfrica
cg.coverage.regionAsia
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1007/s00122-018-3268-2en
cg.isijournalISI Journalen
cg.issn1432-2242en
cg.issue4en
cg.journalTheoretical and Applied Geneticsen
cg.reviewStatusPeer Reviewen
cg.volume132en
dc.contributor.authorNdjiondjop, M.N.en
dc.contributor.authorAlachiotis, N.en
dc.contributor.authorPavlidis, P.en
dc.contributor.authorGoungoulou, Alphonse J.en
dc.contributor.authorKpeki, S.B.en
dc.contributor.authorZhao, D.en
dc.contributor.authorSemagn, K.en
dc.date.accessioned2019-05-25T11:07:42Zen
dc.date.available2019-05-25T11:07:42Zen
dc.identifier.urihttps://hdl.handle.net/10568/101379
dc.titleComparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian riceen
dcterms.abstractPrevious studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1–32.1 and 16.3–37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10−4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10−2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.en
dcterms.accessRightsOpen Access
dcterms.available2018-12-21
dcterms.bibliographicCitationNdjiondjop, M.N., Alachiotis, N., Pavlidis, P., Goungoulou, A., Kpeki, S.B., Zhao, D. and Semagn, K. 2019. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. Theoretical and Applied Genetics 132: 1145.en
dcterms.extentpp. 1145-1158en
dcterms.issued2019-04
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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