Domestication history and geographical adaptation inferred from a SNP map of African rice

Rachel S. Meyer, Jae Young Choi, Michelle Sanches, Anne Plessis, Jonathan M. Flowers, Junrey Amas, Katherine Dorph, Annie Barretto, Briana Gross, Dorian Q. Fuller, Isaac Kofi Bimpong, Marie Noelle Ndjiondjop, Khaled M. Hazzouri, Glenn B. Gregorio, Michael D. Purugganan

Research output: Contribution to journalArticlepeer-review


African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa-3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began-13,000-15,000 years ago with effective population size reaching its minimum value-3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within-300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species.

Original languageEnglish (US)
Pages (from-to)1083-1088
Number of pages6
JournalNature Genetics
Issue number9
StatePublished - Sep 1 2016

ASJC Scopus subject areas

  • Genetics


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