Article

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

Meyer, RS; Choi, JY; Sanches, M; Plessis, A; Flowers, JM; Amas, J; Dorph, K; Barretto, A; Gross, B; Fuller, DQ; Bimpong, IK; Ndjiondjop, MN; Hazzouri, KM; Gregorio, GB; Purugganan, MD

Nature genetics 2016 9

PMID: 27500524

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

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.