Meyer, RS; Choi, JY; Sanches, M; Plessis, A; Flowers, JM; Amas, J; Dorph, K; ... Purugganan, MD; + view all 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; - view fewer (2016) Domestication history and geographical adaptation inferred from a SNP map of African rice. Nature Genetics , 48 (9) pp. 1083-1088. 10.1038/ng.3633.

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Abstract

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.

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