Domestication history and geographical adaptation inferred from a SNP map of African rice
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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 similar to 3,000 years ago(1-3). African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses(4,5). 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 similar to 13,000-15,000 years ago with effective population size reaching its minimum value similar to 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 similar to 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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