title: Domestication history and geographical adaptation inferred from a SNP map of African rice.
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.
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.|Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors: Rachel S
authors: RS
authors: Meyer
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.
authors: Jae Young
authors: JY
authors: Choi
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.
authors: Michelle
authors: M
authors: Sanches
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.
authors: Anne
authors: A
authors: Plessis
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.|Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors: Jonathan M
authors: JM
authors: Flowers
authors: Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.
authors: Junrey
authors: J
authors: Amas
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.
authors: Katherine
authors: K
authors: Dorph
authors: Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.
authors: Annie
authors: A
authors: Barretto
authors: Department of Biology, University of Minnesota, Duluth, Minnesota, USA.
authors: Briana
authors: B
authors: Gross
authors: Institute of Archaeology, University College London, London, UK.
authors: Dorian Q
authors: DQ
authors: Fuller
authors: AfricaRice Sahel Station, Saint-Louis, Senegal.
authors: Isaac Kofi
authors: IK
authors: Bimpong
authors: AfricaRice Centre, Cotonou, Benin.
authors: Marie-Noelle
authors: MN
authors: Ndjiondjop
authors: Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors: Khaled M
authors: KM
authors: Hazzouri
authors: Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.
authors: Glenn B
authors: GB
authors: Gregorio
authors: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA.|Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE.
authors: Michael D
authors: MD
authors: Purugganan
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D018556:Crops, Agricultural; D000071278:Domestication; D017343:Genes, Plant / Q000235:genetics*; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005843:Geography; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D055049:Salt Tolerance