title: The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.
abstract: The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.
authors.forename: Jae Young
authors.initials: JY
authors.lastname: Choi
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.
authors.forename: Adrian E
authors.initials: AE
authors.lastname: Platts
authors.affiliation: Institute of Archaeology, University College London, London, United Kingdom.
authors.forename: Dorian Q
authors.initials: DQ
authors.lastname: Fuller
authors.affiliation: Institute of Plant and Microbial Biology, Academica Sinica, Nankang, Taipei, Taiwan, Republic of China.
authors.forename: Yue-Ie
authors.initials: YI
authors.lastname: Hsing
authors.affiliation: Arizona Genomics Institute, University of Arizona, Tucson, AZ.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.|Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Purugganan
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000483:Alleles; D005075:Biological Evolution; D018556:Crops, Agricultural / Q000235:genetics; D000071278:Domestication; D019143:Evolution, Molecular; D051456:Gene Flow / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D049810:Genetic Speciation; D014644:Genetic Variation / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods
keywords:  crop species; adaptation; gene flow; introgressive hybridization