title: Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice.
abstract: The domestication history of rice remains controversial, with multiple studies reaching different conclusions regarding its origin(s). These studies have generally assumed that populations of living wild rice,O. rufipogon, are descendants of the ancestral population that gave rise to domesticated rice, but relatively little attention has been paid to the origins and history of wild rice itself. Here, we investigate the genetic ancestry of wild rice by analyzing a diverse panel of rice genomes consisting of 203 domesticated and 435 wild rice accessions. We show that most modern wild rice is heavily admixed with domesticated rice through both pollen- and seed-mediated gene flow. In fact, much presumed wild rice may simply represent different stages of feralized domesticated rice. In line with this hypothesis, many presumed wild rice varieties show remnants of the effects of selective sweeps in previously identified domestication genes, as well as evidence of recent selection in flowering genes possibly associated with the feralization process. Furthermore, there is a distinct geographical pattern of gene flow fromaus,indica, andjaponicavarieties into colocated wild rice. We also show that admixture fromausandindicais more recent than gene flow fromjaponica, possibly consistent with an earlier spread ofjaponicavarieties. We argue that wild rice populations should be considered a hybrid swarm, connected to domesticated rice by continuous and extensive gene flow.
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.|College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Hongru
authors.initials: H
authors.lastname: Wang
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, 1350 Copenhagen, Denmark.
authors.forename: Filipe G
authors.initials: FG
authors.lastname: Vieira
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Jacob E
authors.initials: JE
authors.lastname: Crawford
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Chengcai
authors.initials: C
authors.lastname: Chu
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
mesh_terms: D000071278:Domestication; D051456:Gene Flow; D018745:Genome, Plant; D006801:Humans; D006824:Hybridization, Genetic; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D000069600:Plant Breeding; D012641:Selection, Genetic