title: A map of rice genome variation reveals the origin of cultivated rice.
abstract: Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.
authors.affiliation: National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
authors.forename: Nori
authors.initials: N
authors.lastname: Kurata
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
authors.forename: Zi-Xuan
authors.initials: ZX
authors.lastname: Wang
authors.forename: Ahong
authors.initials: A
authors.lastname: Wang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Kunyan
authors.initials: K
authors.lastname: Liu
authors.forename: Hengyun
authors.initials: H
authors.lastname: Lu
authors.forename: Wenjun
authors.initials: W
authors.lastname: Li
authors.forename: Yunli
authors.initials: Y
authors.lastname: Guo
authors.forename: Yiqi
authors.initials: Y
authors.lastname: Lu
authors.forename: Congcong
authors.initials: C
authors.lastname: Zhou
authors.forename: Danlin
authors.initials: D
authors.lastname: Fan
authors.forename: Qijun
authors.initials: Q
authors.lastname: Weng
authors.forename: Chuanrang
authors.initials: C
authors.lastname: Zhu
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.forename: Yongchun
authors.initials: Y
authors.lastname: Wang
authors.forename: Lei
authors.initials: L
authors.lastname: Feng
authors.forename: Hiroyasu
authors.initials: H
authors.lastname: Furuumi
authors.forename: Takahiko
authors.initials: T
authors.lastname: Kubo
authors.forename: Toshie
authors.initials: T
authors.lastname: Miyabayashi
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yuan
authors.forename: Qun
authors.initials: Q
authors.lastname: Xu
authors.forename: Guojun
authors.initials: G
authors.lastname: Dong
authors.forename: Qilin
authors.initials: Q
authors.lastname: Zhan
authors.forename: Canyang
authors.initials: C
authors.lastname: Li
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Tingting
authors.initials: T
authors.lastname: Lu
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.forename: Jiayang
authors.initials: J
authors.lastname: Li
authors.forename: Bin
authors.initials: B
authors.lastname: Han
mesh_terms: D000383:Agriculture / Q000266:history*; D001947:Breeding / Q000266:history; D018556:Crops, Agricultural / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D062305:Geographic Mapping; D049690:History, Ancient; D012275:Oryza / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012641:Selection, Genetic