title: Two evolutionary histories in the genome of rice: the roles of domestication genes.
abstract: Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been "rediscovered" by this approach. In summary, we identified 13 additional candidate genes of domestication.
authors.affiliation: State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Ziwen
authors.initials: Z
authors.lastname: He
authors.forename: Weiwei
authors.initials: W
authors.lastname: Zhai
authors.forename: Haijun
authors.initials: H
authors.lastname: Wen
authors.forename: Tian
authors.initials: T
authors.lastname: Tang
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Xuemei
authors.initials: X
authors.lastname: Lu
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Greenberg
authors.forename: Richard R
authors.initials: RR
authors.lastname: Hudson
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
mesh_terms: D018556:Crops, Agricultural / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant; D012275:Oryza / Q000145:classification / Q000235:genetics*