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.
Highlights
A main objective in the study of natural and domesticated species is to systematically identify genomic regions that have been influenced by selection
If gene flow continues between diverging populations, selection may play a large role in shaping the genealogies of different parts of the same genome
Because phylogenetic studies tend to support the independent domestication hypothesis [8,9,10,11], we may have the unusual opportunity to analyze the course of evolution twice from the same common ancestor, the Asian wild rice O. rufipogon [6]
Summary
A main objective in the study of natural and domesticated species is to systematically identify genomic regions that have been influenced by selection. If gene flow continues between diverging populations, selection may play a large role in shaping the genealogies of different parts of the same genome. The joint action of gene flow and selection could be even stronger in domesticated species than in natural populations as breeders might cross varieties between subspecies that do not readily interbreed in nature. Human selection for desired traits is often intense. In this context, Asian cultivated rice (Oryza sativa) is of particular value as there are two subspecies, indica and japonica, which are partially reproductively isolated [6]. Because phylogenetic studies tend to support the independent domestication hypothesis [8,9,10,11], we may have the unusual opportunity to analyze the course of evolution twice from the same common ancestor, the Asian wild rice O. rufipogon [6]
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