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.
Details
Title
Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes
Author
He, Ziwen : Sun Yat-sen University Zhai, Weiwei : Chinese Academy of Sciences Wen, Haijun : Sun Yat-sen University Tang, Tian : Sun Yat-sen University Wang, Yu : Chinese Academy of Sciences Lu, Xuemei : Chinese Academy of Sciences Greenberg, Anthony J. : Cornell University Hudson, Richard R. : University of Chicago Wu, Chung-I : Sun Yat-sen University Shi, Suhua : Sun Yat-sen University
Funding Information
National Basic Research Program of China, 2007CB815701 National Natural Science Foundation of China, 30730008 National Natural Science Foundation of China, 40976081 National Natural Science Foundation of China, 31000957 National Natural Science Foundation of China, 31071914 National Natural Science Foundation of China, 30970208 National S&T Major Project of China, 2009ZX08010-017B National S&T Major Project of China, 2009ZX08009-149B Yat-Sen innovation project Beijing Institute of Genomics SRF for ROCS Chinese Academy of Sciences, KSCX1-YW-22
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