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水稻重测序2011-PLoS Genetics（ Roles of Domestication gene）
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水稻重测序 2011-06-09—PLoS Genetics
Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes
He Z, Zhai W, Wen H, Tang T, Wang Y, et al. (2011) Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes. PLoS Genet 7(6):e1002100.
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.
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.
研究人员应用Solexa-GA与ABI-Solid 两种二代测序仪器同时对水稻的三个亚种（66株水稻，每个亚种一个pool，平均测序深度30X）进行全基因组重测序，通过对low diversity regions 进行研究，对水稻基因组的两种进化史进行研究探讨，全基因组重测序的结果和部分已经鉴定的驯化相关gene具有一致性。
https://blog.sciencenet.cn/blog-491809-455188.html
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