State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, China.
PLoS Genet. 2011 Jun;7(6):e1002100. doi: 10.1371/journal.pgen.1002100. Epub 2011 Jun 9.
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.
由于基因流和选择的共同影响，不同基因组区域的谱系模式可能不同。栽培稻的两个亚种的存在为分析驯化过程中的这些影响提供了独特的机会。我们选择了来自三个水稻分类群的 66 个品系（约 22 个来自籼稻、22 个来自粳稻和 22 个来自野生稻）进行全基因组测序。在寻找选择的特征时，我们专注于栽培稻共享的低多样性区域 (LDR)。我们发现，这些重叠 LDR 的谱系历史与基因组背景明显不同。虽然籼稻和粳稻的基因组通常似乎是独立起源的，但许多重叠的 LDR 可能仅起源于一次，是选择和随后的基因渗入的结果。有趣的是，许多这样的 LDR 只包含一个水稻驯化的候选基因，并且通过这种方法确实“重新发现”了几个已知的驯化基因。总之，我们鉴定了 13 个额外的驯化候选基因。
