College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Hangzhou, People's Republic of China.
Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA.
Mol Biol Evol. 2017 Apr 1;34(4):908-924. doi: 10.1093/molbev/msw296.
Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a "cost of domestication". Here, we investigated the numbers and frequencies of deleterious variants in Asian rice (Oryza sativa), focusing on two varieties (japonica and indica) and their wild relative (O. rufipogon). We investigated three signals of a potential cost of domestication in Asian rice relative to O. rufipogon: an increase in the frequency of deleterious SNPs (dSNPs), an enrichment of dSNPs compared with synonymous SNPs (sSNPs), and an increased number of deleterious variants. We found evidence for all three signals, and domesticated individuals contained ∼3-4% more deleterious alleles than wild individuals. Deleterious variants were enriched within low recombination regions of the genome and experienced frequency increases similar to sSNPs within regions of putative selective sweeps. A characteristic feature of rice domestication was a shift in mating system from outcrossing to predominantly selfing. Forward simulations suggest that this shift in mating system may have been the dominant factor in shaping both deleterious and neutral diversity in rice.
许多单核苷酸多态性被预测为编码有害的氨基酸变异。这些轻微有害的突变可以为种群历史、选择的动态以及表型的遗传基础提供独特的见解。对于驯化物种来说尤其如此，因为瓶颈和选择的历史可能会影响有害变异的频率，并发出“驯化成本”的信号。在这里，我们研究了亚洲稻（Oryza sativa）中有害变异的数量和频率，重点研究了两个品种（粳稻和籼稻）及其野生亲缘种（O. rufipogon）。我们研究了亚洲稻相对于 O. rufipogon 潜在驯化成本的三个信号：有害单核苷酸多态性（dSNP）频率增加、有害 SNP 与同义 SNP 相比富集（dSNP）以及有害变异数量增加。我们发现了所有这三个信号的证据，并且驯化个体比野生个体多含有约 3-4%的有害等位基因。有害变异在基因组中低重组区域内富集，并在假定的选择清扫区域内经历了类似于 sSNP 的频率增加。水稻驯化的一个特征是交配系统从异交转变为主要自交。正向模拟表明，这种交配系统的转变可能是塑造水稻有害和中性多样性的主要因素。
