Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.
Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.
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DOI：
10.1534/g3.116.028753
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发表时间：
2016-07-07
期刊：
影响因子：
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通讯作者：
Lascoux M
中科院分区：
文献类型：
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作者：
Chen J;Källman T;Ma XF;Zaina G;Morgante M;Lascoux M
选拔和过去人口统计的联合推断仍然是一项代价高昂且要求很高的任务。我们使用下一代测序的两个池48挪威云杉母树，一个对应于Fennoscandian结构域，另一个对应于阿尔卑斯域，以评估88个核基因的核苷酸多态。这些基因是控制植物物候性状的候选基因，大部分属于光周期途径。根据汇集的数据对群体遗传汇总统计数据的估计与之前的估计类似，这表明汇集测序是可靠的。非同义SNPs在两个结构域之间的频率差异和FST值均低于静默SNPs。这些结果表明存在净化选择。基于同义变化的两个结构域之间的分歧约为500万年，这一时间与最近600万年的系统发育估计相似，但比之前基于同工酶的估计要大得多。使用了两种方法，其中一种是新颖的，既考虑了FST，也考虑了两个区域之间的等位基因频率差异，用于在多样化选择下潜在地识别SNPs。检测到了大约20个基因的SNPs，其中包括之前被确定为主要选择目标的基因，如PaPRR3和PagI。
The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.