The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)
The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)
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DOI：
10.1111/mec.13537
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发表时间：
2016-03-01
影响因子：
4.9
通讯作者：
Lascoux, Martin
中科院分区：
文献类型：
--
作者：
Kryvokhyzha, Dmytro;Holm, Karl;Lascoux, Martin
在测试种群间适应性表型差异时，种群结构是一个潜在的问题。观察到的种群间的表型差异可能只是由于遗传漂移，如果不考虑它们之间的遗传距离，这种分化可能被错误地解释为适应性。相反，适应过程和人口统计过程可能是紧密关联的，对种群结构进行修正可能会导致假阴性。在这里，我们在世界性杂草Capsella bursa-Pastoris中评估了这个问题。我们使用RNA-Seq技术分析了24份材料的基因表达差异，这些材料属于一个更大的群体，以前已经确定了开花时间和昼夜节律，并使用测序基因分型(GBS)技术进行了基因分型。我们发现，基因表达的聚类检索到了与以前使用GBS数据获得的相同的三个聚类，即欧洲、中东和亚洲。此外，三个群体还在开花时间和昼夜节律变化上进行了区分。在分析差异基因表达分析时，对群体遗传结构的修正消除了三组之间的所有差异。这可能表明，大多数差异是中性的，只是反映了人口历史。然而，开花时间和昼夜节律的地理差异表明，适应性状的分布可能受到种群结构的干扰。为了绕过这种混淆效应，我们比较了基因组内不同开花生态型之间的基因表达差异。在差异表达的基因中，开花基因C是局部适应调控开花时间的最强候选基因。
Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.