Derome N, Bougas B, Rogers S M, Whiteley A R, Labbe A, Laroche J, Bernatchez L
Department of Biology, University of Laval, Quebec, Canada.
Genetics. 2008 Aug;179(4):1903-17. doi: 10.1534/genetics.107.086306. Epub 2008 Jul 27.
Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied toward investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits, differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from an F(1) hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals and the two sexes treated separately. We identified strikingly more eQTL in the female data set (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed >50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data sets and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to interindividual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family-specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations.
表达数量性状基因座（eQTL）定位是阐明基因调控遗传结构的有力手段。然而，eQTL定位尚未应用于研究参与种群分化过程（最终导致物种形成事件）的基因的调控结构。在此，我们进行了一项eQTL定位实验，以比较适应性性状中转录调控的遗传结构，区分湖白鲑最近进化出的湖沼型（矮型）和底栖型（正常型）物种对。eQTL在来自一个F(1) 杂交 - 矮型回交家系的三个数据集中进行定位：66个基因分型个体的完整数据集以及分别处理的两性数据集。与雄性（54个）和合并（33个）数据集相比，我们在雌性数据集中鉴定出显著更多的eQTL（174个）。这些基因中的大多数在回交家系的雄性和雌性后代之间没有差异表达，从而为转录组调控中强大的多效性性连锁效应提供了证据。在雌性中分离的一个连锁群的亚端粒区域包含了所有eQTL的50%以上，这些eQTL表现出最明显的加性效应。我们还对在受控条件下饲养的纯矮型和正常后代的转录组图谱进行了直接比较。我们检测到34个差异表达的转录本，它们与仅在性别特异性数据集中分离的eQTL相关，并且大多属于区分自然种群中矮型和正常白鲑的功能组。因此，这些eQTL与个体间变异无关，而是与矮型和正常白鲑之间的适应性和历史遗传分化有关。这项研究例证了遗传和转录组数据的整合如何通过将映射家系特异性效应与选择中的遗传因素分离，为剖析对选择的功能基因组反应提供了有力手段，这些遗传因素可能参与自然种群的表型分化。
