eQTL mapping in Lake Whitefish Species Pairs.. Coregonus clupeaformis

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 towards 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 a F1 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 dataset (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 more than 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 inter-individual 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. Keywords: eQTL mapping Overall design: Dissected white muscle tissue (250-350 mg) was sampled for 76 individuals from the hybrid x dwarf backcross mapping family. We used a loop design (YANG and SPEED 2002; CHURCHILL 2002) to maximize the number of sampled meioses. Each of 76 samples was technically replicated on two distinct slides, while performing dye swapping (Cy3 and Alexa) to estimate the dye intensity variation bias. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (KERR et al. 2000). The design file used for the maanova analysis is linked below as a supplementary file.表达数量性状位点（expression quantitative trait loci, eQTL）的定位是解析基因调控遗传结构的有效手段。然而，eQTL定位尚未被应用于研究参与种群分化、最终导致物种形成过程的基因的调控架构。本研究开展eQTL定位实验，以比较近期分化的浮游型（矮化）与底栖型（正常）湖白鲑物种对的适应性性状的转录调控遗传结构。eQTL定位基于来自F1杂种-矮化回交群体的三类数据集：全部66个完成基因分型的个体的合并数据集，以及分别按雄性、雌性拆分的两个性别特异性数据集。与雄性数据集（54个eQTL）和合并数据集（33个eQTL）相比，雌性数据集中共鉴定到显著更多的eQTL（174个）。这些基因中的大多数在回交群体的雄性和雌性后代之间未呈现差异表达，这为转录组调控中存在强烈的多效性连锁性别效应提供了证据。一个在雌性群体中发生分离的连锁群的亚端粒区域涵盖了超过50%的eQTL，这些eQTL表现出最为显著的加性效应。我们还对受控条件下饲养的纯矮化和正常后代的转录组谱进行了直接比较，鉴定到34个差异表达转录本，这些转录本对应的eQTL仅在性别特异性数据集中分离，且大多属于在自然种群中区分矮化与正常湖白鲑的功能类群。因此，这些eQTL并非源于个体间的表达差异，而是与矮化和正常湖白鲑之间的适应性及历史性遗传分化相关。本研究展示了如何通过整合遗传与转录组数据，将作图群体特异性效应与受选择的遗传因素分离，从而解析选择作用下的功能基因组响应，这一策略或可用于揭示自然种群的表型分化机制。 关键词：eQTL定位 整体实验设计：从杂交种×矮化回交作图群体的76个个体中采集解剖得到的白肌组织（250-350 mg）。我们采用循环设计（YANG和SPEED 2002；CHURCHILL 2002）以最大化采样的减数分裂事件数量。76个样本均在两张不同的芯片上进行技术重复，并通过染料交换（Cy3与Alexa荧光染料）估算染料强度变异偏差。在校正局部背景后，原始强度值经以2为底的对数转换，并使用R/MANOVA软件（KERR等，2000）中实现的区域局部加权回归散点平滑法（regional LOWESS method）进行标准化。用于maanova分析的设计文件已作为补充文件附于文末。