Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)

The evolution of reproductive isolation in an ecological context may involve multiple facets of species divergence on which divergent selection may operate. These include variation in quantitative phenotypic traits, regulation of gene expression, and differential transmission of particular allelic combinations. Thus, an integrative approach to the speciation process involves identifying the genetic basis of these traits, in order to understand how they are affected by divergent selection in nature and how they ultimately contribute to reproductive isolation. In the Lake Whitefish (Coregonus clupeaformis), dwarf and normal species pairs sympatrically occur in several North American postglacial lakes. The limnetic dwarf whitefish distinguishes from its normal benthic relative by numerous life history, behavioural, morphological and gene expression traits, in relation with the exploitation of distinct ecological niches. Here, we have applied the RAD-Sequencing method to a hybrid backcross family to reconstruct a high-density genetic linkage map and perform QTL mapping in the Lake Whitefish. The 3061 cM map encompassed 3438 segregating RAD markers distributed over 40 linkage groups, for an average resolution of 0.89 cM. We mapped phenotypic and expression QTL underlying ecologically important traits as well as transmission ratio distortion QTL, and identified genomic regions harbouring clusters of such QTL. A narrow genomic region strongly associated with sex determination was also evidenced. Positional and functional information revealed in this study will be useful in ongoing population genomic studies to illuminate our understanding of the genomic architecture of reproductive isolation between whitefish species pairs.

生态背景下的生殖隔离（reproductive isolation）演化，可能涉及物种分化（species divergence）的多个维度，而这些维度均可成为趋异选择（divergent selection）的作用靶点。此类维度涵盖数量表型性状（quantitative phenotypic traits）变异、基因表达调控（regulation of gene expression），以及特定等位基因组合（allelic combinations）的差异传递。因此，针对物种形成（speciation）过程的整合研究，需先明确这些性状的遗传基础，以此解析自然环境中趋异选择对其产生的影响，以及它们最终如何推动生殖隔离的形成。在湖白鲑（Coregonus clupeaformis，Lake Whitefish）中，矮型与正常型物种对在北美多处冰后湖泊（postglacial lakes）中呈同域分布。浮游型矮白鲑相较于底栖型正常白鲑，在生活史、行为、形态及基因表达等诸多性状上存在差异，这种差异与其对独特生态位（ecological niches）的利用相关。本研究将RAD测序（RAD-Sequencing）技术应用于杂交回交群体，以构建湖白鲑的高密度遗传连锁图谱，并开展数量性状位点（QTL）定位分析。该图谱总长3061厘摩（cM），包含分布于40个连锁群的3438个分离性RAD标记，平均分辨率达0.89 cM。我们对与生态重要性状相关的表型及表达QTL、传递比率畸变（transmission ratio distortion）QTL进行了定位，并鉴定出承载此类QTL簇的基因组区域。同时，还发现了一个与性别决定强相关的狭窄基因组区域。本研究获得的位置与功能信息，将为当前正在进行的种群基因组学（population genomic studies）研究提供助力，以加深我们对白鲑物种对间生殖隔离的基因组架构（genomic architecture）的理解。