Data from: 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.

生态背景下生殖隔离（reproductive isolation）的演化，往往涉及物种分化的多个维度，而分歧选择可对这些维度产生作用。这些维度涵盖数量表型性状的变异、基因表达调控，以及特定等位基因组合的差异传递。因此，针对物种形成过程的整合性研究，需鉴定上述性状的遗传基础，进而阐明自然环境中的分歧选择如何影响这些性状，以及它们最终如何促成生殖隔离。湖白鲑（Coregonus clupeaformis，Lake Whitefish）的矮型与正常型物种对，在北美多处冰后湖泊中呈同域分布。相较于底栖的正常型同类，浮游性矮型白鲑在生活史、行为、形态及基因表达等诸多性状上存在显著差异，以适配不同的生态位。本研究将RAD测序（RAD-Sequencing）技术应用于一个回交杂交家系，构建了湖白鲑的高密度遗传连锁图谱，并开展数量性状位点（Quantitative Trait Locus, 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QTL、表达QTL，以及传递比率偏倚QTL进行了定位，并鉴定出承载此类QTL簇的基因组区域。此外，本研究还发现了一个与性别决定显著相关的狭窄基因组区域。本研究获得的位置信息与功能信息，将为后续的群体基因组学研究提供助力，以深化我们对湖白鲑物种对间生殖隔离的基因组架构的认知。