Data from: Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

Hybridization can lead to phenotypic differences arising from changes in gene expression patterns or new allele combinations. Variation in gene expression is thought to be controlled by differences in transcription regulation of parental alleles, either through cis or trans regulatory elements. A previous study among brook charr hybrids from different populations (Rupert, Laval, and domestic) showing distinct length at age during early life stages also revealed different patterns in transcription regulation inheritance of transcript abundance. In the present study, transcript abundance by means of RNA-seq and qRT-PCR, SNP genotypes and allelic imbalance were assessed in order to understand the molecular mechanisms underlying the observed transcriptomic and differences in length at age among domestic × Rupert hybrids and Laval × domestic hybrids. We found 198 differentially expressed genes between the two hybrid crosses and allelic imbalance could be analyzed for 69 of them. Among these 69 genes, 36 genes exhibited cis acting regulatory effects in both of the two crosses, thus confirming the prevalent role of cis acting regulatory elements in the regulation of differentially expressed genes among intraspecific hybrids. In addition, we detected a significant association between SNP genotypes of three genes and length at age. Our study is thus one of the few that have highlighted some of the molecular mechanisms potentially involved in the differential phenotypic expression in intraspecific hybrids for non-model species.

杂交可引发表型差异，此类差异源自基因表达模式改变或新等位基因组合的产生。基因表达变异被认为由亲本等位基因的转录调控差异所介导，可通过顺式（cis）或反式（trans）调控元件实现。此前一项针对不同种群（Rupert、Laval及家养种群）溪红点鲑杂交后代的研究显示，其早期生命阶段的体长存在显著差异，同时还揭示了转录本丰度的转录调控遗传模式存在差异。本研究通过RNA测序（RNA-seq）与实时定量聚合酶链式反应（qRT-PCR）、单核苷酸多态性（SNP）基因型分析及等位基因失衡检测，对家养×Rupert杂交后代与Laval×家养杂交后代的转录本丰度、观测到的转录组差异以及体长差异背后的分子机制进行解析。本研究在两类杂交组合间共鉴定出198个差异表达基因，其中69个可用于等位基因失衡分析。在这69个基因中，有36个在两类杂交组合中均表现出顺式调控效应，由此证实顺式调控元件在种内杂交后代差异表达基因的调控中发挥普遍作用。此外，本研究还检测到3个基因的SNP基因型与体长存在显著关联。因此，本研究是为数不多的揭示非模式物种种内杂交后代表型差异表达潜在分子机制的研究之一。