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（Hybridization）可通过改变基因表达模式或形成新的等位基因组合，引发表型差异。现有研究认为，基因表达变异由亲本等位基因的转录调控差异所控制，调控路径涵盖顺式调控元件（cis-regulatory elements）与反式调控元件（trans-regulatory elements）。此前针对不同种群（Rupert、Laval及驯养种群）溪鳟（brook charr）杂交后代的研究显示，该类群体在早期生活阶段呈现出体长随年龄的显著差异，同时还发现转录本丰度（transcript abundance）的转录调控遗传模式存在分化。本研究通过RNA测序（RNA-seq）与实时定量聚合酶链反应（qRT-PCR）检测转录本丰度，并分析单核苷酸多态性（SNP）基因型与等位基因失衡（allelic imbalance）情况，旨在解析驯养种群×Rupert种群杂交后代与Laval种群×驯养种群杂交后代中，观测到的转录组差异及体长随年龄差异背后的分子机制。本研究在两类杂交组合间共鉴定出198个差异表达基因（differentially expressed genes），其中69个可开展等位基因失衡分析。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作用，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，本研究还发现3个基因的SNP基因型与体长随年龄的表型存在显著关联。综上，本研究是少数针对非模式物种（non-model species）种内杂交后代差异表型表达潜在分子机制的研究之一，阐明了部分相关作用机制。