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.