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

Abstract

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 using RNA-sequencing and quantitative real-time PCR, single-nucleotide polymorphism (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 nonmodel species.

Signatures of selection in tilapia revealed by whole genome resequencing

“…5 ). Previous studies showed significant associations of their homologous genes with economic traits in animals 42 43 , supporting the notion that these genes could be selected during breeding for genetic improvement. These candidate genes under selection identified in our study could provide useful information for rapidly identifying DNA markers associated with economically important traits in Tilapia.…”

A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions

“…report the use of reciprocal hybrids, whereas in this study, hybrid eggs originated only from domesticated animals. Third, since parental effects vary over time, and seem to be most pronounced at the yolk sac resorption stage, and tend to decrease over time, the sampling time-point selected could also have contributed to the gene expression differences of the hybrids [ 73 ]. Indeed, in the current study a higher proportion of genes showed a dominant inheritance pattern at the yolk sac stage (52%) then during exogenous feeding (42%), suggesting stronger maternal influence at the earlier life stage.…”

Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions inDrosophila pseudoobscura

“…Genes were classified as either dominant, underdominant, overdominant, or additive. Following convention ( Gibson et al 2004 ; McManus et al 2010 ; Bougas et al 2013 ; Schaefke et al 2013 ), here dominant, overdominant, and underdominant refer to the mode of inheritance, not selection or fitness. These categories of expression patterns were defined similarly to previous studies ( McManus et al 2010 ; Bell et al 2013 ).…”