Differential gene expression in small and large rainbow trout derived from two seasonal spawning groups

Abstract

BackgroundGrowth in fishes is regulated via many environmental and physiological factors and is shaped by the genetic background of each individual. Previous microarray studies of salmonid growth have examined fish experiencing either muscle wastage or accelerated growth patterns following refeeding, or the influence of growth hormone and transgenesis. This study determines the gene expression profiles of genetically unmanipulated large and small fish from a domesticated salmonid strain reared on a typical feeding regime. Gene expression profiles of white muscle and liver from rainbow trout (Oncorhynchus mykiss) from two seasonal spawning groups (September and December lots) within a single strain were examined when the fish were 15 months of age to assess the influence of season (late fall vs. onset of spring) and body size (large vs. small).ResultsAlthough IGFBP1 gene expression was up-regulated in the livers of small fish in both seasonal lots, few expression differences were detected in the liver overall. Faster growing Dec. fish showed a greater number of differences in white muscle expression compared to Sept. fish. Significant differences in the GO Generic Level 3 categories ‘response to external stimulus’, ‘establishment of localization’, and ‘response to stress’ were detected in white muscle tissue between large and small fish. Larger fish showed up-regulation of cytoskeletal component genes while many genes related to myofibril components of muscle tissue were up-regulated in small fish. Most of the genes up-regulated in large fish within the ‘response to stress’ category are involved in immunity while in small fish most of these gene functions are related to apoptosis.ConclusionsA higher proportion of genes in white muscle compared to liver showed similar patterns of up- or down-regulation within the same size class across seasons supporting their utility as biomarkers for growth in rainbow trout. Differences between large and small Sept. fish in the ‘response to stress’ and ‘response to external stimulus’ categories for white muscle tissue, suggests that smaller fish have a greater inability to handle stress compared to the large fish. Sampling season had a significant impact on the expression of genes related to the growth process in rainbow trout.

Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

“…On 10 December 2008 a second set of five females was crossed with a different XY male to produce the Dec. XY male lot. Information on the mortality, specific growth rates, thermal growth coefficients, and tank densities of the lots have been reported previously (Kocmarek et al 2014(Kocmarek et al , 2015.…”

“…The locations of the sequences within the stickleback genome were coupled with stickleback and rainbow trout synteny information (Guyomard et al 2012) to identify the most likely location of the Agilent sequences within the rainbow trout genome. If the genes were localized with a detected QTL, biological process gene ontology (GO) terms were assigned based on the results presented in the microarray analysis (Kocmarek et al 2014(Kocmarek et al , 2015. Due to the fact that most of the significant differences between large and small fish were seen at GO level 3, the results from this level are presented.…”

“…We used a comparative analysis to determine whether 108 unique sequences (Supplementary File 5 1 ), which had shown a ≥2.4-fold DGE between large and small fish in microarray studies (Kocmarek et al 2014(Kocmarek et al , 2015, mapped to the same chromosomes as the QTL detected above. The large and small fish used in the microarray studies are a subset of the fish used in the QTL analysis.…”

“…Comparisons of GH-transgenic and domestic salmonids with slower growing wildtype controls suggest the somatrophic axis may influence growth via a variety of genes, including those related to carbohydrate, lipid, and energy metabolism, cell/tissue structure, development, and the response to stress (Rise et al 2006;Devlin et al 2009Devlin et al , 2013Tymchuk et al 2009;White et al 2013;Xu et al 2013). Similarly, RNAseq analysis and additional microarray studies using rainbow trout muscle have identified genes related to lipid and carbohydrate metabolism, ATP production (Salem et al 2012;Kocmarek et al 2014), muscle components (Salem et al 2012), and transcription factors (Kocmarek et al 2014) to be differentially expressed between large and small fish. Although these studies have been effective at identifying which genes are differentially expressed in fish with different growth phenotypes they are less able to link expression of the gene to particular QTL.…”

“…We screened the families for variation at marker loci located on 11 linkage groups known to contain body weight QTL (Wringe et al 2010;Magee 2011). We then tested whether candidate genes known to be differently expressed between large and small fish in a microarray analysis of a subset of the fish from the same families (Kocmarek et al 2014(Kocmarek et al , 2015 used in the current QTL analysis localize with the chromosomal regions containing the QTL for body weight and length. Using the rainbow trout genome published by Berthelot et al (2014) and synteny between the rainbow trout and stickleback genomes, we identified the location of the candidate genes within the rainbow trout genome.…”