A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush)

Abstract

In Lake Superior there are three principal forms of lake trout (Salvelinus namaycush): lean, siscowet and humper. Wild lean and siscowet differ in the shape and relative size of the head, size of the fins, location and size of the eyes, caudal peduncle shape and lipid content of the musculature. To investigate the basis for these phenotypic differences, lean and siscowet lake trout, derived from gametes of wild populations in Lake Superior, were reared communally under identical environmental conditions for 2.5 years. Fish were analysed for growth, morphometry and lipid content, and differences in liver transcriptomics were investigated using Roche 454 GS-FLX pyrosequencing. The results demonstrate that key phenotypic differences between wild lean and siscowet lake trout such as condition factor, morphometry and lipid levels, persist in these two forms when reared in the laboratory under identical environmental conditions. This strongly suggests that these differences are genetic and not a result of environmental plasticity. Transcriptomic analysis involving the comparison of hepatic gene frequencies (RNAseq) and expression (quantitative reverse transcription-polymerase chain reaction (qPCR)) between the two lake trout forms, indicated two primary gene groups that were differentially expressed; those involving lipid synthesis, metabolism and transport (acylCoA desaturase, acyl-CoA binding protein, peroxisome proliferator-activated receptor gamma, and apolipoproteins), and those involved with immunity (complement component C3, proteasome, FK506 binding protein 5 and C1q proteins). The results demonstrate that RNA-seq can be used to identify differentially expressed genes; however, some discrepancies between RNA-seq analysis and qPCR indicate that methods for deep sequencing may need to be refined and ⁄ or different RNA-seq platforms utilized.

An Overview of the Immunological Defenses in Fish Skin

“…NGS is revolutionizing the approaches taken to study both transcriptomics and genomics, due to the massive amount of sequence information that can be generated in a relatively short length of time [363]. There are some reports describing NGS on salmonid fish, both wild (Salvelinus namaycush and Coregonus clupeaformis) [364,365] and farmed (S. salar and Oncorhynchus mykiss) [366,367].…”

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

“…Microarrays and, more recently, RNA-seq by means of NGS technologies have been used to compare the transcriptomes of phenotypically distinct individuals, namely in salmonid fishes St-Cyr et al, 2008;Goetz et al, 2010;Jeukens et al, 2010;Xu et al, 2010). Typically, many transcriptomic differences involved genes with functions related to energy production, muscular activity, immunity and cell cycle regulation processes.…”

“…Numerous studies have characterized genomewide patterns of gene expression among populations exhibiting phenotypic variation. In fishes in particular, the majority of such studies have not only used microarrays (Oleksiak et al, 2002;Whitehead and Crawford, 2005;Whitehead and Crawford, 2006;St-Cyr et al, 2008;Whiteley et al, 2008), but also next-generation sequencing to a lower extent (Elmer et al, 2010;Goetz et al, 2010;Jeukens et al, 2010;Shen et al, 2012). Hybridization can also lead to different modes of transcription regulation.…”

Evolution and origin of sympatric shallow-water morphotypes of Lake Trout, Salvelinus namaycush, in Canada’s Great Bear Lake

“…For example, in the Laurentian Great Lakes (LGLs), up to three depthsegregated morphs differing in morphology and ecology have been reported (Krueger and Ihssen, 1995;Moore and Bronte, 2001). The origin of these morphs is not completely understood, but there appears to be a genetic component to these differences (Page et al, 2004;Goetz et al, 2010). Sympatric morphs in the LGLs have been heavily impacted, even extirpated in some cases, owing to overharvesting, invasive Sea Lamprey (Petromyzon marinus) predation and the long history of Lake Trout hatchery supplementation (Krueger and Ihssen, 1995;Page et al, 2004), making the study of their evolutionary origin problematic.…”