Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon

Type Article
Acceptance Date 2021-01 IN PRESS
Language English
Author(s) Christensen Kris A1, 2, Le Luyer JeremyORCID3, Chan Michelle T T1, 4, Rondeau Eric B1, 2, Koop Ben F2, Bernatchez Louis3, Devlin Robert H1
Affiliation(s) 1 : Fisheries and Oceans Canada, West Vancouver, BC, Canada V7V 1N6
2 : Department of Biology, University of Victoria, Victoria, BC, Canada V8P 5C2
3 : Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada G1V OA6
4 : Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
Source G3 Genes|Genomes|Genetics (2160-1836) (Oxford University Press (OUP)) In Press
DOI 10.1093/g3journal/jkab021
Keyword(s) epigenetics, transcriptome, GxE, transgenic, growth hormone, salmonid
Abstract

Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.

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Christensen Kris A, Le Luyer Jeremy, Chan Michelle T T, Rondeau Eric B, Koop Ben F, Bernatchez Louis, Devlin Robert H Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon. G3 Genes|Genomes|Genetics IN PRESS. Publisher's official version : https://doi.org/10.1093/g3journal/jkab021 , Open Access version : https://archimer.ifremer.fr/doc/00677/78890/