FN Archimer Export Format
PT J
TI Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon
BT 
AF Christensen, Kris A
   LE LUYER, Jeremy
   Chan, Michelle T T
   Rondeau, Eric B
   Koop, Ben F
   Bernatchez, Louis
   Devlin, Robert H
AS 1:1,2;2:3;3:1,4;4:1,2;5:2;6:3;7:1;
FF 1:;2:;3:;4:;5:;6:;7:;
C1 Fisheries and Oceans Canada, West Vancouver, BC, Canada V7V 1N6
   Department of Biology, University of Victoria, Victoria, BC, Canada V8P 5C2
   Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada G1V OA6
   Molecular Biology and Biochemistry Department, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
C2 MPO, CANADA
   UNIV VICTORIA, CANADA
   UNIV LAVAL, CANADA
   UNIV SIMON FRASER, CANADA
IN DOAJ
IF 3.542
TC 1
UR https://archimer.ifremer.fr/doc/00677/78890/81188.pdf
LA English
DT Article
DE ;epigenetics;transcriptome;GxE;transgenic;growth hormone;salmonid
AB 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. 
PY 2021
PD FEB
SO G3-genes Genomes Genetics
SN 2160-1836
PU Oxford University Press (OUP)
VL 11
IS 2
UT 000651850600049
DI 10.1093/g3journal/jkab021
ID 78890
ER

EF