Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon

Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fi...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2017-12, Vol.114 (49), p.12964-12969
Main Authors: Le Luyer, Jérémy, Laporte, Martin, Beacham, Terry D., Kaukinen, Karia H., Withler, Ruth E., Leong, Jong S., Rondeau, Eric B., Koop, Ben F., Bernatchez, Louis
Format: Article
Language:English
Subjects:
Abundance
Biological Sciences
Deoxyribonucleic acid
DNA
DNA methylation
Epigenetics
Fish
Fish stocking
Fisheries
Fitness
Genomes
Hatcheries
Life Sciences
Oncorhynchus kisutch
Reproductive fitness
Rivers
Salmon
Salmonids
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Summary:Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatcheryborn smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1711229114