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Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration

ABSTRACT: Abstract Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize human‐induced genomic variation, human‐induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modifications. Major questions remain pertaining to how much epigenomic variation arises from environmental heterogeneity, whether this variation can persist throughout life, and whether it can be transmitted across generations. We performed whole genome bisulfite sequencing (WGBS) on the sperm of genetically indistinguishable hatchery and wild‐born migrating adults of Coho salmon (Oncorhynchus kisutch) from two geographically distant rivers at different epigenome scales. Our results showed that coupling WGBS with fine‐scale analyses (local and chromosomal) allows the detection of parallel early‐life hatchery‐induced epimarks that differentiate wild from hatchery‐reared salmon. Four chromosomes and 183 differentially methylated regions (DMRs) displayed a significant signal of methylation differentiation between hatchery and wild‐born Coho salmon. Moreover, those early‐life epimarks persisted in germ line cells despite about 1.5 year spent in the ocean following release from hatchery, opening the possibility for transgenerational inheritance. Our results strengthen the hypothesis that epigenomic modifications environmentally induced during early‐life development persist in germ cells of adults until reproduction, which could potentially impact their fitness.

SUBMITTER: Leitwein M

PROVIDER: S-EPMC8549618 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Enrichment of rearing environment with natural elements has been suggested to improve the welfare and post-release survival of cultured fish. We studied the combined effects of shelter structures, periodical water flow and water level changes on pre- and post-release performance of critically endangered landlocked Atlantic salmon (Salmo salar m. sebago). Relative to standard (plain) rearing tanks, provision of enrichment improved fish condition factor and survival during the first year of rearing when most mortality was attributable to parasitic and bacterial infections. The consequent higher density in enriched tanks probably induced greater growth variation and more dorsal fin damages than found in fish of standard tanks. Possibly this was partly due to the applied changes in water level. Experimentally determined smolt migration tendency at age 3 did not differ, on average, between the rearing groups, but enriched-reared fish showed clearly less variation in total movement activity than standard-reared fish. Experimental angling in earthen ponds did not suggest divergent vulnerability between the differentially reared fish at age 3, but decreased condition during the preceding growth season increased vulnerability to fishing. Based on long-term post-stocking tag returns in large-lake fisheries, fish length at release but not rearing method affected the capture rates of fish released at age 2. When released at age 3 the fish grown in enriched environment had a higher risk to be captured with stationary gears and earlier by hook and line gears compared to standard-reared conspecifics. Earlier time of maximal smolt migration activity was associated with an increased risk of being captured. We suggest that environmental enrichment may modulate growth- and behavior-related qualities that indirectly increased the vulnerability to fishing in natural conditions but not in experimental setting. The favorable effects of enrichment on early survival encourages adopting enriched rearing practices in supportive breeding of landlocked salmon.

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Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration

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