Venney Clare J, Bouchard Raphaël, April Julien, Normandeau Eric, Lecomte Laurie, Côté Guillaume, Bernatchez Louis
Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada.
Département de Biologie, Université Laval, Québec, Quebec, Canada.
Mol Ecol Resour. 2023 Feb 9. doi: 10.1111/1755-0998.13766.
Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec, Canada. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F offspring from four groups (pure wild, pure hatchery origin and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F . There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.
即使在没有基因变化的情况下，鲑鱼孵化场的圈养养殖在一代之内也会对鱼类的表型和适应性产生相当大的影响。孵化场诱导DNA甲基化变化的证据越来越多，不过这些影响的性别特异性、它们在产卵前的持续性以及传递给后代的可能性等问题仍然存在。在此，我们对16条来自孵化场和16条来自野生的大西洋鲑（Salmo salar）的鳍组织进行了全基因组甲基化测序，这些鲑鱼回到加拿大魁北克省里穆斯基河产卵。通过甲基化分析，我们识别出两组孵化场养殖的鲑鱼，其中一组在表观遗传学上与野生鱼类相似，这表明补充养殖的努力或许能够将孵化场养殖的表观遗传效应降至最低。我们发现孵化场养殖存在相当大的性别特异性效应，在雄性和雌性中受影响的基因组区域很少。我们还分析了来自四组（纯野生、纯孵化场来源以及正反交杂种）的32个F1代后代的甲基化组。我们发现，尽管遗传模式似乎很复杂，涉及非加性效应，但亲本孵化场养殖引起的表观遗传变化在F1代后代中很少持续存在。我们的结果表明，孵化场养殖的表观遗传效应在F1代中可能最小。与孵化场养殖相关的表观遗传遗传可能也最小，表观遗传变化会迅速消失。然而，由于性别特异性和非加性遗传模式，圈养养殖引起的甲基化变化相当复杂，该领域将受益于进一步研究，以在保护工作中尽量减少圈养养殖的表观遗传效应。
