Epigenetic considerations in aquaculture

Abstract

Epigenetics has attracted considerable attention with respect to its potential value in many areas of agricultural production, particularly under conditions where the environment can be manipulated or natural variation exists. Here we introduce key concepts and definitions of epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, review the current understanding of epigenetics in both fish and shellfish, and propose key areas of aquaculture where epigenetics could be applied. The first key area is environmental manipulation, where the intention is to induce an ‘epigenetic memory’ either within or between generations to produce a desired phenotype. The second key area is epigenetic selection, which, alone or combined with genetic selection, may increase the reliability of producing animals with desired phenotypes. Based on aspects of life history and husbandry practices in aquaculture species, the application of epigenetic knowledge could significantly affect the productivity and sustainability of aquaculture practices. Conversely, clarifying the role of epigenetic mechanisms in aquaculture species may upend traditional assumptions about selection practices. Ultimately, there are still many unanswered questions regarding how epigenetic mechanisms might be leveraged in aquaculture.

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

“…The epigenetic molecular component of phenotypic variability in salmonids is relatively poorly understood but holds promise for translational research relevant to stock enhancement in aquaculture (for recent reviews, see Gavery & Roberts ; Best et al . ).…”

Is Good Fish Culture Management Harming Recovery Efforts in Aquaculture‐Assisted Fisheries?

“…Moghadam et al. () and Gavery and Roberts () suggested that customizing epigenetic modification would improve fish and profits in food fish farming. Their idea has even greater relevance in imperiled‐species culture programs.…”

“…The fish hatchery environment and management practices used to raise fish can produce stable, heritable, nongenetic changes in fish (Salinas and Munch 2012;Evans et al 2014;McGhee and Bell 2014;Shao et al 2014;Jonsson and Jonsson 2016). Moghadam et al (2015) and Gavery and Roberts (2017) suggested that customizing epigenetic modification would improve fish and profits in food fish farming. Their idea has even greater relevance in imperiled-species culture programs.…”

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation?

“…Importantly, they are known to facilitate phenotypic plasticity through genotype-epigenotypeenvironment interactions (Cosseau et al, 2017). In the context of anthropogenic climate change, understanding the specific contributions of genetic and epigenetic information to adaptive potential of populations and the underlying mechanisms are crucial to assess species' evolution in fast-changing and often unstable environments, in particular when applied to ecological and aquaculture challenges (Gavery and Roberts, 2017;Eirin-lopez and Putnam, 2019). For instance, recent studies in environmental epigenetics applied to marine species (e.g., bivalves, fish) have brought the concept of assisted evolution via epigenetically mediated adaptation to light for aquaculture and conservation applications.…”

“…For instance, recent studies in environmental epigenetics applied to marine species (e.g., bivalves, fish) have brought the concept of assisted evolution via epigenetically mediated adaptation to light for aquaculture and conservation applications. The possibility to generate environment-specific phenotypes mediated through heritable epigenetic-based events has been suggested in several species and for a number of traits (e.g., sex ratio, growth, immunity) relevant for the aquaculture industry, even if the precise mechanisms underlying these are poorly described (Gavery and Roberts, 2017;Le Luyer et al, 2017;Panserat et al, 2017;Balasubramanian et al, 2019;Gavery et al, 2019).…”