Environmental induced methylation changes associated with seawater adaptation in brown trout

Current Advances in Functional Genomics in Aquaculture

“…As for migration traits, Baerwald et al [212] identiied several DMRs between migratory smolts and resident rainbow trout juveniles in which most DMRs encoded proteins associated with migration showing that epigenetic variations were linked to migration traits in anadromous ish. Their indings were in concordance with Morán et al [17] who found genome-wide methylation diferences between hatchery reared and seawater brown trout. In addition, Morán et al [17] showed that salt diets used during the seawater phase triggered genome-wide methylation changes when administered in freshwater reared trout indicating that DNA methylation could play a vital role in enabling anadromous ish acclimatize to seawater after transfer from freshwater.…”

“…Their indings were in concordance with Morán et al [17] who found genome-wide methylation diferences between hatchery reared and seawater brown trout. In addition, Morán et al [17] showed that salt diets used during the seawater phase triggered genome-wide methylation changes when administered in freshwater reared trout indicating that DNA methylation could play a vital role in enabling anadromous ish acclimatize to seawater after transfer from freshwater. DNA methylation and histone modiication have also been associated with adaptation changes induced by adverse environmental conditions as shown in Nile tilapia exposed to industrial pollutions [231], eels to cadmium exposure [232], sea urchin (G. crenularis) exposure to perluoroctane sulfonate (PFOS) [216] and the three-spine stickleback (G. aculeatus) hexabromocyclododecane (HBCD) exposed to 17-β oestradiol (E 2 ) and 5-aza 2′ deoxycytidine (5AdC) pollutants [233].…”

“…As a result of these advances, epigenetics studies in aquaculture have tremendously increased in the last decades with the view to identifying biological markers relevant for improving the production of farmed aquatic organisms. Technologies used for epigenetics analyses in aquaculture include (i) RNA-seq in Medaka [207] and Nile tilapia [208]; (ii) genome-wide methylated DNA immunoprecipitation sequencing (MeDIP-seq) in Nile tilapia [209] and Medaka [207]; (iii) bisulite sequencing (BS-seq) in smooth tongue sole (Cynoglossus semilaevis) [210,211], rainbow trout [212] and Nile tilapia [208]; (iv) genetic linkage map analysis using simple sequence length polymorphisms (SSLPs) in medaka [213,214]; (v) methylation sensitivity ampliied polymorphism (MSAP) in Atlantic salmon [18], grass carp [215], brown trout [17], sea urchin (Glyptocidaris crenularis) [216] and sea cucumber (Apostichopus japonicas) [217]; (vi) 5-methylcytosine immunolocation in sea lamprey (Petromyzon marinus) [218]; (vii) restriction endonuclease hydrolysis of DNA using methylation enzymes in Zebraish [219] and (viii) bisulite sequencing PCR in Paciic Oyster (Crassostrea gigas) [220] and grass carp [221]. As shown in Table 3, epigenetics studies carried out this far include studies on reproduction, growth and adaptation traits.…”

“…And as shown from recent studies, their applications in aquaculture have accelerated our ability to identify emerging pathogens [9], monitor the microbiomes of diferent aquatic environments [10], develop nutritional diets with less side efects [11,12] and understand the cellular networks that regulate diferent biological processes in aquatic organisms [13][14][15]. It is evident from studies carried out this far that an integrated use of different omics technologies is bound to improve our production systems in aquaculture [10,12,[16][17][18]. Hence, this chapter provides an overview of diferent omics technologies currently used in aquaculture mainly focusing on their overall contribution to transforming genomics studies into functional applications.…”

An integrated transcriptomic and comparative genomic analysis of differential gene expression in Arctic charr (Salvelinus alpinus) following seawater exposure

“…Because the gene sets that affect hyper-and hypo-osmoregulation are different, changes in methylation states should be anticipated when transcription is compared between freshwater-and seawaterexposed fish. Observations from other species support these findings: seawater-induced changes in methylation states have been observed in brown trout (Morán et al, 2013), and transcription of the betain-homocysteine S-methyltransferase gene in ayu (Plecoglossus altivelis) gill is reduced after transfer from freshwater to brackish water (Lu et al, 2010). Thus, changes in methylation states are likely to be part of the physiological transition to seawater in anadromous fishes.…”