1
|
Risha KS, Rasal KD, Reang D, Iquebal MA, Sonwane A, Brahmane M, Chaudhari A, Nagpure N. DNA Methylation Profiling in Genetically Selected Clarias magur (Hamilton, 1822) Provides Insights into the Epigenetic Regulation of Growth and Development. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:776-789. [PMID: 39037491 DOI: 10.1007/s10126-024-10346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals.
Collapse
Affiliation(s)
- K Shasti Risha
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India.
| | - Dhalongsaih Reang
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Arvind Sonwane
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Manoj Brahmane
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Aparna Chaudhari
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Naresh Nagpure
- Fish Genetics and Biotechnology, ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| |
Collapse
|
2
|
Tawfik MM, Betancor MB, McMillan S, Norambuena F, Tocher DR, Douglas A, Martin SAM. Modulation of metabolic and immunoregulatory pathways in the gut transcriptome of Atlantic salmon ( Salmo salar L.) after early nutritional programming during first feeding with plant-based diet. Front Immunol 2024; 15:1412821. [PMID: 39015564 PMCID: PMC11249740 DOI: 10.3389/fimmu.2024.1412821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/27/2024] [Indexed: 07/18/2024] Open
Abstract
Introduction Plant-based nutritional programming is the concept of exposing fish at very early life stages to a plant-based diet for a short duration to improve physiological responses when exposed to a similar plant-rich diet at a later developmental stage. The mechanisms of action underlying nutritional programming have not been fully deciphered, and the responses may be controlled at multiple levels. Methods This 22-week study examines gut transcriptional changes after nutritional programming. Triplicate groups of Atlantic salmon were fed with a plant (V) vs. a marine-rich (M, control) diet for 2 weeks (stimulus phase) at the first exogenous feeding. Both stimulus fish groups (M and V fish) were then fed the M diet for 12 weeks (intermediate phase) and lastly fed the V diet (challenge phase) for 6 weeks, generating two dietary regimes (MMV and VMV) across phases. This study used a whole-transcriptome approach to analyse the effects of the V diet at the end of stimulus (short-term effects) and 22 weeks post-first feeding (long-term effects). After the stimulus, due to its developmental stage, the whole intestine was used, whereas, after the challenge, pyloric caeca and middle and distal intestines were examined. Results and discussion At the stimulus end, genes with increased expression in V fish enriched pathways including regulatory epigenetic responses and lipid metabolism, and genes involved in innate immune response were downregulated. In the middle intestine at the end of the challenge, expression levels of genes of lipid, carbohydrate, and energy metabolism were increased in V fish, while M fish revealed increased expression of genes associated with autoimmune and acute adaptive immune response. The distal intestine of V fish showed increased expression of genes associated with immune response and potential immune tolerance. Conversely, the distal intestine of M fish at challenge revealed upregulation of lipid and carbohydrate metabolic pathways, tissue degeneration, and apoptotic responses. The present study demonstrated nutritional programming-associated changes in the intestinal transcriptome, with altered expression of genes involved in both immune responses and different metabolic processes. While there were limited changes in growth between the groups, the results show that there were transcriptional differences, suggesting a programming response, although the mechanism of this response still requires to be fully elucidated.
Collapse
Affiliation(s)
- Marwa Mamdouh Tawfik
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Hydrobiology Department, Veterinary Research Institute, National Research Centre, Giza, Egypt
| | - Mónica B. Betancor
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Stuart McMillan
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | | | - Douglas R. Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, Guangdong, China
| | - Alex Douglas
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Samuel A. M. Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
3
|
Sequence, Expression, and Anti-GCRV Function of the Ferritin from the Grass Carp, Ctenopharyngodon idellus. Int J Mol Sci 2022; 23:ijms23126835. [PMID: 35743279 PMCID: PMC9224801 DOI: 10.3390/ijms23126835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Ferritin possesses an immune function to defend against pathogen infection. To elucidate the immunity-protecting roles of ferritin from Ctenopharyngodon idellus (Ciferritin) against virus infection, the cDNA and promoter sequences of Ciferritin were determined, and the correlations between Ciferrtin expressions and promoter methylation levels were analyzed. In addition, the functional role of Ciferrtin on GCRV (grass carp reovirus) infection was assessed. The full-length cDNA of Ciferritin is 1053 bp, consists of a 531 bp open-reading frame, and encodes 176 amino acids. Ciferritin showed the highest sequence identity with the ferritin middle subunit of Mylopharyngodon piceus (93.56%), followed by the subunits of Megalobrama amblycephala and Sinocyclocheilus rhinocerous. Ciferritin contains a conserved ferritin domain (interval: 10−94 aa), and the caspase recruitment domain (CARD) and Rubrerythrin domain were also predicted. In the spleen and kidney, significantly higher Ciferritin expressions were observed at 6, 12, 24, or 168 h post GCRV infection than those in the PBS injection group (p < 0.05). The Ciferrtin expression level in the progeny of maternal-immunized grass carp was significantly higher than that in the progeny of common grass carp (p < 0.05). Ciferritin promoter methylation level in the progeny from common grass carp was 1.27 ± 0.15, and in the progeny of the maternal-immunized group was 1.00 ± 0.14. In addition, methylation levels of “CpG9” and “CpG10” loci were significantly lower in the progeny of maternal-immunized fish than those in the common group. Except for the “CpG5”, methylation levels of all other detected “CpG” loci negatively correlated with Ciferritin expression levels. Furthermore, the total methylation level of “CpG1−10” negatively correlated with the Ciferritin expressions. The Ciferritin expression level was significantly up-regulated, and the VP7 protein levels were significantly reduced, at 24 h post GCRV infection in the Ciferritin over-expression cells (p < 0.05). The results from the present study provide sequence, epigenetic modification and expression, and anti-GCRV functional information of Ciferritin, which provide a basis for achieving resistance to GCRV in grass carp breeding.
Collapse
|
4
|
Kwasek K, Patula S, Wojno M, Oliaro F, Cabay C, Pinnell LJ. Does Exposure of Broodstock to Dietary Soybean Meal Affect Its Utilization in the Offspring of Zebrafish (Danio rerio)? Animals (Basel) 2022; 12:ani12121475. [PMID: 35739814 PMCID: PMC9219465 DOI: 10.3390/ani12121475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Replacement of fishmeal in fish diets with plant protein has been an ongoing challenge. High-quality plant protein concentrates are widely used since their digestibility can be comparable to fishmeal. However, their price can exceed the cost of marine raw materials. Progress with utilization of lower-quality plant protein sources has been made but a number of concerns must be overcome to maintain acceptable growth rates at high fishmeal substitution levels. Nutritional programming represents a promising approach to offset the negative effects of dietary plant protein through its exposure in early life. We tested an unconventional programming strategy by exposing parental zebrafish to soybean meal diet to improve dietary soybean meal utilization in progeny fish. The study observed a strong trend showing better growth performance between progeny zebrafish fed soybean meal diet that originated from broodstock exposed to soybean meal as opposed to progeny fish fed soybean meal diet that originated from fishmeal diet fed broodstock. However, the study found no changes in the richness, diversity, or composition of gut microbial communities associated with progeny fish from fishmeal or soybean meal fed broodstock. Hence, the mechanism behind nutritional programming does not seem to be associated with modified gut microbiome. Abstract Nutritional programming (NP) is a concept in which early nutritional events alter the physiology of an animal and its response to different dietary regimes later in life. The objective of this study was to determine if NP via broodstock with dietary plant protein (PP) has any effect on the gut microbiome of the progeny fish and whether this modified gut microbiome leads to better utilization of PP diet. The experiment consisted of four different treatments as follows: (1) progeny that received FM diet obtained from fishmeal (FM)-fed broodstock (FMBS-FM, +control); (2) progeny that received PP diet obtained from FM-fed parents (FMBS-PP); (3) progeny that received PP diet obtained from “nutritionally programmed” parents (PPBS-PP; −control); and (4) progeny that received FM diet obtained from “nutritionally programmed” parents (PPBS-FM). Zebrafish was used as a model species. This study found that parental programming seems to have some positive effect on dietary PP utilization in progeny. However, the influence of NP with PP through broodstock on gut microbiota of the offspring fish was not detected.
Collapse
Affiliation(s)
- Karolina Kwasek
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University, 1125 Lincoln Dr. Life Science II, Room 251, Carbondale, IL 62901, USA; (S.P.); (M.W.)
- Correspondence: ; Tel.: +1-618-453-2890
| | - Samuel Patula
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University, 1125 Lincoln Dr. Life Science II, Room 251, Carbondale, IL 62901, USA; (S.P.); (M.W.)
| | - Michal Wojno
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University, 1125 Lincoln Dr. Life Science II, Room 251, Carbondale, IL 62901, USA; (S.P.); (M.W.)
| | - Frank Oliaro
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA; (F.O.); (C.C.)
| | - Chrissy Cabay
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA; (F.O.); (C.C.)
| | - Lee J. Pinnell
- Veterinary Education, Research, and Outreach Program, Texas A&M University, Canyon, TX 79015, USA;
| |
Collapse
|
5
|
Metabolic and molecular signatures of improved growth in Atlantic salmon ( Salmo salar) fed surplus levels of methionine, folic acid, vitamin B 6 and B 12 throughout smoltification. Br J Nutr 2022; 127:1289-1302. [PMID: 34176547 DOI: 10.1017/s0007114521002336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A moderate surplus of the one carbon (1C) nutrients methionine, folic acid, vitamin B6 and B12 above dietary recommendations for Atlantic salmon has shown to improve growth and reduce hepatosomatic index in the on-growing saltwater period when fed throughout smoltification. Metabolic properties and molecular mechanisms determining the improved growth are unexplored. Here, we investigate metabolic and transcriptional signatures in skeletal muscle taken before and after smoltification to acquire deeper insight into pathways and possible nutrient–gene interactions. A control feed (Ctrl) or 1C nutrient surplus feed (1C+) were fed to Atlantic salmon 6 weeks prior to smoltification until 3 months after saltwater transfer. Both metabolic and gene expression signatures revealed significant 1C nutrient-dependent changes already at pre-smolt, but differences intensified when analysing post-smolt muscle. Transcriptional differences revealed lower expression of genes related to translation, growth and amino acid metabolisation in post-smolt muscle when fed additional 1C nutrients. The 1C+ group showed less free amino acid and putrescine levels, and higher methionine and glutathione amounts in muscle. For Ctrl muscle, the overall metabolic profile suggests a lower amino acid utilisation for protein synthesis, and increased methionine metabolisation in polyamine and redox homoeostasis, whereas transcription changes are indicative of compensatory growth regulation at local tissue level. These findings point to fine-tuned nutrient–gene interactions fundamental for improved growth capacity through better amino acid utilisation for protein accretion when salmon was fed additional 1C nutrients throughout smoltification. It also highlights potential nutritional programming strategies on improved post-smolt growth through 1C+ supplementation before and throughout smoltification.
Collapse
|
6
|
Abstract
To date, genomic prediction has been conducted in about 20 aquaculture species, with a preference for intra-family genomic selection (GS). For every trait under GS, the increase in accuracy obtained by genomic estimated breeding values instead of classical pedigree-based estimation of breeding values is very important in aquaculture species ranging from 15% to 89% for growth traits, and from 0% to 567% for disease resistance. Although the implementation of GS in aquaculture is of little additional investment in breeding programs already implementing sib testing on pedigree, the deployment of GS remains sparse, but could be boosted by adaptation of cost-effective imputation from low-density panels. Moreover, GS could help to anticipate the effect of climate change by improving sustainability-related traits such as production yield (e.g., carcass or fillet yields), feed efficiency or disease resistance, and by improving resistance to environmental variation (tolerance to temperature or salinity variation). This chapter synthesized the literature in applications of GS in finfish, crustaceans and molluscs aquaculture in the present and future breeding programs.
Collapse
Affiliation(s)
- François Allal
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France.
| | - Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| |
Collapse
|
7
|
Patula S, Wojno M, Pinnell LJ, Oliaro F, Cabay C, Molinari GS, Kwasek K. Nutritional Programming with Dietary Soybean Meal and Its Effect on Gut Microbiota in Zebrafish ( Danio rerio). Zebrafish 2021; 18:125-138. [PMID: 33761297 DOI: 10.1089/zeb.2020.1952] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nutritional programming (NP) is considered a promising approach that can counteract the negative effects of dietary plant protein (PP) by introducing PP to fish in the early developmental stages. Therefore the objective of our study was to assess the effect of NP on PP utilization and the gut microbiome in zebrafish Danio rerio. The study included four treatment groups: (1) a positive control group that received a fishmeal (FM) diet throughout the entire trial (+ control); (2) a negative control group that received PP diet throughout the entire trial (- control); (3) an NP group that received dietary PP during the larval stage followed by FM-based diet during the juvenile stage and PP diet again during a PP challenge in the grow-out phase (NP-PP); and (4) an FM-group that received FM-based diet during the larval and juvenile stages and was challenged with a PP diet during the grow-out phase (NP-FM). During the PP challenge, the NP-PP group achieved the highest weight gain compared to the (-) control and NP-FM groups. The relative abundance of certain phyla such as Chloroflexi, Planctomycetes, and Bacteroidetes presented higher values in some groups at early juvenile stage. The fish gut microbiome also presented differences throughout the study.
Collapse
Affiliation(s)
- Samuel Patula
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Michal Wojno
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Lee J Pinnell
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois, USA
| | - Frank Oliaro
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois, USA
| | - Chrissy Cabay
- A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, Illinois, USA
| | - Giovanni S Molinari
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| | - Karolina Kwasek
- Center for Fisheries, Aquaculture, and Aquatic Sciences, School of Biological Sciences, Southern Illinois University, Carbondale, Illinois, USA
| |
Collapse
|
8
|
Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout ( Oncorhynchus mykiss) Breeding Strains by Using Next-Generation Sequencing. Genes (Basel) 2020; 11:genes11080841. [PMID: 32722051 PMCID: PMC7464081 DOI: 10.3390/genes11080841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 11/24/2022] Open
Abstract
Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (Oncorhynchus mykiss), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.
Collapse
|
9
|
Molinari GS, McCracken VJ, Wojno M, Rimoldi S, Terova G, Kwasek K. Can intestinal absorption of dietary protein be improved through early exposure to plant-based diet? PLoS One 2020; 15:e0228758. [PMID: 32497052 PMCID: PMC7272038 DOI: 10.1371/journal.pone.0228758] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Nutritional Programming (NP) has been studied as a means of mitigating the negative effects of dietary plant protein (PP), but the optimal timing and mechanism behind NP are still unknown. The objectives of this study were: 1) To determine whether zebrafish (Danio rerio) can be programmed to soybean meal (SBM) through early feeding and broodstock exposure to improve SBM utilization; 2) To determine if NP in zebrafish affects expression of genes associated with intestinal nutrient uptake; 3) To determine if early stage NP and/or broodstock affects gene expression associated with intestinal inflammation or any morphological changes in the intestinal tract that might improve dietary SBM utilization. Two broodstocks were used to form the six experimental groups. One broodstock group received fishmeal (FM) diet (FMBS), while the other was fed ("programmed with") SBM diet (PPBS). The first ((+) Control) and the second group ((-) Control) received FM and SBM diet for the entire study, respectively, and were progeny of FMBS. The last four groups consisted of a non-programmed (FMBS-X-PP and PPBS-X-PP) and a programmed group (FMBS-NP-PP and PPBS-NP-PP) from each of the broodstocks. The programming occurred through feeding with SBM diet during 13-23 dph. The non-control groups underwent a PP-Challenge, receiving SBM diet during 36-60 dph. During the PP-Challenge, both PPBS groups experienced significantly lower weight gains than the (+) Control group. NP in early life stages significantly increased the expression of PepT1 in PPBS-NP-PP, compared to PPBS-X-PP. NP also tended to increase the expression of fabp2 in the programmed vs. non-programmed groups of both broodstocks. The highest distal villus length-to-width ratio was observed in the dual-programmed group, suggesting an increase in surface area for nutrient absorption within the intestine. The results of this study suggest that NP during early life stages may increase intestinal absorption of nutrients from PP-based feeds.
Collapse
Affiliation(s)
- Giovanni S. Molinari
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University, Carbondale, Illinois, United States of America
| | - Vance J. McCracken
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
| | - Michal Wojno
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University, Carbondale, Illinois, United States of America
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Karolina Kwasek
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Southern Illinois University, Carbondale, Illinois, United States of America
- * E-mail:
| |
Collapse
|
10
|
Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
Collapse
Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| |
Collapse
|
11
|
Piferrer F, Anastasiadi D, Valdivieso A, Sánchez-Baizán N, Moraleda-Prados J, Ribas L. The Model of the Conserved Epigenetic Regulation of Sex. Front Genet 2019; 10:857. [PMID: 31616469 PMCID: PMC6775248 DOI: 10.3389/fgene.2019.00857] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022] Open
Abstract
Epigenetics integrates genomic and environmental information to produce a given phenotype. Here, the model of Conserved Epigenetic Regulation of Sex (CERS) is discussed. This model is based on our knowledge on genes involved in sexual development and on epigenetic regulation of gene expression activation and silencing. This model was recently postulated to be applied to the sexual development of fish, and it states that epigenetic and gene expression patterns are more associated with the development of a particular gonadal phenotype, e.g., testis differentiation, rather than with the intrinsic or extrinsic causes that lead to the development of this phenotype. This requires the existence of genes with different epigenetic modifications, for example, changes in DNA methylation levels associated with the development of a particular sex. Focusing on DNA methylation, the identification of CpGs, the methylation of which is linked to sex, constitutes the basis for the identification of Essential Epigenetic Marks (EEM). EEMs are defined as the number and identity of informative epigenetic marks that are strictly necessary, albeit perhaps not sufficient, to bring about a specific, measurable, phenotype of interest. Here, we provide a summary of the genes where DNA methylation has been investigated so far, focusing on fish. We found that cyp19a1a and dmrt1, two key genes for ovary and testis development, respectively, consistently show an inverse relationship between their DNA methylation and expression levels, thus following CERS predictions. However, in foxl2a, a pro-female gene, and amh, a pro-male gene, such relationship is not clear. The available data of other genes related to sexual development such as sox9, gsdf, and amhr2 are also discussed. Next, we discuss the use of CERS to make testable predictions of how sex is epigenetically regulated and to better understand sexual development, as well as the use of EEMs as tools for the diagnosis and prognosis of sex. We argue that CERS can aid in focusing research on the epigenetic regulation of sexual development not only in fish but also in vertebrates in general, particularly in reptiles with temperature sex-determination, and can be the basis for possible practical applications including sex control in aquaculture and also in conservation biology.
Collapse
Affiliation(s)
- Francesc Piferrer
- Institut de Ciències del Mar (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
12
|
Podgorniak T, Brockmann S, Konstantinidis I, Fernandes JMO. Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication. Epigenetics 2019; 14:818-836. [PMID: 31131688 PMCID: PMC6597363 DOI: 10.1080/15592294.2019.1618164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/02/2019] [Accepted: 05/04/2019] [Indexed: 01/14/2023] Open
Abstract
Growth is a complex trait whose variability within a population cannot be explained solely by genetic variation. Epigenetic regulation is often suggested as an important factor shaping the phenotype, but its association with growth can be highly context- and species-dependent. Nevertheless, the mechanisms involved in epigenetic regulation of growth in fish are poorly understood. We have used reduced representation bisulphite sequencing to determine the genome-wide CpG methylation patterns in male and female Nile tilapia of different sizes but at the same early stage of domestication. The average CpG methylation level in the reduced genome representation was 63% across groups but many sites displayed group-specific methylation patterns. The number of differentially methylated (DM) CpGs was much higher when the interaction between sex and weight was included rather than when these factors were considered separately. There were 1128 DM CpGs between large and small females and 970 DM CpGs between large and small males. We have found many growth-related genes associated with DM CpGs, namely map3k5 and akt3 in females and gadd45g and ppargc1a in males. Only 5% of CpG locations associated with growth were common to both sexes. In particular, the autophagy-related gene atg14 displayed a high association of methylation with growth exclusively in males. The sexually dimorphic association between atg14 methylation and growth may uncover novel metabolic mechanisms at play during mouth brooding in Nile tilapia females. Taken together, our data suggest that epigenetic regulation of growth in Nile tilapia involves different gene networks in males and females.
Collapse
Affiliation(s)
- Tomasz Podgorniak
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Sven Brockmann
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Ioannis Konstantinidis
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jorge M. O. Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| |
Collapse
|
13
|
Anastasiadi D, Vandeputte M, Sánchez-Baizán N, Allal F, Piferrer F. Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination. Epigenetics 2018; 13:988-1011. [PMID: 30265213 PMCID: PMC6284782 DOI: 10.1080/15592294.2018.1529504] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/10/2018] [Accepted: 09/22/2018] [Indexed: 12/13/2022] Open
Abstract
The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between cyp19a1a methylation and expression is relevant to the epigenetic regulation of vertebrate sex, and we report the evidence of such relationship only below a methylation threshold, ~ 80%, and that it was sex-specific: negatively correlated in females but positively correlated in males. From parents to offspring, the methylation in gonads was midway between oocytes and sperm, with bias towards oocytes for amh-r2, er-β2, fsh-r and cyp19a1a. In contrast, dmrt1 levels resembled those of sperm. The methylation of individual CpGs from foxl2, er-β2 and nr3c1 were conserved from parents to offspring, whereas those of cyp19a1a, dmrt1 and amh-r2 were affected by temperature. Utilizing a machine-learning procedure based on the methylation levels of a selected set of CpGs, we present the first, to our knowledge, system based on epigenetic marks capable of predicting sex in an animal with ~ 90% accuracy and discuss possible applications.
Collapse
Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Marc Vandeputte
- MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD, Palavas-les-Flots, France
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Núria Sánchez-Baizán
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD, Palavas-les-Flots, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| |
Collapse
|
14
|
Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
Collapse
|
15
|
Bach A, Aris A, Guasch I. Consequences of supplying methyl donors during pregnancy on the methylome of the offspring from lactating and non-lactating dairy cattle. PLoS One 2017; 12:e0189581. [PMID: 29228040 PMCID: PMC5724855 DOI: 10.1371/journal.pone.0189581] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 11/29/2017] [Indexed: 12/02/2022] Open
Abstract
The aim of this study was to evaluate the potential effects of methyl donor supplementation of pregnant animals in the presence or absence of a concomitant lactation on the methylome of the offspring. Twenty Holstein cows, 10 nulliparous (non-lactating while pregnant) and 10 multiparous (lactating while pregnant) were blocked by parity and randomly assigned to an i.m. weekly injections of a placebo (CTRL) or a solution containing methyl donors (MET). After calving, 5 calves randomly selected from each treatment (two born to non-lactating and three to lactating dams) were blood-sampled to determine their full methylome. There were more than 2,000 CpG differentially methylated between calves born to CTRL and those born to MET, and also between calves born to lactating and non-lactating dams. Most of the differences affected genes involved in immune function, cell growth regulation and differentiation, kinase activity, and ion channeling. We conclude that the coexistence of pregnancy and lactation affects the methylome of the offspring, and that supplementation of methyl donors early in gestation has also consequences on the methylome.
Collapse
Affiliation(s)
- Alex Bach
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Department of Ruminant Production, IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Caldes de Montbui, Spain
- * E-mail:
| | - Anna Aris
- Department of Ruminant Production, IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Caldes de Montbui, Spain
| | | |
Collapse
|
16
|
Gavery MR, Roberts SB. Epigenetic considerations in aquaculture. PeerJ 2017; 5:e4147. [PMID: 29230373 PMCID: PMC5723431 DOI: 10.7717/peerj.4147] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
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.
Collapse
Affiliation(s)
- Mackenzie R Gavery
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Steven B Roberts
- School of Aquatic & Fishery Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
17
|
García-Fernández P, García-Souto D, Almansa E, Morán P, Gestal C. Epigenetic DNA Methylation Mediating Octopus vulgaris Early Development: Effect of Essential Fatty Acids Enriched Diet. Front Physiol 2017; 8:292. [PMID: 28559849 PMCID: PMC5432645 DOI: 10.3389/fphys.2017.00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022] Open
Abstract
The common octopus, Octopus vulgaris, is a good candidate for aquaculture but a sustainable production is still unviable due to an almost total mortality during the paralarvae stage. DNA methylation regulates gene expression in the eukaryotic genome, and has been shown to exhibit plasticity throughout O. vulgaris life cycle, changing profiles from paralarvae to adult stages. This pattern of methylation could be sensitive to small alterations in nutritional and environmental conditions during the species early development, thus impacting on its health, growth and survival. In this sense, a full understanding of the epigenetic mechanisms operating during O. vulgaris development would contribute to optimizing the culture conditions for this species. Paralarvae of O. vulgaris were cultured over 28 days post-hatching (dph) using two different Artemia sp. based diets: control and a long chain polyunsaturated fatty acids (LC-PUFA) enriched diet. The effect of the diets on the paralarvae DNA global methylation was analyzed by Methyl-Sensitive Amplification Polymorphism (MSAP) and global 5-methylcytosine enzyme-linked immunosorbent assay (ELISA) approaches. The analysis of different methylation states over the time revealed a global demethylation phenomena occurring along O. vulgaris early development being directly driven by the age of the paralarvae. A gradual decline in methylated loci (hemimethylated, internal cytosine methylated, and hypermethylated) parallel to a progressive gain in non-methylated (NMT) loci toward the later sampling points was verified regardless of the diet provided and demonstrate a pre-established and well-defined demethylation program during its early development, involving a 20% of the MSAP loci. In addition, a differential behavior between diets was also observed at 20 dph, with a LC-PUFA supplementation effect over the methylation profiles. The present results show significant differences on the paralarvae methylation profiles during its development and a diet effect on these changes. It is characterized by a process of demethylation of the genome at the paralarvae stage and the influence of diet to favor this methylation loss.
Collapse
Affiliation(s)
- Pablo García-Fernández
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (Consejo Superior de Investigaciones Científicas)Vigo, Spain.,Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Danie García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Eduardo Almansa
- Instituto Español de Oceanografía, Centro Oceanográfico de CanariasTenerife, Spain
| | - Paloma Morán
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de VigoVigo, Spain
| | - Camino Gestal
- Aquatic Molecular Pathobiology Group, Instituto de Investigaciones Marinas (Consejo Superior de Investigaciones Científicas)Vigo, Spain
| |
Collapse
|
18
|
Shiel BP, Hall NE, Cooke IR, Robinson NA, Strugnell JM. Epipodial Tentacle Gene Expression and Predetermined Resilience to Summer Mortality in the Commercially Important Greenlip Abalone, Haliotis laevigata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:191-205. [PMID: 28349286 PMCID: PMC5405107 DOI: 10.1007/s10126-017-9742-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/06/2017] [Indexed: 05/05/2023]
Abstract
"Summer mortality" is a phenomenon that occurs during warm water temperature spikes that results in the mass mortality of many ecologically and economically important mollusks such as abalone. This study aimed to determine whether the baseline gene expression of abalone before a laboratory-induced summer mortality event was associated with resilience to summer mortality. Tentacle transcriptomes of 35 greenlip abalone (Haliotis laevigata) were sequenced prior to the animals being exposed to an increase in water temperature-simulating conditions which have previously resulted in summer mortality. Abalone derived from three source locations with different environmental conditions were categorized as susceptible or resistant to summer mortality depending on whether they died or survived after the water temperature was increased. We detected two genes showing significantly higher expression in resilient abalone relative to susceptible abalone prior to the laboratory-induced summer mortality event. One of these genes was annotated through the NCBI non-redundant protein database using BLASTX to an anemone (Exaiptasia pallida) Transposon Ty3-G Gag Pol polyprotein. Distinct gene expression signatures were also found between resilient and susceptible abalone depending on the population origin, which may suggest divergence in local adaptation mechanisms for resilience. Many of these genes have been suggested to be involved in antioxidant and immune-related functions. The identification of these genes and their functional roles have enhanced our understanding of processes that may contribute to summer mortality in abalone. Our study supports the hypothesis that prestress gene expression signatures are indicative of the likelihood of summer mortality.
Collapse
Affiliation(s)
- Brett P Shiel
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia.
| | - Nathan E Hall
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia
- Life Sciences Computation Centre, VLSCI, Parkville, VIC, Australia
- Department of Molecular and Cell Biology, James Cook University, Townsville, Australia
| | - Ira R Cooke
- Life Sciences Computation Centre, VLSCI, Parkville, VIC, Australia
- Department of Molecular and Cell Biology, James Cook University, Townsville, Australia
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia
| | - Nicholas A Robinson
- Nofima, P.O. Box 210, 1431, Ås, Norway
- Sustainable Aquaculture Laboratory-Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Kingsbury Drive, Melbourne, VIC, 3086, Australia
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| |
Collapse
|
19
|
Polakof S, Panserat S. How Tom Moon's research highlighted the question of glucose tolerance in carnivorous fish. Comp Biochem Physiol B Biochem Mol Biol 2016; 199:43-49. [DOI: 10.1016/j.cbpb.2015.11.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/30/2015] [Accepted: 11/01/2015] [Indexed: 11/15/2022]
|
20
|
González-Recio O, Toro MA, Bach A. Past, present, and future of epigenetics applied to livestock breeding. Front Genet 2015; 6:305. [PMID: 26442117 PMCID: PMC4585102 DOI: 10.3389/fgene.2015.00305] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/12/2015] [Indexed: 11/27/2022] Open
Abstract
This article reviews the concept of Lamarckian inheritance and the use of the term epigenetics in the field of animal genetics. Epigenetics was first coined by Conrad Hal Waddington (1905–1975), who derived the term from the Aristotelian word epigenesis. There exists some controversy around the word epigenetics and its broad definition. It includes any modification of the expression of genes due to factors other than mutation in the DNA sequence. This involves DNA methylation, post-translational modification of histones, but also linked to regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. There is little evidence of the existence of transgenerational epigenetic inheritance in mammals, which may commonly be confounded with environmental forces acting simultaneously on an individual, her developing fetus and the germ cell lines of the latter, although it could have an important role in the cellular energetic status of cells. Finally, we review some of the scarce literature on the use of epigenetics in animal breeding programs.
Collapse
Affiliation(s)
- Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid Spain
| | - Miguel A Toro
- Departamento de Producción Animal, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid Madrid, Spain
| | - Alex Bach
- Department of Ruminant Production, Institució Catalana de Recerca i Estudis Avançats - Institut de Recerca i Tecnologia Agroalimentàries, Caldes de Montbui Spain
| |
Collapse
|