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Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
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Holland OJ, Toomey M, Ahrens C, Hoffmann AA, Croft LJ, Sherman CDH, Miller AD. Whole genome resequencing reveals signatures of rapid selection in a virus affected commercial fishery. Mol Ecol 2022; 31:3658-3671. [PMID: 35555938 PMCID: PMC9327721 DOI: 10.1111/mec.16499] [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: 09/29/2021] [Revised: 04/11/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Infectious diseases are recognized as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australian blacklip abalone (Haliotis rubra) following a major population crash associated with an infectious disease. Genome scans on H. rubra were performed using pooled whole genome resequencing data from commercial fishing stocks varying in historical exposure to haliotid herpesvirus‐1 (HaHV‐1). Approximately 25,000 single nucleotide polymorphism loci associated with virus exposure were identified, many of which mapped to genes known to contribute to HaHV‐1 immunity in the New Zealand pāua (Haliotis iris) and herpesvirus response pathways in haliotids and other animal systems. These findings indicate genetic changes across a single generation in H. rubra fishing stocks decimated by HaHV‐1, with stock recovery potentially determined by rapid evolutionary changes leading to virus resistance. This is a novel example of apparently rapid adaptation in natural populations of a nonmodel marine organism, highlighting the pace at which selection can potentially act to counter disease in wildlife communities.
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Affiliation(s)
- Owen J Holland
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Madeline Toomey
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Collin Ahrens
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.,Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, Royal Botanic Garden, Sydney, NSW, 2000, Australia
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Laurence J Croft
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
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The Role of Anti-Viral Effector Molecules in Mollusc Hemolymph. Biomolecules 2022; 12:biom12030345. [PMID: 35327536 PMCID: PMC8945852 DOI: 10.3390/biom12030345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/06/2022] [Accepted: 02/21/2022] [Indexed: 02/04/2023] Open
Abstract
Molluscs are major contributors to the international and Australian aquaculture industries, however, their immune systems remain poorly understood due to limited access to draft genomes and evidence of divergences from model organisms. As invertebrates, molluscs lack adaptive immune systems or ‘memory’, and rely solely on innate immunity for antimicrobial defence. Hemolymph, the circulatory fluid of invertebrates, contains hemocytes which secrete effector molecules with immune regulatory functions. Interactions between mollusc effector molecules and bacterial and fungal pathogens have been well documented, however, there is limited knowledge of their roles against viruses, which cause high mortality and significant production losses in these species. Of the major effector molecules, only the direct acting protein dicer-2 and the antimicrobial peptides (AMPs) hemocyanin and myticin-C have shown antiviral activity. A better understanding of these effector molecules may allow for the manipulation of mollusc proteomes to enhance antiviral and overall antimicrobial defence to prevent future outbreaks and minimize economic outbreaks. Moreover, effector molecule research may yield the description and production of novel antimicrobial treatments for a broad host range of animal species.
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Rosani U, Abbadi M, Green T, Bai CM, Turolla E, Arcangeli G, Wegner KM, Venier P. Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1. BMC Genomics 2020; 21:620. [PMID: 32912133 PMCID: PMC7488030 DOI: 10.1186/s12864-020-07026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Background Since 2008, the aquaculture production of Crassostrea gigas was heavily affected by mass mortalities associated to Ostreid herpesvirus 1 (OsHV-1) microvariants worldwide. Transcriptomic studies revealed the major antiviral pathways of the oyster immune response while other findings suggested that also small non-coding RNAs (sncRNA) such as microRNAs might act as key regulators of the oyster response against OsHV-1. To explore the explicit connection between small non-coding and protein-coding transcripts, we performed paired whole transcriptome analysis of sncRNA and messenger RNA (mRNA) in six oysters selected for different intensities of OsHV-1 infection. Results The mRNA profiles of the naturally infected oysters were mostly governed by the transcriptional activity of OsHV-1, with several differentially expressed genes mapping to the interferon, toll, apoptosis, and pro-PO pathways. In contrast, miRNA profiles suggested more complex regulatory mechanisms, with 15 differentially expressed miRNAs (DE-miRNA) pointing to a possible modulation of the host response during OsHV-1 infection. We predicted 68 interactions between DE-miRNAs and oyster 3′-UTRs, but only few of them involved antiviral genes. The sncRNA reads assigned to OsHV-1 rather resembled mRNA degradation products, suggesting the absence of genuine viral miRNAs. Conclusions We provided data describing the miRNAome during OsHV-1 infection in C. gigas. This information can be used to understand the role of miRNAs in healthy and diseased oysters, to identify new targets for functional studies and, eventually to disentangle cause and effect relationships during viral infections in marine mollusks.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 35121, Padova, Italy. .,Coastal Ecology Section, AWI - Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, 25992, List, Germany.
| | - Miriam Abbadi
- Istituto Zooprofilattico delle Venezie, Legnaro, Italy
| | - Timothy Green
- Centre for Shellfish Research & Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, BC, V9R 5S5, Canada
| | - Chang-Ming Bai
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | | | | | - K Mathias Wegner
- Coastal Ecology Section, AWI - Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, 25992, List, Germany
| | - Paola Venier
- Department of Biology, University of Padova, 35121, Padova, Italy.
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Abalone Viral Ganglioneuritis. Pathogens 2020; 9:pathogens9090720. [PMID: 32882932 PMCID: PMC7558354 DOI: 10.3390/pathogens9090720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/23/2020] [Accepted: 08/29/2020] [Indexed: 11/17/2022] Open
Abstract
Abalone viral ganglioneuritis (AVG), caused by Haliotid herpesvirus-1 (HaHV-1; previously called abalone herpesvirus), is a disease that has been responsible for extensive mortalities in wild and farmed abalone and has caused significant economic losses in Asia and Australia since outbreaks occurred in the early 2000s. Researchers from Taiwan, China, and Australia have conducted numerous studies encompassing HaHV-1 genome sequencing, development of molecular diagnostic tests, and evaluation of the susceptibility of various abalone species to AVG as well as studies of gene expression in abalone upon virus infection. This review presents a timeline of the most significant research findings on AVG and HaHV-1 as well as potential future research avenues to further understand this disease in order to develop better management strategies.
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