What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?
Abstract
:Simple Summary
Abstract
1. Introduction
2. Conventional Disease Control Methods
3. Breeding for Disease Resistance in Fish
3.1. Conventional Selection
3.2. Candidate Genes and Marker Assisted Selection
AFLP | Amplified Fragment Length Polymorphisms | Restriction enzymes are used for genomic DNA digestion. A subset of the restriction fragments is selected for amplification by primers complementary to the ligation adaptor sequence, the restriction site sequence, and a few nucleotides inside the restriction site fragments. The markers are a cost-effective alternative in species for which economic resources are limited. |
RAPD | Random Amplified Polymorphic DNA | The genome is amplified using several arbitrary short primers (10–12 nucleotides). AFLP markers are usually preferred to RAPD because of their greater reproducibility. |
RFLP | Restriction Fragment Length Polymorphic DNA | Genomic DNA is digested by restriction enzymes; the fragments separate on agarose gel and create different patterns. The markers are poorly polymorphic, however, which is a major drawback. |
SSR/STR/VNTR | Microsatellite Repeats | Specific sequences of DNA containing tandem repeats. The number of repeats differs for alleles at a specific locus; a specific set of primers is used in simplex or multiplex PCR for loci amplification. These markers are commonly used because of their high polymorphic information content and their wide distribution throughout the genome. |
ESTs | Expressed Sequence Tags | ESTs derived from c-DNA libraries, constructed using mRNA expressed in tissues. They are useful tools for marker development in species where the full genome is not yet available. |
SNP | Single Nucleotide Polymorphism | DNA sequence variations at a single nucleotide level are used as genetic markers. They are the most frequent polymorphism in any organism, adaptable to automation, and reveal hidden polymorphisms not detected by other methods. |
ddRAD | Double-Digest Restriction-Site-Associated DNA Sequencing | This method is based on the enzymatic digestion of the whole genomic DNA and the creation of multiplexed libraries, with consequent binding to specific adapters (reduced representation libraries) which are more laborious and less accurate than SNP analysis. |
3.3. Genomic Selection
3.4. Genome Editing
3.5. Novel Approaches
4. Pathogen Characterization
4.1. Conventional Methods
4.2. Molecular Methods
4.3. Whole Genome Sequencing (WGS)
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genetic Approach | Species | Pathogen/Disease | Reference |
---|---|---|---|
Marker-assisted Selection | Rainbow trout | Rhabdovirus | [24] |
Rainbow trout | Aeromonassalmonicida | [25] | |
Rainbow trout | Vibrioanguillarum | [26] | |
Rainbow trout | Flavobacterium psychrophilum | [27] | |
Rainbow trout | Viral hemorrhagic septicemia virus | [27] | |
Rainbow trout | Flavobacterium columnare | [28] | |
Rainbow trout | Flavobacterium psychrophilum | [29] | |
Atlantic salmon | Infectious Pancreatic Necrosis Virus | [22,23] | |
Atlantic salmon | Caligus rogercresseyi | [31] | |
Atlantic salmon | Neoparamoeba perurans | [30] | |
Atlantic salmon | Lepeophtheirus salmonis | [32] | |
Shrimp | White spot syndrome virus | [33] | |
Gene-assisted Selection | Atlantic salmon | Infectious pancreatic necrosis virus | [34] |
Atlantic salmon | Infectious pancreatic necrosis virus | [35] | |
Rainbow trout | Lactococcus garvieae | [36] | |
Rainbow trout | Flavobacterium psychrophilum | [37] | |
Atlantic salmon | Infectious salmon anaemia | [38] | |
Atlantic salmon | Aeromonas salmonicida | [39] | |
Oyster | Perkinsus marinus | [41] | |
Genomic Selection | Rainbow trout | Flavobacterium psychrophilum | [44] |
Shrimp–Oyster | - | [46] | |
Sea bass–Sea bream | - | [47] | |
Atlantic salmon | Caligus rogercresseyi | [49] | |
Atlantic salmon | - | [48] | |
Atlantic salmon | Lepeophtheirus salmonis | [49] | |
Atlantic salmon | - | [52] | |
Atlantic salmon | Neoparamoeba perurans | [30] | |
Catfish | Edwardsiella ictaluri | [50] | |
Catfish | Flavobacterium columnare | [51] | |
Shrimp | White spot syndrome virus | [52] | |
Genome Editing | Sea bream | - | [54] |
Catfish | - | [55] |
Typing Technique | Repeatability | Reproducibility | Time (Days) | Cost |
---|---|---|---|---|
MLST | high | high | 3+ | medium–high |
PFGE | medium–high | medium–high | 3 | high |
RFLP | medium–high | medium | 1–3 | medium |
AFLP | high | medium–high | 2 | low–medium |
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Sciuto, S.; Colli, L.; Fabris, A.; Pastorino, P.; Stoppani, N.; Esposito, G.; Prearo, M.; Esposito, G.; Ajmone-Marsan, P.; Acutis, P.L.; et al. What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals 2022, 12, 2176. https://doi.org/10.3390/ani12172176
Sciuto S, Colli L, Fabris A, Pastorino P, Stoppani N, Esposito G, Prearo M, Esposito G, Ajmone-Marsan P, Acutis PL, et al. What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals. 2022; 12(17):2176. https://doi.org/10.3390/ani12172176
Chicago/Turabian StyleSciuto, Simona, Licia Colli, Andrea Fabris, Paolo Pastorino, Nadia Stoppani, Giovanna Esposito, Marino Prearo, Giuseppe Esposito, Paolo Ajmone-Marsan, Pier Luigi Acutis, and et al. 2022. "What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?" Animals 12, no. 17: 2176. https://doi.org/10.3390/ani12172176