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Shen X, Niu YC, Uichanco JAV, Phua N, Bhandare P, Thevasagayam NM, Prakki SRS, Orbán L. Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer). BMC Genomics 2023; 24:449. [PMID: 37558985 PMCID: PMC10413685 DOI: 10.1186/s12864-023-09513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND For Asian seabass (Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading causes of disease, causing tens of millions of dollars of annual economic losses. Over the years, we conducted farm-based challenges by exposing Asian seabass juveniles to complex natural environmental conditions. In one of these challenges, we collected a total of 1,250 fish classified as either 'sensitive' or 'robust' individuals during the 28-day observation period. RESULTS We constructed a high-resolution linkage map with 3,089 SNPs for Asian seabass using the double digest Restriction-site Associated DNA (ddRAD) technology and a performed a search for Quantitative Trait Loci (QTL) associated with robustness. The search detected a major genome-wide significant QTL for increased robustness in pathogen-infected marine environment on linkage group 11 (ASB_LG11; 88.9 cM to 93.6 cM) with phenotypic variation explained of 81.0%. The QTL was positioned within a > 800 kb genomic region located at the tip of chromosome ASB_LG11 with two Single Nucleotide Polymorphism markers, R1-38468 and R1-61252, located near to the two ends of the QTL. When the R1-61252 marker was validated experimentally in a different mass cross population, it showed a statistically significant association with increased robustness. The majority of thirty-six potential candidate genes located within the QTL have known functions related to innate immunity, stress response or disease. By utilizing this ddRAD-based map, we detected five mis-assemblies corresponding to four chromosomes, namely ASB_LG8, ASB_LG9, ASB_LG15 and ASB_LG20, in the current Asian seabass reference genome assembly. CONCLUSION According to our knowledge, the QTL associated with increased robustness is the first such finding from a tropical fish species. Depending on further validation in other stocks and populations, it might be potentially useful for selecting robust Asian seabass lines in selection programs.
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Affiliation(s)
- Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.
- Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore.
| | | | - Joseph Angelo V Uichanco
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- James Cook University Singapore, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present Address: School of Chemical & Life Sciences, Life Sciences Applied Research Group, Nanyang Polytechnic, Singapore, Singapore
| | - Pranjali Bhandare
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present address: Theodor Boven Institute (Biocenter), University of Würzburg, Würzburg, Germany
| | - Natascha May Thevasagayam
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present address: Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sai Rama Sridatta Prakki
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present address: Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary.
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Karami AM, Marana MH, Mathiessen H, Dalsgaard I, Nielsen TF, Kania PW, Buchmann K. Validation of a QTL associated with resistance to Vibrio anguillarum in rainbow trout (Oncorhynchus mykiss). Acta Vet Scand 2023; 65:28. [PMID: 37365572 DOI: 10.1186/s13028-023-00692-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/22/2023] [Indexed: 06/28/2023] Open
Abstract
Vibriosis is a bacterial disease in fish caused by the Gram negative bacterium Vibrio anguillarum with severe impact on rainbow trout (Oncorhynchus mykiss) farming. Sustainable control methods should be developed and we here show that marker assisted selective breeding of fish naturally resistant to the disease is feasible. We have validated the use of a single nucleotide polymorphism (SNP) marker SNP AX-89,945,921 (QTL on chromosome 21). The QTL was previously found associated with resistance to vibriosis and described following a genome wide association analysis (GWAS) of trout exposed to the bacterium. For this validation spawners were genotyped by use of the 57 K Axiom®Trout Microarray (Affymetrix) and homozygous male fish carrying the allele with the SNP AX-89,945,921 were then selected and used to fertilize eggs from outbred female trout resulting in fish all carrying the SNP (QTL-fish). Control fish (non-QTL fish) were produced by fertilizing the same batch of eggs by use of male parents negative for the SNP. The fish were exposed in freshwater to V. anguillarum (water bath infection) at 19 C°. A total of 900 fish were challenged in a common garden set-up in triplicate. A bacterial solution of V. anguillarum (serotype O1) was added to each of three freshwater fish tanks, each with 150 QTL and 150 non-QTL fish. Fish were tagged by tail fin cut (upper/lower) to discern the two groups, whereafter fish were monitored around the clock to detect disease signs and remove moribund fish. Clinical vibriosis developed within two days in non-QTL-fish (overall morbidity of 70%). QTL fish developed clinical signs later and the morbidity was significantly lower and did not reach 50%. Rainbow trout farming may benefit from using the QTL associated with higher resistance towards vibriosis. The effect may be optimized in the future by use of both male and female parents homozygous for the marker allele.
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Affiliation(s)
- Asma Mohammad Karami
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870, Frederiksberg C, Denmark
| | - Moonika Haahr Marana
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870, Frederiksberg C, Denmark
| | - Heidi Mathiessen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870, Frederiksberg C, Denmark
| | - Inger Dalsgaard
- National Institute of Aquatic Resources, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | | | - Per Walter Kania
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870, Frederiksberg C, Denmark
| | - Kurt Buchmann
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870, Frederiksberg C, Denmark.
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3
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Yang Q, Yang XD, Liu MQ, Zeng C, Zhao HK, Xiang KW, Hou ZS, Wen HS, Li JF. Transcriptome analysis of liver, gill and intestine in rainbow trout (Oncorhynchus mykiss) symptomatically or asymptomatically infected with Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108643. [PMID: 36871630 DOI: 10.1016/j.fsi.2023.108643] [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: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss), an important economic cold-water fish worldwide, is severely threatened by viruses and bacteria in the farming industry. The vibriosis outbreak has caused a significant setback to aquaculture. Vibrio anguillarum, one of the common disease-causing vibriosis associated with severe lethal vibriosis in aquaculture, infects fish mainly by adsorption and invasion of the skin, gills, lateral line and intestine. To investigate the defense mechanism of rainbow trout against the pathogen after infection with Vibrio anguillarum, trout were intraperitoneally injected by Vibrio anguillarum and divided into symptomatic group (SG) and asymptomatic group (AG) according to the phenotype. RNA-Seq technology was used to evaluate the transcriptional signatures of liver, gill and intestine of trout injected with Vibrio anguillarum (SG and AG) and corresponding control groups (CG(A) and CG(B)). The GO and KEGG enrichment analyses were used to investigate the mechanisms underlying the differences in susceptibility to Vibrio anguillarum. Results showed that in SG, immunomodulatory genes in the cytokine network were activated and tissue function-related genes were down-regulated, while apoptosis mechanisms were activated. However, AG responded to Vibrio anguillarum infection by activating complement related immune defenses, while metabolism and function related genes were up-regulated. Conclusively, a rapid and effective immune and inflammatory response can successfully defend Vibrio anguillarum infection. However, a sustained inflammatory response can lead to tissue and organ damage and cause death. Our results may provide a theoretical basis for breeding rainbow trout for disease resistance.
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Affiliation(s)
- Qian Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Xiao-Dong Yang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Meng-Qun Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Chu Zeng
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Hong-Kui Zhao
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Kai-Wen Xiang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Zhi-Shuai Hou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Hai-Shen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Ji-Fang Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Ocean University of China, Qingdao, China.
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4
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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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5
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Calboli FCF, Iso-Touru T, Bitz O, Fischer D, Nousiainen A, Koskinen H, Tapio M, Tapio I, Kause A. Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus. J Anim Sci 2023; 101:skad333. [PMID: 37777972 PMCID: PMC10583997 DOI: 10.1093/jas/skad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023] Open
Abstract
Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.
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Affiliation(s)
| | - Terhi Iso-Touru
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Oliver Bitz
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Daniel Fischer
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Antti Nousiainen
- Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland
| | - Heikki Koskinen
- Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland
| | - Miika Tapio
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Ilma Tapio
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Antti Kause
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
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Sánchez-Roncancio C, García B, Gallardo-Hidalgo J, Yáñez JM. GWAS on Imputed Whole-Genome Sequence Variants Reveal Genes Associated with Resistance to Piscirickettsia salmonis in Rainbow Trout ( Oncorhynchus mykiss). Genes (Basel) 2022; 14:114. [PMID: 36672855 PMCID: PMC9859203 DOI: 10.3390/genes14010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWAS) allow the identification of associations between genetic variants and important phenotypes in domestic animals, including disease-resistance traits. Whole Genome Sequencing (WGS) data can help increase the resolution and statistical power of association mapping. Here, we conduced GWAS to asses he facultative intracellular bacterium Piscirickettsia salmonis, which affects farmed rainbow trout, Oncorhynchus mykiss, in Chile using imputed genotypes at the sequence level and searched for candidate genes located in genomic regions associated with the trait. A total of 2130 rainbow trout were intraperitoneally challenged with P. salmonis under controlled conditions and genotyped using a 57K single nucleotide polymorphism (SNP) panel. Genotype imputation was performed in all the genotyped animals using WGS data from 102 individuals. A total of 488,979 imputed WGS variants were available in the 2130 individuals after quality control. GWAS revealed genome-wide significant quantitative trait loci (QTL) in Omy02, Omy03, Omy25, Omy26 and Omy27 for time to death and in Omy26 for binary survival. Twenty-four (24) candidate genes associated with P. salmonis resistance were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism and apoptotic process. Our results provide further knowledge on the genetic variants and genes associated with resistance to intracellular bacterial infection in rainbow trout.
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Affiliation(s)
- Charles Sánchez-Roncancio
- Doctorado en Acuicultura, Programa Cooperativo: Universidad de Chile. Universidad Católica del Norte. Pontificia Universidad Católica de Valparaíso, Chile
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
| | - Baltasar García
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
| | - Jousepth Gallardo-Hidalgo
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
| | - José M. Yáñez
- Center for Research and Innovation in Aquaculture (CRIA), Universidad de Chile, Santiago 8820808, Chile
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, La Pintana, Santiago 8820808, Chile
- Núcleo Milenio de Salmonidos Invasores Australes (INVASAL), Concepcion 4030000, Chile
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Abstract
Finfish aquaculture in freshwater and marine environments is continuously expanding globally, and the potential for a substantial further increase is well documented. The industry is supplying fish products for human consumption to the same extent as capture fisheries, and new fish species for domestication are still being selected by the industry. The challenge faced by all aquacultured species, classical and novel, is the range of pathogens associated with each new fish type. A fish host in its natural environment carries a series of more or less specific parasites (specialists and generalists). Some of these show a marked ability to propagate in aquaculture settings. They may then elicit disease when infection intensities in the confined aquaculture environment reach high levels. In addition, the risk of transmission of parasites from aquaculture enterprises to wild fish stocks adds to the parasitic challenge. Control programmes of various kinds are needed and these may include chemotherapeutants and medicines as the farmer's first and convenient choice, but mechanical, biological, immunological and genetic control methods are available solutions. New methods are still to be developed by scrutinizing the life cycle of each particular parasite species and pin-pointing the vulnerable stage to be targeted. As parasites exhibit a huge potential for adaptation to environmental changes, one must realize that only one approach rarely is sufficient. The present work therefore elaborates on and advocates for implementation of integrated control strategies for diseases caused by protozoan and metazoan parasites.
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Quezada‐Rodriguez PR, Taylor RS, Downes J, Egan F, White S, Brenan A, Rigby M, Nowak BF, Ruane NM, Wynne JW. Prevalence of epitheliocystis in freshwater Atlantic salmon reared in flow-through and recirculation aquaculture systems. JOURNAL OF FISH DISEASES 2022; 45:1721-1731. [PMID: 36017570 PMCID: PMC9805179 DOI: 10.1111/jfd.13694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Epitheliocystis, an intracellular bacterial infection in the gills and skin epithelium, has been frequently reported in Atlantic salmon (Salmo salar) during freshwater production in a number of countries. This study describes the prevalence and intensity of a natural epitheliocystis infection present in the gills of two strains of Atlantic salmon reared in either a flow-through (FT) or a recirculation aquaculture system (RAS) in Ireland. Repeated sampling of gills prior to and throughout seawater transfer, histology and quantitative real-time PCR were used to determine infection prevalence and intensity. Despite no clinical gill disease, and minor histopathological changes, epitheliocystis lesions were identified in histology at all time points. Specific PCR confirmed the presence of Candidatus Clavichlamydia salmonicola in both strains and its number of copies was correlated with intensity of epitheliocystis lesions. A significant interaction between hatchery system and fish strain on the prevalence and intensity of gill epitheliocystis was found both using histological and molecular methods. Specifically, fish from FT had higher prevalence and intensity than RAS reared fish and within FT, the Irish cohort were more affected than Icelandic.
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Affiliation(s)
- Petra R. Quezada‐Rodriguez
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaLauncestonTasmaniaAustralia
| | - Richard S. Taylor
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
| | | | | | | | | | - Megan Rigby
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaLauncestonTasmaniaAustralia
| | | | - James W. Wynne
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
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Karami AM, Duan Y, Kania PW, Buchmann K. Responses towards eyefluke (Diplostomum pseudospathaceum) in different genetic lineages of rainbow trout. PLoS One 2022; 17:e0276895. [PMID: 36301982 PMCID: PMC9612474 DOI: 10.1371/journal.pone.0276895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022] Open
Abstract
Marker-assisted selective breeding of fish with higher levels of resistance towards specific pathogens may improve fish health, but the impact of host genotype on susceptibility to multiple pathogen infections is still poorly investigated. This study examined the resistance in rainbow trout Oncorhynchus mykiss towards infection with the eye fluke Diplostomum pseudospathaceum. We used genetically selected rainbow trout, carrying SNPs associated with resistance towards the parasitic ciliate Ichthyophthirius multifiliis, and exposed the fish to eye fluke cercariae. We showed that fish partly resistant to I. multifiliis were more susceptible to eye fluke invasion. The expression of immune relevant genes (encoding innate and adaptive factors) was also affected as these genotypes responded less strongly to a secondary fluke infection. The complexity of genome architecture in disease resistance towards multiple pathogens is discussed.
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Affiliation(s)
- Asma M. Karami
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
| | - Yajiao Duan
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Per W. Kania
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Kurt Buchmann
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Kurpe SR, Sukhovskaya IV, Borvinskaya EV, Morozov AA, Parshukov AN, Malysheva IE, Vasileva AV, Chechkova NA, Kuchko TY. Physiological and Biochemical Characteristics of Rainbow Trout with Severe, Moderate and Asymptomatic Course of Vibrio anguillarum Infection. Animals (Basel) 2022; 12:ani12192642. [PMID: 36230384 PMCID: PMC9559680 DOI: 10.3390/ani12192642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary During the past decades, bacterial infections have been a serious problem in aquaculture that causes very large economic losses. Currently, antibiotics are the most common method of disease prevention and control. A combination of water quality monitoring, early detection of fish infections, and other preventive biosecurity measures in fish farms can help prevent the spread of infection. We investigated the natural bacterial infection in fish farms and characterized the parameters of the health status of rainbow trout Oncorhynchus mykiss (Walbaum, 1792) during disease. Depending on the course of the disease (severity of the pathology, leukocyte profile, and expression of immune-related genes), three subpopulations of fish with severe damage, a moderate course of the infectious process, and asymptomatic fish were characterized. An unexpected result was a small metabolic difference between fish with moderate symptoms and fish with weak signs of pathology. Thus, we have described the characteristics of a trout subpopulation with a mild course of infection which has potential for recovery after infection. Abstract This article describes the clinical manifestation of natural Vibrio anguillarum infection in rainbow trout (Oncorhynchus mykiss) during an outbreak on a fish farm. (i) Using an integrated approach, we characterized the pathogenesis of vibriosis from the morphological, hematological, and biochemical points of view. The molecular mechanisms associated with the host immune response were investigated using mass spectrometric analysis of trout plasma proteins. (ii) According to the severity of infection (the extent of tissue damage, the level of expression of pro-inflammatory genes, and changes in the leukocyte profile) three fish populations were identified among infected trout: fish with severe lesions (SL), fish with the moderate infectious process (IP) and asymptomatic fish (AS). (iii) Lymphopenia, granulocytosis, and splenomegaly were strong trends during the progression of infection and informative indicators of severe manifestation of disease, associated with hemorrhagic shock, metabolic acidosis, and massive tissue damage. (iv) As expected, pro-inflammatory interleukins, complement components, acute phase proteins, and antimicrobial peptides were implicated in the acute pathogenesis. Systemic coagulopathy was accompanied by increased antithrombotic reactions. (v) Reconstruction of metabolic pathways also revealed a high energy requirement for the immune response in severely affected fish. (vi) An unexpected result was a small difference between fish with moderate symptoms and fish with no or minor external signs of pathology (putatively resistant to infection). Increased production of antiproteases and enhanced blood coagulation cascade were observed in healthier fish, which may underlie the mechanisms of a controlled, non-self-damaging immune response to infection. (vii) Depending on the progression of the disease and the presence of the pathogen, a stepwise or linear change in the abundance of some plasma proteins was revealed. These proteins could be proposed as molecular markers for diagnosing the health and immune status of trout when cultured in fish farms.
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Affiliation(s)
- Stanislav Rimaso Kurpe
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University (PetrSU), 185640 Petrozavodsk, Russia
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence: (S.R.K.); (I.V.S.)
| | - Irina Viktorovna Sukhovskaya
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University (PetrSU), 185640 Petrozavodsk, Russia
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 11 Pushkinskaya Street, 185910 Petrozavodsk, Russia
- Correspondence: (S.R.K.); (I.V.S.)
| | | | - Alexey Anatolievich Morozov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences (LIN SB RAS), 3 Ulan-Batorskaya Street, 664033 Irkutsk, Russia
| | - Aleksey Nikolaevich Parshukov
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 11 Pushkinskaya Street, 185910 Petrozavodsk, Russia
| | - Irina Evgenyevna Malysheva
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University (PetrSU), 185640 Petrozavodsk, Russia
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences (IB KarRC RAS), 11 Pushkinskaya Street, 185910 Petrozavodsk, Russia
| | - Alina Valeryevna Vasileva
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University (PetrSU), 185640 Petrozavodsk, Russia
| | - Natalia Alexandrovna Chechkova
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University (PetrSU), 185640 Petrozavodsk, Russia
| | - Tamara Yurevna Kuchko
- Institute of Biology, Ecology and Agricultural Technologies of the Petrozavodsk State University (PetrSU), 185640 Petrozavodsk, Russia
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What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals (Basel) 2022; 12:ani12172176. [PMID: 36077896 PMCID: PMC9454762 DOI: 10.3390/ani12172176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Infectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture. Abstract Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.
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Bernard M, Dehaullon A, Gao G, Paul K, Lagarde H, Charles M, Prchal M, Danon J, Jaffrelo L, Poncet C, Patrice P, Haffray P, Quillet E, Dupont-Nivet M, Palti Y, Lallias D, Phocas F. Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping. Front Genet 2022; 13:941340. [PMID: 35923696 PMCID: PMC9340366 DOI: 10.3389/fgene.2022.941340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip.
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Affiliation(s)
- Maria Bernard
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, SIGENAE, Jouy-en-Josas, France
| | - Audrey Dehaullon
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Guangtu Gao
- USDA, REE, ARS, NEA, NCCCWA, Kearneysville, WV, United States
| | - Katy Paul
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Henri Lagarde
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Mathieu Charles
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, SIGENAE, Jouy-en-Josas, France
| | - Martin Prchal
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia, Vodňany, Czechia
| | - Jeanne Danon
- INRAE-UCA, Plateforme Gentyane, UMR GDEC, Clermont-Ferrand, France
| | - Lydia Jaffrelo
- INRAE-UCA, Plateforme Gentyane, UMR GDEC, Clermont-Ferrand, France
| | - Charles Poncet
- INRAE-UCA, Plateforme Gentyane, UMR GDEC, Clermont-Ferrand, France
| | | | | | - Edwige Quillet
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Yniv Palti
- USDA, REE, ARS, NEA, NCCCWA, Kearneysville, WV, United States
| | - Delphine Lallias
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Florence Phocas
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
- *Correspondence: Florence Phocas,
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Abstract
Introduction Neutrophilic granulocytes are short‐lived cells continuously circulating in the vascular system of vertebrates. They play a basic and decisive role in the innate immune defence of the hosts against all types of pathogenic microorganisms. Methods Based on a literature study, the functions of neutrophils and cells with similar functions are described. The study places special emphasis on organisms in the aquatic environment and the pathogens occurring in that particular environment. Results The evolutionary origin of this specific cell type is not clear, but its most basic traits (recognition of foreign elements, extracellular trap release, phagocytosis and elimination of ingested material) are found in phagocytes in members of evolutionary ancient invertebrate groups spanning from amoebae, sponges, sea‐anemones, mollusks (snails and mussels), arthropods (crustaceans and insects) to echinoderms (sea stars and sea urchins). Their functions as innate immune sentinels and effector cells in these groups are well described. Neutrophilic granulocytes with elongated and lobed nuclei (possibly allowing cell movements through narrow extracellular spaces and leaving space for phagosomes) occur in vertebrates including fish, amphibians, reptiles, birds and mammals although the morphology of the nucleus, stainability of cytoplasmic granula, and the antimicrobial armament vary among groups. Following the pathogen invasion of a fish host, the neutrophils migrates from the vascular system into the infection focus. They apply their PRRs (including TLRs) to recognize the invader as non‐self, produce netosis by casting extracellular chromatin containing traps in the microenvironment. These nets assist the immobilization of invading microbes and prevents their further spread. The cells attach to and engulf the microbes by phagocytosis, whereafter they eliminate the pathogen in phagolysosomes equipped with a range of killing mechanisms and attract, by release of chemokines, additional immune cells (monocytes, macrophages and lymphocytes) to the site of invasion. Their role in innate immunity of fish hosts towards aquatic pathogens has been elucidated by in vivo and in vitro studies. Neutrophils interact with virus (e.g. IPNV and VHSV), bacteria (e.g. Aeromonas, Vibrio, Edwardsiella, Mycobacterium and Renibacterium) and parasites, including monogeneans (Gyrodactylus), cestodes (Diphyllobothrium), trematodes (Diplostomum) and ciliates (Ichthyophthirius and Philasterides). Despite the decisive function of neutrophils in innate immunity and early protection, the excessive production of ROS, RNS and NETs may lead to pathological disturbances in the host, which are exacerbated if the pathogens evolve immune evasion mechanisms. Conclusion Neutrophils in aquatic organisms play a central role in innate immunity but may serve as a toll and a support in acquired protection. The strong impact of the cellular reactions not only on pathogen but also on host tissues emphasizes that an optimal immune reaction is balanced, involves targeted and specific effector mechanisms, which leaves a minimum of collateral damage in host organs.
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Affiliation(s)
- Kurt Buchmann
- Laboratory of Aquatic Pathobiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass. Animals (Basel) 2022; 12:ani12030277. [PMID: 35158601 PMCID: PMC8833606 DOI: 10.3390/ani12030277] [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: 11/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary In the present study, the genetic architecture of the stress response, body weight, and disease resistance in European seabass were studied, providing fruitful results for further research. Initially, the above traits were recorded and genotyping on a large scale was performed in those fish. The recorded data and genotypes were combined and analyzed to find genomic areas affecting them as well as to estimate the heritability of those traits. Stress response traits and body weight were medium heritable, while genomic regions affecting them were detected. However, no genomic areas related to disease resistance were revealed. These findings improve our knowledge of the genetic structure of those traits and can be utilized in a breeding program for the genetic improvement of aquaculture broodstocks. Abstract The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits.
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Whole-genome association study searching for QTL for Aeromonas salmonicida resistance in rainbow trout. Sci Rep 2021; 11:17857. [PMID: 34497310 PMCID: PMC8426485 DOI: 10.1038/s41598-021-97437-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis, has extensive negative effects on wild and farmed salmonids worldwide. Vaccination induces some protection under certain conditions but disease outbreaks occur even in vaccinated fish. Therefore, alternative disease control approaches are required to ensure the sustainable expansion of rainbow trout aquaculture. Selective breeding can be applied to enhance host resistance to pathogens. The present work used genome-wide association study (GWAS) to identify quantitative trait loci (QTL) associated with A. salmonicida resistance in rainbow trout. A total 798 rainbow trout exposed to A. salmonicida by bath challenge revealed 614 susceptible and 138 resistant fish. Genotyping was conducted using the 57 K single nucleotide polymorphism (SNP) array and the GWAS was performed for survival and time to death phenotypes. We identified a QTL on chromosome 16 and located positional candidate genes in the proximity of the most significant SNPs. In addition, samples from exposed fish were examined for expression of 24 immune-relevant genes indicating a systematic immune response to the infection. The present work demonstrated that resistance to A. salmonicida is moderately heritable with oligogenic architecture. These result will be useful for the future breeding programs for improving the natural resistance of rainbow trout against furunculosis.
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