1
|
Choi HD, Baek EJ, Hong S, Kim YC, Jeong JM, Kwon MG, Il Kim K. Development and validation of reverse-transcription cross-priming amplification-based lateral flow assay for the detection of infectious hematopoietic necrosis virus. J Virol Methods 2024; 329:115008. [PMID: 39153529 DOI: 10.1016/j.jviromet.2024.115008] [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: 05/26/2024] [Revised: 07/08/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024]
Abstract
Infectious hematopoietic necrosis virus (IHNV) severely and lethally infects salmonid fish, including Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) worldwide. Rapid and accurate viral detection is crucial for preventing pathogen spread and minimizing damage. Although several IHNV detection assays have been developed, their analytical and diagnostic performances have not been evaluated and field usability assessments have not been completely validated. Here, we developed a reverse-transcription cross-priming amplification-based lateral flow assay (RT-CPA-LFA) and validated its diagnostic performance. To detect the IHNV, primers were designed based on the consensus sequence of the nucleocapsid (N) gene. Notably, when combined with a lateral flow dipstick, it could visualize the IHNV amplification products within 5 min and the detection limit of the developed RT-CPA-LFA was 3.28×105 copies/μL. The diagnostic sensitivity and specificity in fish samples (n=140) were 98.88 % and 96.08 %, respectively. Moreover, the IHNV detection rate by RT-CPA-LFA in dead rainbow trout artificially injected with the virus was 100 %, consistent with to the results obtained from second conventional and real-time PCR, indicating its applicability for rapid IHNV detection and presumptive IHN diagnosis during the endemic period.
Collapse
Affiliation(s)
- Hyun Deok Choi
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Eun Jin Baek
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Suhee Hong
- Department of Aquatic Life Medicine, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Young Chul Kim
- Department of Aquatic Life Medicine, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Ji Min Jeong
- Aquatic Disease Control Division, National Fishery Products Quality Management Service (NFQS), Republic of Korea
| | - Mun Gyeong Kwon
- Aquatic Disease Control Division, National Fishery Products Quality Management Service (NFQS), Republic of Korea
| | - Kwang Il Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea.
| |
Collapse
|
2
|
Palti Y, Vallejo RL, Purcell MK, Gao G, Shewbridge KL, Long RL, Setzke C, Fragomeni BO, Cheng H, Martin KE, Naish KA. Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci. Front Genet 2024; 15:1394656. [PMID: 38854430 PMCID: PMC11162110 DOI: 10.3389/fgene.2024.1394656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/30/2024] [Indexed: 06/11/2024] Open
Abstract
Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were naïve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the naïve lines. A total of 1,859 and 1,768 offspring from two commercial aquaculture strains were phenotyped for resistance to IHNV and genotyped with the rainbow trout Axiom 57K SNP array. Moderate heritability values (0.15-0.25) were estimated. Two statistical methods were used for genome wide association analyses in the two populations. No major QTL were detected despite the naïve status of the two lines. Further, our analyses confirmed an oligogenic architecture for genetic resistance to IHNV in rainbow trout. Overall, 17 QTL with notable effect (≥1.9% of the additive genetic variance) were detected in at least one of the two rainbow trout lines with at least one of the two statistical methods. Five of those QTL were mapped to overlapping or adjacent chromosomal regions in both lines, suggesting that some loci may be shared across commercial lines. Although some of the loci detected in this GWAS merit further investigation to better understand the biological basis of IHNV disease resistance across populations, the overall genetic architecture of IHNV resistance in the two rainbow trout lines suggests that genomic selection may be a more effective strategy for genetic improvement in this trait.
Collapse
Affiliation(s)
- Yniv Palti
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States
| | - Roger L. Vallejo
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States
| | - Maureen K. Purcell
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, United States
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States
| | - Kristy L. Shewbridge
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States
| | - Roseanna L. Long
- National Center for Cool and Cold Water Aquaculture, USDA-ARS, Kearneysville, WV, United States
| | - Christopher Setzke
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States
| | - Breno O. Fragomeni
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | | | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States
| |
Collapse
|
3
|
Ziafati Kafi Z, Ghalyanchilangeroudi A, Nikaein D, Marandi A, Rahmati‐Holasoo H, Sadri N, Erfanmanesh A, Enayati A. Phylogenetic analysis and genotyping of Iranian infectious haematopoietic necrosis virus (IHNV) of rainbow trout (
Oncorhynchus mykiss
) based on the glycoprotein gene. Vet Med Sci 2022; 8:2411-2417. [DOI: 10.1002/vms3.931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Zahra Ziafati Kafi
- Faculty of Veterinary Medicine Department of Microbiology and Immunology University of Tehran Tehran Iran
| | - Arash Ghalyanchilangeroudi
- Faculty of Veterinary Medicine Department of Microbiology and Immunology University of Tehran Tehran Iran
| | - Donya Nikaein
- Faculty of Veterinary Medicine Department of Microbiology and Immunology University of Tehran Tehran Iran
| | - Amin Marandi
- Faculty of Veterinary Medicine Department of Aquatic Animal Health University of Tehran Tehran Iran
| | - Hooman Rahmati‐Holasoo
- Faculty of Veterinary Medicine Department of Aquatic Animal Health University of Tehran Tehran Iran
- Centre of Excellence for Warm Water Fish Health and Disease Shahid Chamran University of Ahvaz Ahvaz Iran
| | - Naser Sadri
- Faculty of Veterinary Medicine Department of Microbiology and Immunology University of Tehran Tehran Iran
| | - Ahmad Erfanmanesh
- Academic Center for Education, Culture and Research (ACECR) Tehran Organization Tehran Iran
| | - Ala Enayati
- Academic Center for Education, Culture and Research (ACECR) Tehran Organization Tehran Iran
| |
Collapse
|
4
|
Liyanage DS, Lee S, Yang H, Lim C, Omeka WKM, Sandamalika WMG, Udayantha HMV, Kim G, Ganeshalingam S, Jeong T, Oh SR, Won SH, Koh HB, Kim MK, Jones DB, Massault C, Jerry DR, Lee J. Genome-wide association study of VHSV-resistance trait in Paralichthys olivaceus. FISH & SHELLFISH IMMUNOLOGY 2022; 124:391-400. [PMID: 35462004 DOI: 10.1016/j.fsi.2022.04.021] [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: 12/20/2021] [Revised: 03/26/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
In flounder aquaculture, selective breeding plays a vital role in the development of disease-resistant traits and animals with high growth rates. Moreover, superior animals are required to achieve high profits. Unlike growth-related traits, disease-resistant experiments need to be conducted in a controlled environment, as the improper measurement of traits often leads to low genetic correlation and incorrect estimation of breeding values. In this study, viral hemorrhagic septicemia virus (VHSV) resistance was studied using a genome-wide association study (GWAS), and the genetic parameters were estimated. Genotyping was performed using a high-quality 70 K single nucleotide polymorphism (SNP) Affymetrix® Axiom® myDesign™ Genotyping Array of olive flounder. A heritability of ∼0.18 for resistance to VHSV was estimated using genomic information of the fish. According to the GWAS, significant SNPs were detected in chromosomes 21, 24, and contig AGQT02032065.1. Three SNPs showed significance at the genome-wide level (p < 1 × 10-6), while others showed significance above the suggestive cutoff (p < 1 × 10-4). The 3% phenotypic variation was explained by the highest significant SNP, named AX-419319631. Of the important genes for disease resistance, SNPs were associated with plcg1, epha4, clstn2, pik3cb, hes6, meis3, prx6, cep164, siae, and kirrel3b. Most of the genes associated with these SNPs have been previously reported with respect to viral entry, propagation, and immune mechanisms. Therefore, our study provides helpful information regarding VHSV resistance in olive flounder, which can be used for breeding applications.
Collapse
Affiliation(s)
- D S Liyanage
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Sukkyoung Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Hyerim Yang
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Chaehyeon Lim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - W K M Omeka
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - W M Gayashani Sandamalika
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - H M V Udayantha
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Gaeun Kim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Subothini Ganeshalingam
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea
| | - Taehyug Jeong
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea
| | - Seong-Rip Oh
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - Seung-Hwan Won
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - Hyoung-Bum Koh
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - Mun-Kwan Kim
- Ocean and Fisheries Research Institute, Jeju Self-Governing Province, 63629, Republic of Korea
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Cecile Massault
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia; Tropical Futures Institute, James Cook University, Singapore.
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju Self-Governing Province, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju Self-Governing Province, 63333, Republic of Korea.
| |
Collapse
|
5
|
Vallejo RL, Fragomeni BO, Cheng H, Gao G, Long RL, Shewbridge KL, MacMillan JR, Towner R, Palti Y. Assessing Accuracy of Genomic Predictions for Resistance to Infectious Hematopoietic Necrosis Virus With Progeny Testing of Selection Candidates in a Commercial Rainbow Trout Breeding Population. Front Vet Sci 2020; 7:590048. [PMID: 33251271 PMCID: PMC7674624 DOI: 10.3389/fvets.2020.590048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/19/2020] [Indexed: 01/17/2023] Open
Abstract
Infectious hematopoietic necrosis (IHN) is an economically important disease of salmonid fish caused by the IHN virus (IHNV). Under industrial aquaculture settings, IHNV can cause substantial mortality and losses. Actually, there is no confirmed and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been performing family-based selective breeding to increase genetic resistance to IHNV in their rainbow trout breeding program. In an earlier study, we used siblings cross-validation to estimate the accuracy of genomic prediction (GP) for IHNV resistance in this breeding population. In the present report, we used empirical progeny testing data to evaluate whether genomic selection (GS) can improve the accuracy of breeding value predictions over traditional pedigree-based best linear unbiased predictions (PBLUP). We found that the GP accuracy with single-step GBLUP (ssGBLUP) outperformed PBLUP by 15% (from 0.33 to 0.38). Furthermore, we found that ssGBLUP had higher GP accuracy than weighted ssGBLUP (wssGBLUP) and single-step Bayesian multiple regression (ssBMR) models with BayesB and BayesC priors which supports our previous findings that the underlying liability of genetic resistance against IHNV in this breeding population might be polygenic. Our results show that GS can be more effective than either the traditional pedigree-based PBLUP model or the marker-assisted selection approach for improving genetic resistance against IHNV in this commercial rainbow trout population.
Collapse
Affiliation(s)
- Roger L. Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Breno O. Fragomeni
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Roseanna L. Long
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Kristy L. Shewbridge
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - John R. MacMillan
- Clear Springs Foods Inc., Research Division, Buhl, ID, United States
| | | | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| |
Collapse
|
6
|
Zuo S, Karami AM, Ødegård J, Mathiessen H, Marana MH, Jaafar RM, von Gersdorff Jørgensen L, Abdu M, Kania PW, Dalsgaard I, Nielsen T, Buchmann K. Immune gene expression and genome-wide association analysis in rainbow trout with different resistance to Yersinia ruckeri infection. FISH & SHELLFISH IMMUNOLOGY 2020; 106:441-450. [PMID: 32791094 DOI: 10.1016/j.fsi.2020.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 05/04/2023]
Abstract
Selective breeding programmes involving marker assisted selection of innately pathogen resistant strains of rainbow trout rely on reliable controlled infection studies, extensive DNA typing of individual fish and recording of expression of relevant genes. We exposed juvenile rainbow trout (6 h bath to 2.6 × 105 CFU mL-1) to the fish pathogen Yersinia ruckeri serotype O1, biotype 2, eliciting Enteric Red Mouth Disease ERM, and followed the disease progression over 21 days. Cumulative mortality reached 42% at 12 days post challenge (dpc) after which no disease signs were recorded. All fish were sampled for DNA-typing (50 k SNP chip, Affymetrix®) throughout the course of infection when they showed clinical signs of disease (susceptible fish) or at day 21 when fish showed no clinical signs of disease (survivors - resistant fish). Genome-wide association analyses of 1027 trout applying single nucleotide polymorphisms (SNPs) as markers revealed an association between traits (susceptible/resistant) and certain regions of the trout genome. It was indicated that multiple genes are involved in rainbow trout resistance towards ERM whereby it is considered a polygenic trait. A corresponding trout group was kept as non-exposed controls and a comparative expression analysis of central innate and adaptive immune genes in gills, spleen and liver was performed for three fish groups: 1) moribund trout exhibiting clinical signs 7 dpc (CS), 2) exposed fish without clinical signs at the same sampling point (NCS) and 3) surviving fish at 21 dpc (survivors). Immune genes encoding inflammatory cytokines (IL-1β, IL-2A, IL-6A, IL-8, IL-10A, IL-12, IL-17A/F2A, IL-17C1, IL-17C2, IL-22, IFNγ, TNFα), acute phase reactants (SAA, C3, cathelicidins, lysozyme) were expressed differently in CS and NCS fish. Correlation (negative or positive) between expression of genes and bacterial load suggested involvement of immune genes in protection. Down-regulation of adaptive immune genes including IgDm, IgDs, IgT and TCR-β was seen primarily in CS and NCS fish whereas survivors showed up-regulation of effector molecule genes such as cathelicidins, complement and lysozyme suggesting their role in clearing the infection. In conclusion, SNP analyses indicated that ERM resistance in rainbow trout is a multi-locus trait. The gene expression in surviving fish suggested that several immune genes are associated with the trait conferring resistance.
Collapse
Affiliation(s)
- Shaozhi Zuo
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Asma M Karami
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark.
| | | | - Heidi Mathiessen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Moonika H Marana
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Rzgar M Jaafar
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Louise von Gersdorff Jørgensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Mohamed Abdu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Per W Kania
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Inger Dalsgaard
- Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Kurt Buchmann
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| |
Collapse
|
7
|
Srisapoome P, Chatchaiphan S, Bunnoy A, Koonawootrittriron S, Na-Nakorn U. Heritability of immunity traits and disease resistance of bighead catfish, Clarias macrocephalus Günther, 1864. FISH & SHELLFISH IMMUNOLOGY 2019; 92:209-215. [PMID: 31181340 DOI: 10.1016/j.fsi.2019.05.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/25/2019] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
Disease outbreak is a major obstruction for intensive aquaculture worldwide. One of the promising solutions is genetic improvement by selective breeding, providing that a sufficient proportion of additive genetic variance (measured by heritability-h2) of disease resistance traits exists. In addition, immunity traits are of interest as potential indirect targeted traits for disease resistance. In this study, the genetic parameters of resistance to Aeromonas hydrophila were reported for the first time in the bighead catfish, Clarias macrocephalus Günther, 1864 which is an important parental species for the production of the commercially important hybrid C. macrocephalus × C. gariepinus. The analyses were performed on 736 data records obtained from 74 full-sib families (31 half-sib families) produced by factorial mating design. The results showed that the heritability of survival rate after disease (Aeromonas hydrophila) challenge (intraperitoneal injection with 0.1 ml containing 1 × 106 CFU/ml of A. hydrophila) was low to moderate (0.05 ± 0.02-0.27 ± 0.15). The immune traits (bactericidal activity-BA, lysozyme activity-LA, and alternative complement activity-ACH50) had low to moderate heritability (h2BA = 0.05 ± 0.02; h2LA = 0.16 ± 0.04; h2ACH50 = 0.31 ± 0.06) while heritability of hematocrit (Hct) was also low (h2Hct = 0.17 ± 0.04). The results suggested the possibility to improve resistance to A. hydrophila by selection, while the possibility to use immunity traits as indirect selection criteria for disease resistance is still unclear.
Collapse
Affiliation(s)
- Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Jatujak, Bangkok, 10900, Thailand
| | - Satid Chatchaiphan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Jatujak, Bangkok, 10900, Thailand
| | - Anurak Bunnoy
- Doctoral Program in Aquaculture, Graduate School of Kasetsart University, Kasetsart University, Jatujak, Bangkok, 10900, Thailand
| | - Skorn Koonawootrittriron
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Jatujak, Bangkok, 10900, Thailand
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Jatujak, Bangkok, 10900, Thailand.
| |
Collapse
|
8
|
Vallejo RL, Cheng H, Fragomeni BO, Shewbridge KL, Gao G, MacMillan JR, Towner R, Palti Y. Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population. Genet Sel Evol 2019; 51:47. [PMID: 31455244 PMCID: PMC6712688 DOI: 10.1186/s12711-019-0489-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 08/18/2019] [Indexed: 11/10/2022] Open
Abstract
Background Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. Currently, there is no proven and cost-effective method for IHNV control. Clear Springs Foods, Inc. has been applying selective breeding to improve genetic resistance to IHNV in their rainbow trout breeding program. The goals of this study were to elucidate the genetic architecture of IHNV resistance in this commercial population by performing genome-wide association studies (GWAS) with multiple regression single-step methods and to assess if genomic selection can improve the accuracy of genetic merit predictions over conventional pedigree-based best linear unbiased prediction (PBLUP) using cross-validation analysis. Results Ten moderate-effect quantitative trait loci (QTL) associated with resistance to IHNV that jointly explained up to 42% of the additive genetic variance were detected in our GWAS. Only three of the 10 QTL were detected by both single-step Bayesian multiple regression (ssBMR) and weighted single-step GBLUP (wssGBLUP) methods. The accuracy of breeding value predictions with wssGBLUP (0.33–0.39) was substantially better than with PBLUP (0.13–0.24). Conclusions Our comprehensive genome-wide scan for QTL revealed that genetic resistance to IHNV is controlled by the oligogenic inheritance of up to 10 moderate-effect QTL and many small-effect loci in this commercial rainbow trout breeding population. Taken together, our results suggest that whole genome-enabled selection models will be more effective than the conventional pedigree-based method for breeding value estimation or the marker-assisted selection approach for improving the genetic resistance of rainbow trout to IHNV in this population.
Collapse
Affiliation(s)
- Roger L Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA.
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, CA, USA
| | - Breno O Fragomeni
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Kristy L Shewbridge
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | | | | | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| |
Collapse
|
9
|
Boonthai T, Loch TP, Standish I, Faisal M. Susceptibility of Representative Great Lakes Fish Species to the North Carolina Strain of Spring Viremia of Carp Virus (SVCV). JOURNAL OF AQUATIC ANIMAL HEALTH 2017; 29:214-224. [PMID: 29072534 DOI: 10.1080/08997659.2017.1360410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Spring viremia of carp virus (SVCV) is a notifiable pathogen of the World Organization of Animal Health. Since SVCV was isolated in Lake Ontario in 2007, concern has grown about its spread in the Great Lakes basin and its potential negative impacts on fish species of importance in stock enhancement programs basinwide. The susceptibility of representative fish species from the families Cyprinidae (Fathead Minnow Pimephales promelas, Golden Shiner Notemigonus crysoleucas, Spotfin Shiner Cyprinella spiloptera, and Creek Chub Semotilus atromaculatus), Centrarchidae (Largemouth Bass Micropterus salmoides), Percidae (Walleye Sander vitreus), Salmonidae (Rainbow Trout Oncorhynchus mykiss), and Esocidae (Muskellunge Esox masquinongy) to SVCV was evaluated by experimental infection under laboratory conditions. Morbidity and mortality were recorded, and virus re-isolation, seminested reverse transcription PCR, and histopathological assessments were performed. Using intraperitoneal (i.p.) injection, Fathead Minnows and Golden Shiners were highly susceptible to SVCV (40-70% mortality). All dead or moribund and apparently healthy surviving Fathead Minnows and Golden Shiners were SVCV positive. The SVCV was also detected in challenged but healthy Spotfin Shiners (30%) and Creek Chub (5%). However, noncyprinid species exhibited no morbidity or mortality and were free of SVCV following an observation period of 30 d. In a follow-up experimental challenge, Fathead Minnows and Golden Shiners were SVCV challenged at 103 and 105 PFU/mL by means of waterborne immersion. After immersion, Fathead Minnows and Golden Shiners exhibited characteristic SVCV disease signs, but mortality was less (30% and 10% mortality, respectively) than that in fish with i.p. injections. The SVCV was detected in all mortalities and a subset of healthy Fathead Minnows and Golden Shiners. Necrotic changes were observed in the kidneys, liver, spleen, ovaries, and heart, and other histopathological lesions also occurred. These findings suggest that two of the four cyprinids tested are susceptible to SVCV-induced disease and that all four can act as potential carriers of SVCV in the Laurentian Great Lakes. Received January 11, 2017; accepted July 17, 2017.
Collapse
Affiliation(s)
- Traimat Boonthai
- a Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 1129 Farm Lane, Room 177K, East Lansing , Michigan 48824 , USA
| | - Thomas P Loch
- a Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 1129 Farm Lane, Room 177K, East Lansing , Michigan 48824 , USA
| | - Isaac Standish
- a Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 1129 Farm Lane, Room 177K, East Lansing , Michigan 48824 , USA
| | - Mohamed Faisal
- a Department of Pathobiology and Diagnostic Investigation , College of Veterinary Medicine, Michigan State University , 1129 Farm Lane, Room 177K, East Lansing , Michigan 48824 , USA
- b Department of Fisheries and Wildlife , College of Agriculture and Natural Resources, Michigan State University , 1129 Farm Lane, Room 177K, East Lansing , Michigan 48824 , USA
| |
Collapse
|
10
|
Breyta R, Brito I, Ferguson P, Kurath G, Naish KA, Purcell MK, Wargo AR, LaDeau S. Transmission routes maintaining a viral pathogen of steelhead trout within a complex multi-host assemblage. Ecol Evol 2017; 7:8187-8200. [PMID: 29075442 PMCID: PMC5648648 DOI: 10.1002/ece3.3276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/22/2017] [Accepted: 06/28/2017] [Indexed: 01/06/2023] Open
Abstract
This is the first comprehensive region wide, spatially explicit epidemiologic analysis of surveillance data of the aquatic viral pathogen infectious hematopoietic necrosis virus (IHNV) infecting native salmonid fish. The pathogen has been documented in the freshwater ecosystem of the Pacific Northwest of North America since the 1950s, and the current report describes the disease ecology of IHNV during 2000-2012. Prevalence of IHNV infection in monitored salmonid host cohorts ranged from 8% to 30%, with the highest levels observed in juvenile steelhead trout. The spatial distribution of all IHNV-infected cohorts was concentrated in two sub-regions of the study area, where historic burden of the viral disease has been high. During the study period, prevalence levels fluctuated with a temporal peak in 2002. Virologic and genetic surveillance data were analyzed for evidence of three separate but not mutually exclusive transmission routes hypothesized to be maintaining IHNV in the freshwater ecosystem. Transmission between year classes of juvenile fish at individual sites (route 1) was supported at varying levels of certainty in 10%-55% of candidate cases, transmission between neighboring juvenile cohorts (route 2) was supported in 31%-78% of candidate cases, and transmission from adult fish returning to the same site as an infected juvenile cohort was supported in 26%-74% of candidate cases. The results of this study indicate that multiple specific transmission routes are acting to maintain IHNV in juvenile fish, providing concrete evidence that can be used to improve resource management. Furthermore, these results demonstrate that more sophisticated analysis of available spatio-temporal and genetic data is likely to yield greater insight in future studies.
Collapse
Affiliation(s)
- Rachel Breyta
- Microbiology Oregon State University Corvallis OR USA.,Cary Institute for Ecosystems Studies Millbrook NY USA
| | - Ilana Brito
- Biomedical Engineering Cornell University Ithaca NY USA
| | - Paige Ferguson
- Biological Sciences University of Alabama Tuscaloosa AL USA
| | - Gael Kurath
- US Geological Survey, Western Fisheries Research Center Seattle WA USA
| | - Kerry A Naish
- School of Aquatic and Fisheries Sciences University of Washington Seattle WA USA
| | - Maureen K Purcell
- US Geological Survey, Western Fisheries Research Center Seattle WA USA
| | - Andrew R Wargo
- Department of Aquatic Health Sciences Virginia Institute of Marine Science Gloucester Point VA USA
| | | |
Collapse
|