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Nguyen NH. Genetics and Genomics of Infectious Diseases in Key Aquaculture Species. BIOLOGY 2024; 13:29. [PMID: 38248460 PMCID: PMC10813283 DOI: 10.3390/biology13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.
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Affiliation(s)
- Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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2
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Xu A, Xu S, Tu Q, Qiao H, Lin W, Li J, He Y, Xie T, Pan L, Pan Q, Zhao Y, Su X, Tong Y. A novel virus in the family Marnaviridae as a potential pathogen of Penaeus vannamei glass post-larvae disease. Virus Res 2023; 324:199026. [PMID: 36529302 DOI: 10.1016/j.virusres.2022.199026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
As an aquatic animal of great commercial relevance, Penaeus vannamei is currently the dominant species of cultured shrimp in China and many other countries worldwide. In recent years, the outbreak of glass post-larvae disease (GPD), which accounts for more than 90% of the mortality of shrimp seedlings in serious cases, in many regions of China has caused significant losses and threatened the sustainability of the aquaculture industry and the economy. It is extremely urgent to determine the infectious agent of GPD in P. vannamei. In this work, we performed metagenomic sequencing of glass post-larvae collected from diseased prawns in Tangshan Hebei, where GPD broke out recently. An evolutionary tree was constructed by MEGA 7 to understand the evolutionary history and relationship of the pathogen genome. A novel virus in the family Marnaviridae was first identified in P. vannamei suffering from GPD, and we tentatively named this virus Baishivirus (GenBank: ON550424). The identified pathogen was validated according to Koch's rule with a pathogenic challenge assay and reverse transcription-polymerase chain reaction. There was only 8% query coverage with 64.96% identity in the Baishivirus genome when compared with its most closely related genome sequence of Wenzhou picorna-like virus 21 reported in 2016. Baishivirus genomic RNA is 9.895 kb in length and encodes three potential open reading frames (ORFs). The identification of Baishivirus in P. vannamei enriches the family Marnaviridae and potentially provides a new candidate to study and prevent GPD in the aquaculture industry.
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Affiliation(s)
- Ailan Xu
- The First Affiliated Hospital of Jiamusi University, 348 Dexiang Street, Jiamusi, Heilongjiang 154003, China
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | - Qihang Tu
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | - Huanao Qiao
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | - Jing Li
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | - Yugan He
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | - Tie Xie
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China
| | | | - Qiang Pan
- Qingdao Nuoanbaite Biotechnology Co., China
| | - Yunwei Zhao
- The First Affiliated Hospital of Jiamusi University, 348 Dexiang Street, Jiamusi, Heilongjiang 154003, China.
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, No. 15 Beisanhuan East Road, Chaoyang, Beijing 100089, China.
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Wang Z, Aweya JJ, Yao D, Zheng Z, Wang C, Zhao Y, Li S, Zhang Y. Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival. MICROBIOME 2022; 10:213. [PMID: 36464721 PMCID: PMC9721036 DOI: 10.1186/s40168-022-01414-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/05/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Numerous microorganisms are found in aquaculture ponds, including several pathogenic bacteria. Infection of cultured animals by these pathogens results in diseases and metabolic dysregulation. However, changes in the metabolic profiles that occur at different infection stages in the same ponds and how these metabolic changes can be modulated by exogenous metabolites in Penaeus vannamei remain unknown. RESULTS Here, we collected gastrointestinal tract (GIT) samples from healthy, diseased, and moribund P. vannamei in the same aquaculture pond for histological, metabolic, and transcriptome profiling. We found that diseased and moribund shrimp with empty GITs and atrophied hepatopancreas were mainly infected with Vibrio parahaemolyticus and Vibrio harveyi. Although significant dysregulation of crucial metabolites and their enzymes were observed in diseased and moribund shrimps, diseased shrimp expressed high levels of taurine and taurine metabolism-related enzymes, while moribund shrimp expressed high levels of hypoxanthine and related metabolism enzymes. Moreover, a strong negative correlation was observed between taurine levels and the relative abundance of V. parahaemolyticus and V. harveyi. Besides, exogenous taurine enhanced shrimp survival against V. parahaemolyticus challenge by increasing the expression of key taurine metabolism enzymes, mainly, cysteine dioxygenase (CDO) and cysteine sulfinic acid decarboxylase (CSD). CONCLUSIONS Our study revealed that taurine metabolism could be modulated by exogenous supplementation to improve crustacean immune response against pathogenic microbes. Video Abstract.
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Affiliation(s)
- Zhongyan Wang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
| | - Jude Juventus Aweya
- College of Ocean Food and Biological Engineering, Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, 361021, Fujian, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
| | - Zhihong Zheng
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
| | - Chuanqi Wang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
| | - Yongzhen Zhao
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, 530021, China
| | - Shengkang Li
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, Guangdong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, College of Science, Shantou University, Shantou, 515063, Guangdong, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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4
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Rapid sample preparation and low-resource molecular detection of hepatopancreatic parvoviruses (HPV) by recombinase polymerase amplification lateral flow detection assay in shrimps (Fenneropenaeus merguiensis). PLoS One 2022; 17:e0276164. [PMID: 36350876 PMCID: PMC9645652 DOI: 10.1371/journal.pone.0276164] [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: 05/17/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Viral diseases are a major problem in shrimp aquaculture facilities as these diseases reduce growth rates, which inevitably lead to production and profit losses. Hepatopancreatic parvoviruses (HPV) are common diseases in shrimp that appear to be associated with high or low levels of replication in specific genetic lineages. Selective breeding may result in resistance to HPV and improved body traits such as body weight, meat yield and shrimp colour, facilitating shrimp farming. HPV virus titre is commonly determined by quantitative PCR (qPCR), which is a time-consuming method requiring laboratory equipment unsuitable for field implementation. The aim of this study was to develop a simple, robust, rapid and reliable method to detect HPV in low-resource environments. Methods We developed a rapid shrimp HPV test that uses (1) a simple three-step sample preparation protocol, followed by (2) isothermal recombinase polymerase amplification (RPA) and lateral flow strip detection (LFD). Analytical sensitivity testing was performed in a background banana shrimp sample matrix, and retrospective testing of Fenneropenaeus merguiensis hepatopancreas tissues (n = 33) with known qPCR viral titres was used to determine diagnostic sensitivity and specificity. Results The rapid shrimp HPV test could detect as little as 35 genome-equivalent copies per reaction in homogenized F. merguiensis banana shrimp. Retrospective testing of stored tissues (n = 33) indicated 100% diagnostic sensitivity (95% confidence interval, CI: 86–100%) and 100% specificity (95% CI: 66–100%) for detection of HPV. Conclusion The rapid shrimp HPV test could be completed in only 40 minutes, and required only homogenization pestles, some pipettors, and a small heating block for single temperature incubation at 39°C. Critically, our procedure eliminated the time-consuming purification of nucleic acids from samples and when combined with RPA-LFD offers a user-friendly HPV detection format that can potentially be performed on-site. Our approach represents a major step forward in the development of a simple and sensitive end-point method for quick determination of unfavourable HPV virus numbers in shrimp, and has great potential to advance on-site management of shrimps in aquaculture.
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Liu L, Shan LP, Zhou Y, Chen J. Small Molecule Inhibitors of White Spot Syndrome Virus: Promise in Shrimp Seedling Culture. Int J Mol Sci 2021; 22:ijms22073450. [PMID: 33810591 PMCID: PMC8036603 DOI: 10.3390/ijms22073450] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/29/2022] Open
Abstract
Rapid production of prawn (Litopenaeus vannamei) under artificial pressure can result in a series of obvious challenges and is vulnerable to serious losses related to aquatic environmental issues and the unrestrained outbreak of white spot syndrome (WSS). However, to date, there are no therapeutic strategies to contain the spread of the virus. Here, we synthesized 27 coumarin derivatives and evaluated their anti-white spot syndrome virus (WSSV) activity in L. vannamei larvae. We demonstrated that electron-withdrawing and electron-giving substituent groups play an important role in reducing toxicity and WSSV replication, respectively. Two coumarin C2 (2-amino-5-oxo-4-(p-tolyl)-4H,5H-pyrano[3,2-c]chromene-3-carbonitrile) and C7 (2-amino-4-(4-chlorophenyl)-5-oxo-4H,5H-pyrano[3,2-c]chromene-3-carbonitrile) were regarded as the most promising anti-WSSV compounds with maximum antiviral response <5% and median effective concentration <10 mg/L. The mortality of WSSV-infected larvae decreased by more than 60% after exposure to C2 and C7. With continuous immersion of C2 and C7 exchange, the mortality further decreased to 40% at 120 h. Additionally, C2 and C7 are the relatively stable in aquacultural water, making these agents suitable for use in inhibiting WSSV horizontal transmission in static aquaculture systems. These results showed the marked advantages of using C2 and C7 in the shrimp industry, and suggest that they hold potential for the treatment and prevention of WSSV infection in shrimp seedling culture.
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Affiliation(s)
- Lei Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; (L.L.); (L.-P.S.); (Y.Z.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Li-Peng Shan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; (L.L.); (L.-P.S.); (Y.Z.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Yan Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; (L.L.); (L.-P.S.); (Y.Z.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo 315832, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; (L.L.); (L.-P.S.); (Y.Z.)
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Meishan Campus, Ningbo University, Ningbo 315832, China
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Meishan Campus, Ningbo University, Ningbo 315832, China
- Correspondence:
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Jiang S, Zhang H, Ni P, Yu S, Dong H, Zhang A, Cao H, Zhang L, Ruan Y, Cui Z. Genome-Wide Association Study Dissects the Genetic Architecture of Maize Husk Tightness. FRONTIERS IN PLANT SCIENCE 2020; 11:861. [PMID: 32695127 PMCID: PMC7338587 DOI: 10.3389/fpls.2020.00861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/27/2020] [Indexed: 06/01/2023]
Abstract
The husk is a leafy outer tissue that encloses a maize ear. Previously, we identified the optimum husk structure by measuring the husk length, husk layer number, husk thickness and husk width. Husk tightness (HTI) is a combined trait based on the above four husk measurements. Unveiling the genetic basis of HTI will aid in guiding the genetic improvement of maize for mechanical harvesting and for protecting the ear from pest damage and pathogen infection. Here, we used a maize associate population of 508 inbred lines with tropical, subtropical and temperate backgrounds to analyze the genetic architecture of HTI. Evaluating the phenotypic diversity in three different environments showed that HTI exhibited broad natural variations and a moderate heritability level of 0.41. A diversity analysis indicated that the inbred lines having a temperate background were more loosely related than those having a tropical or subtropical background. HTI showed significant negative correlations with husk thickness and width, which indicates that thicker and wider husks wrapped the ear tighter than thinner and slimmer husks. Combining husk traits with ∼1.25 million single nucleotide polymorphisms in a genome-wide association study revealed 27 variants that were significantly associated with HTI above the threshold of P < 7.26 × 10-6. We found 27 candidate genes for HTI that may participate in (1) husk senescence involving lipid peroxidation (GRMZM2G017616) and programmed cell death (GRMZM2G168898 and GRMZM2G035045); (2) husk morphogenesis involving cell division (GRMZM5G869246) and cell wall architecture (GRMZM2G319798); and (3) cell signal transduction involving protein phosphorylation (GRMZM2G149277 and GRMZM2G004207) and the ABSISIC ACID INSENSITIVE3/VIVIPAROUS1 transcription factor (GRMZM2G088427). These results provide useful information for understanding the genetic basis of husk development. Further studies of identified candidate genes will help elucidate the molecular pathways that regulate HTI in maize.
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Affiliation(s)
- Siqi Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Haibo Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Pengzun Ni
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Haixiao Dong
- College of Plant Sciences, Jilin University, Changchun, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Huiying Cao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Lijun Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Zhenhai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
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Du J, Wang W, Chan JFW, Wang G, Huang Y, Yi Y, Zhu Z, Peng R, Hu X, Wu Y, Zeng J, Zheng J, Cui X, Niu L, Zhao W, Lu G, Yuen KY, Yin F. Identification of a Novel Ichthyic Parvovirus in Marine Species in Hainan Island, China. Front Microbiol 2019; 10:2815. [PMID: 31866980 PMCID: PMC6907010 DOI: 10.3389/fmicb.2019.02815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/20/2019] [Indexed: 01/27/2023] Open
Abstract
Parvoviruses are a diverse group of viruses that are capable of infecting a wide range of animals. In this study, we report the discovery of a novel parvovirus, tilapia parvovirus HMU-HKU, in the fecal samples of crocodiles and intestines of tilapia in Hainan Province, China. The novel parvovirus was firstly identified from crocodiles fed with tilapia using next-generation sequencing (NGS). Screening studies revealed that the prevalence of the novel parvovirus in crocodile feces samples fed on tilapia (75–86%) was apparently higher than that in crocodiles fed with chicken (4%). Further studies revealed that the prevalence of the novel parvovirus in tilapia feces samples collected at four areas in Hainan Province was between 40 and 90%. Four stains of the novel parvovirus were identified in this study based on sequence analyses of NS1 and all the four strains were found in tilapia in contrast only two of them were detected in crocodile feces. The nearly full-length genome sequence of the tilapia parvovirus HMU-HKU-1 was determined and showed less than 45.50 and 40.38% amino acid identity with other members of Parvoviridae in NS1 and VP1 genes, respectively. Phylogenetic analysis based on the complete helicase domain amino acid sequences showed that the tilapia parvovirus HMU-HKU-1 formed a relatively independent branch in the newly proposed genus Chaphamaparvovirus in the subfamily Hamaparvovirinae according to the ICTV’s most recent taxonomic criteria for Parvoviridae classification. Tilapia parvovirus HMU-HKU-1 likely represented a new species within the new genus Chaphamaparvovirus. The identification of tilapia parvovirus HMU-HKU provides further insight into the viral and genetic diversity of parvoviruses and its infections in tilapia populations need to be evaluated in terms of pathogenicity and production losses in tilapia farming.
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Affiliation(s)
- Jiang Du
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wenqi Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jasper Fuk-Woo Chan
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Gaoyu Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yi Huang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yufang Yi
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Zheng Zhu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ruoyan Peng
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xiaoyuan Hu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yue Wu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jifeng Zeng
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Haikou, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Haikou, China
| | - Jiping Zheng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiuji Cui
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Lina Niu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wei Zhao
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Gang Lu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Kwok-Yung Yuen
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Feifei Yin
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
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8
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Van Khang P, Van Nha V, Nguyen NH. Resistance to Streptococcus iniae and its genetic associations with traits of economic importance in Asian seabass (Lates calcarifer). JOURNAL OF FISH DISEASES 2019; 42:1657-1666. [PMID: 31591734 DOI: 10.1111/jfd.13092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Streptococcus iniae is one of the most serious aquatic pathogens, causing significant economic losses in marine and freshwater species, including Asian seabass (Lates calcarifer). Controlling this gram-positive bacterial pathogen has been an issue in aquaculture systems, due to the combined effects of aquaculture intensification and climatic impacts. To date, there have not been any genetic parameter estimates for S. iniae resistance in Asian seabass. The main aim of this study was to examine genetic variation in S. iniae resistance and its genetic correlations with growth and cannibalism in Asian seabass families produced from a breeding programme for high growth in 2016 and 2017. The study included a total of 5,835 individual fish that were offspring of 41 sires and 60 dams (31 half-sib and 34 full-sib families). The experimental fish were challenged by intraperitoneal injection with a volume containing 105 CFU (colony-forming unit)/fish. Resistance to S. iniae was measured as survival rate at 6 hr, 3, 5, 7, 10 and 15 days post-challenge test. There were significant variations in S. iniae resistance among families at different observation periods (ranging from 24.4% to 80%). Restricted maximum-likelihood method and mixed model analysis were applied to estimate heritability for S. iniae resistance. The heritability for S. iniae resistance ranged from 7% to 18% across different statistical models used. The common full-sib effects accounted for 0.1%-2% of the total variation in resistance to S. iniae. Genetic correlations of the S. iniae resistance at 6 hr and 3 days with later post-challenge test periods were low to moderate. However, these estimates for S. iniae resistance between successive measurement times (5, 7, 10 and 15 days) were high and close to 1. The genetic correlations of resistance with body weights at 180, 270 and 360 days post-hatch were not significant as well with cannibalism. It is concluded that there is substantial additive genetic variation in resistance to S. iniae, suggesting there is potential for genetic improvement of Asian seabass for resistance to S. iniae through selective breeding.
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Affiliation(s)
- Pham Van Khang
- GenCology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Maroochydore, Qld, Australia
- Department of Science, Technology and Environment, Ministry of Agriculture and Rural Development, Nha Trang, Vietnam
| | - Vo Van Nha
- Research Institute for Aquaculture No. 3, Nha Trang, Khanh Hoa, Vietnam
| | - Nguyen Hong Nguyen
- GenCology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Maroochydore, Qld, Australia
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Nguyen NH, Phuthaworn C, Knibb W. Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis. Genomics 2019; 112:2021-2027. [PMID: 31765824 DOI: 10.1016/j.ygeno.2019.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 01/12/2023]
Abstract
Conventional genetic improvement of disease resistance in aquatic animal species involves challenge tests or using qPCR to quantify viral load that is costly, time-consuming and causing biosecurity concerns. Recent developments in high throughput next generation genome sequencing platforms such as genotyping by sequencing (GBS) have opened new possibilities for improving disease traits based on DNA information. The principal aim of this study was thus to examine potential application of genomic selection to improve resistance to hepatopancreatic parvovirus (HPV) in banana shrimp Fenneropenaeus merguiensis. Specifically, we used a total of 9472 single nucleotide polymorphisms (SNPs) developed de novo from GBS platforms to assess accuracy of genomic prediction for HPV resistance and growth, carcass and quality-related traits in this white shrimp species. Our multi-locus mixed model analysis showed moderate heritabilities for HPV resistance (h2 = 0.46) and other traits studied (0.10 to 0.55). Genetic correlations of HPV titre with growth and carcass traits, estimated using SNPs markers, were negative (i.e., favourable), suggesting that selection for improved growth and carcass traits may have increased HPV resistance (i.e., reduced HPV titre). More importantly, our gBLUP model demonstrated that the accuracy of gBLUP prediction was moderate for HPV disease resistance (0.46). The genomic prediction accuracy was somewhat greater for growth and carcass related traits especially for body weight (0.76) and meat or tail weight (0.77). On the other hand, the prediction accuracy was from 0.25 to 0.41 for quality traits (raw and cooked colour and flesh streaks). Collectively, it is concluded that there are prospects to apply genomic selection in the genetic improvement for increased disease resistance, carcass and quality-related traits in this population of banana shrimp F. merguiensis.
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Affiliation(s)
- Nguyen Hong Nguyen
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia.
| | - Chontida Phuthaworn
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia
| | - Wayne Knibb
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia
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10
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Selection for improved white spot syndrome virus resistance increased larval survival and growth rate of Pacific Whiteleg shrimp, Liptopenaeus vannamei. J Invertebr Pathol 2019; 166:107219. [PMID: 31330143 DOI: 10.1016/j.jip.2019.107219] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/23/2022]
Abstract
Outbreaks of contagious diseases, including White spot syndrome virus (WSSV), occur more frequently due to environment changes and as commercial shrimp production becomes intensified. The over-arching aim of this study was to examine new traits to improve disease resistance of Whiteleg shrimp, Liptopenaeus vannamei, to WSSV. Specifically, we made a compressive evaluation of the breeding population to determine a suitable selection criterion for improved WSSV resistance. To achieve this objective, we analysed five traits (viral titre, WSSV resistance, larval survival, body weight and standard length) recorded for 120,000 individual shrimps that were offspring of 228 sires and 300 dams produced over two generations of selection in 2017 and 2018. Our restricted maximum likelihood mixed model analysis showed that there is additive genetic variation in viral copy number (or viral titre, viral load) with the heritability that equals 0.18 ± 0.02. Viral titre displayed a moderate and negative genetic correlation with WSSV resistance (rg = -0.55). These results suggest that viral titre can be used as a selection criterion to improve WSSV resistance, but selection for decreased viral titre (i.e., increased resistance) may not capture all genetic expression in WSSV resistance. In addition to the estimation of population genetic parameters, we evaluated direct response to selection for increased WSSV resistance, which was measured as differences in estimated breeding values between the high and low resistant lines. The direct genetic gain achieved for WSSV resistance averaged 12.9% after one generation of selection in this Whiteleg shrimp population. The selection program also resulted in positive impacts on growth and larval survival by 7% and 17%, respectively. There is abundant genetic variation in WSSV resistance (h2 = 0.19-0.27), suggesting that the tested Whiteleg shrimp population will continue to respond to future selection. Collectively, the results obtained in our study provide important information to assist the design and implementation of genetic improvement programs for disease traits in aquaculture species, including L. vannamei.
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Trang TT, Hung NH, Ninh NH, Knibb W, Nguyen NH. Genetic Variation in Disease Resistance Against White Spot Syndrome Virus (WSSV) in Liptopenaeus vannamei. Front Genet 2019; 10:264. [PMID: 30984244 PMCID: PMC6447704 DOI: 10.3389/fgene.2019.00264] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 03/08/2019] [Indexed: 01/20/2023] Open
Abstract
White Spot Syndrome Virus (WSSV) is the most damaging pathogen in terms of production and economic losses for the shrimp sector world-wide. Estimation of heritability for WSSV resistance was made in this study to obtain necessary parameter inputs for broadening the breeding objectives of an ongoing selective breeding programme for Whiteleg shrimp (Liptopenaeus vannamei) that has focussed exclusively on improving growth performance since 2014. The present study involved a disease challenge test experiment using a total of 15,000 shrimps from 150 full- and half-sib families (100 individuals per family). Survival rates were recorded at six different experimental periods: 1–3 days (S1), 1–5 days (S2), 1–7 days (S3), 1–9 days (S4), 1–12 days (S5), and 1–15 days (S6) and were used as measures of WSSV resistance. There was significant variation in WSSV resistance among families studied. Quantitative-real time PCR (qPCR) analysis showed that the amount of viral titer (viral load) was significantly lower in high than low resistance families. Analyses of heritability were carried out using linear mixed model (LMM) and threshold logistic generalized model (TLGM). Both linear and threshold models used showed that the heritability (h2) for WSSV resistance was moderate in the early infection phases (S1–S4), whilst a low h2 value was observed for survival after 12 and 15 days of the challenge test (S5 and S6). The transformed heritabilities for WSSV resistance ranged from 1 to 31% which were somewhat lower than those estimated on the liability scale. Genetic correlations between survival rates measured over six different days post-infection were high and positive (0.82–0.99). The phenotypic correlations ranged from 0.31 ± 0.01 to 0.97 ± 0.01. The genetic correlations between body weights and WSSV resistance were negative. Our results on the heritability and genetic correlations show that improvement of WSSV resistance can be achieved through selective breeding in this population of Whiteleg shrimp.
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Affiliation(s)
- Trinh Thi Trang
- Faculty of Science, Health, Education and engineering, GeneCology Research Centre, University of the Sunshine Coast, Maroochydore, QLD, Australia.,Vietnam National University of Agriculture, Gia Lâm, Vietnam
| | - Nguyen Huu Hung
- Research Institute for Aquaculture No. 3, Nha Trang, Vietnam
| | - Nguyen Huu Ninh
- Research Institute for Aquaculture No. 3, Nha Trang, Vietnam
| | - Wayne Knibb
- Vietnam National University of Agriculture, Gia Lâm, Vietnam
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Nguyen NH, Fitzgibbon QP, Quinn J, Smith G, Battaglene S, Knibb W. Can metamorphosis survival during larval development in spiny lobster Sagmariasus verreauxi be improved through quantitative genetic inheritance? BMC Genet 2018; 19:27. [PMID: 29728054 PMCID: PMC5936031 DOI: 10.1186/s12863-018-0621-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 04/30/2018] [Indexed: 11/17/2022] Open
Abstract
Background One of the major impediments to spiny lobster aquaculture is the high cost of hatchery production due to the long and complex larval cycle and poor survival during the many moult stages, especially at metamorphosis. We examined if the key trait of larval survival can be improved through selection by determining if genetic variance exists for this trait. Specifically, we report, for the first time, genetic parameters (heritability and correlations) for early survival rates recorded at five larval phases; early-phyllosoma stages (instars 1–6; S1), mid-phyllosoma stages (instars; 7–12; S2), late-phyllosoma stages (instars 13–17; S3), metamorphosis (S4) and puerulus stage (S5) in hatchery-reared spiny lobster Sagmariasus verreauxi. Results The data were collected from a total of 235,060 larvae produced from 18 sires and 30 dams over nine years (2006 to 2014). Parentage of the offspring and full-sib families was verified using ten microsatellite markers. Analysis of variance components showed that the estimates of heritability for all the five phases of larval survival obtained from linear mixed model were generally similar to those obtained from threshold logistic generalised models (0.03–0.47 vs. 0.01–0.50). The heritability estimates for survival traits recorded in the early larval phases (S1 and S2) were higher than those estimated in later phases (S3, S4 and S5). The existence of the additive genetic component in larval survival traits indicate that they could be improved through selection. Both phenotypic and genetic correlations among the five survival measures studied were moderate to high and positive. The genetic associations between successive rearing periods were stronger than those that are further apart. Conclusions Our estimates of heritability and genetic correlations reported here in a spiny lobster species indicate that improvement in the early survival especially during metamorphosis can be achieved through genetic selection in this highly economic value species. Electronic supplementary material The online version of this article (10.1186/s12863-018-0621-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nguyen H Nguyen
- GeneCology Research Center, The University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.
| | - Quinn P Fitzgibbon
- Fisheries and Aquaculture, Institute of Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia
| | - Jane Quinn
- GeneCology Research Center, The University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
| | - Greg Smith
- Fisheries and Aquaculture, Institute of Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia
| | - Stephen Battaglene
- Fisheries and Aquaculture, Institute of Marine and Antarctic Studies, University of Tasmania, Private Bag 49, Hobart, TAS, 7001, Australia
| | - Wayne Knibb
- GeneCology Research Center, The University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia
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