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Chen Q, Ma X, Wang J, Shi M, Hu G, Chen S, Zhou Q. Multi-organ transcriptomic profiles and gene-regulation network underlying vibriosis resistance in tongue sole. Sci Data 2024; 11:819. [PMID: 39048589 PMCID: PMC11269662 DOI: 10.1038/s41597-024-03651-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: 02/21/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Vibrio spp. are major pathogens responsible for mortality and disease in various marine aquaculture organisms. Effective disease control and genetic breeding strategies rely heavily on understanding host vibriosis resistance mechanisms. The Chinese tongue sole (Cynoglossus semilaevis) is economically vital but suffers from substantial mortalities due to vibriosis. Through continuous selective breeding, we have successfully obtained vibriosis-resistant families of this species. In this study, we conducted RNA-seq analysis on three organs, including liver, spleen and intestine from selected resistant and susceptible tongue soles. Additionally, we integrated these data with our previously published RNA-seq datasets of skin and gill, enabling the construction of organ-specific transcriptional profiles and a comprehensive gene co-expression network elucidating the differences in vibriosis resistance. Furthermore, we identified 12 modules with organ-specific functional implications. Overall, our findings provide a valuable resource for investigating the molecular basis of vibriosis resistance in fish, offering insights into target genes and pathways essential for molecular selection and genetic manipulation to enhance vibriosis resistance in fish breeding programs.
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Affiliation(s)
- Quanchao Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xinran Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Jie Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Meng Shi
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Guobin Hu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
| | - Qian Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
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Wang L, Tian M, Chen S. Differentially expressed proteins and microbial communities of the skin regulate disease resistance to Chinese tongue sole ( Cynoglossus semilaevis). Front Immunol 2024; 15:1352469. [PMID: 38711504 PMCID: PMC11071164 DOI: 10.3389/fimmu.2024.1352469] [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: 12/11/2023] [Accepted: 03/20/2024] [Indexed: 05/08/2024] Open
Abstract
Vibriosis, caused by Vibrio, seriously affects the health of fish, shellfish, and shrimps, causing large economic losses. Teleosts are represent the first bony vertebrates with both innate and adaptive immune responses against pathogens. Aquatic animals encounter hydraulic pressure and more pathogens, compared to terrestrial animals. The skin is the first line of defense in fish, constituting the skin-associated lymphoid tissue (SALT), which belongs to the main mucosa-associated lymphoid tissues (MALT). However, little is known about the function of immunity related proteins in fish. Therefore, this study used iTRAQ (isobaric tags for relative and absolute quantitation) to compare the skin proteome between the resistant and susceptible families of Cynoglossus semilaevis. The protein integrin beta-2, the alpha-enolase isoform X1, subunit B of V-type proton ATPase, eukaryotic translation initiation factor 6, and ubiquitin-like protein ISG15, were highly expressed in the resistant family. The 16S sequencing of the skin tissues of the resistant and susceptible families showed significant differences in the microbial communities of the two families. The protein-microbial interaction identified ten proteins associated with skin microbes, including immunoglobulin heavy chain gene (IGH), B-cell lymphoma/leukemia 10 (BCL10) and pre-B-cell leukemia transcription factor 1 isoform X2 (PBX2). This study highlights the interaction between skin proteins and the microbial compositions of C. semilaevis and provides new insights into understanding aquaculture breeding research.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Min Tian
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, China
- Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
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Ma X, Chen Q, Chen Z, Chen S, Zhou Q. Genome-wide DNA methylation mediates the resistance to vibriosis in Cynoglossus semilaevis. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109144. [PMID: 37805114 DOI: 10.1016/j.fsi.2023.109144] [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: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine fish in China. However, vibriosis has caused huge mortality and economic losses in its culturing industry. To reveal the effect of DNA methylation on the resistance to vibriosis in tongue sole, we conducted RNA sequencing and whole genome bisulfite sequencing (WGBS), and compared the gene expressions and DNA methylation patterns between the resistant and susceptible families. We identified a total of 741 significantly differentially expressed genes (DEGs) in kidney and 17460 differentially methylated genes (DMGs), which were both enriched in immune-related pathways, such as "cAMP signaling pathway" and "NOD-like receptor signaling pathway". Through the correlation analysis of DEGs and DMGs, we identified two important immune pathways, including "complement and coagulation cascades", and "cytokine-cytokine receptor interaction", which played important roles in regulating the inflammation level and immune homeostasis. For example, the expression of proinflammatory cytokine il17c was down-regulated under the regulation of DNA methylation; in addition, the expression of protease-activated receptor 3 (par3) was up-regulated, which could induce the up-expressionof il8. These results demonstrated that the regulation of DNA methylation on the genes involved in immune responses might contribute to the resistance to vibriosis in tongue sole, and provided a basis for the control of diseases in fish aquaculture.
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Affiliation(s)
- Xinran Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Shandong Key Laboratory for Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, Shandong, 266071, China; Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Ocean University, Lianyungang, 222000, China
| | - Quanchao Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Shandong Key Laboratory for Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, Shandong, 266071, China
| | - Zhangfan Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Shandong Key Laboratory for Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, Shandong, 266071, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Shandong Key Laboratory for Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, Shandong, 266071, China
| | - Qian Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China; Shandong Key Laboratory for Marine Fisheries Biotechnology and Genetic Breeding, Qingdao, Shandong, 266071, China.
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Zhou Q, Chen Y, Chen Z, Wang L, Ma X, Wang J, Zhang Q, Chen S. Genomics and transcriptomics reveal new molecular mechanism of vibriosis resistance in fish. Front Immunol 2022; 13:974604. [PMID: 36304468 PMCID: PMC9592550 DOI: 10.3389/fimmu.2022.974604] [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: 06/21/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Infectious diseases have caused dramatic production decline and economic loss for fish aquaculture. However, the poor understanding of fish disease resistance severely hampered disease prevention. Chinese tongue sole (Cynoglossus semilaevis) is an important economic flatfish suffering from vibriosis. Here we used genomic, transcriptomic and experimental approaches to investigate the molecular genetic mechanisms underlying fish vibriosis resistance. A genome-wide comparison revealed that the genes under selective sweeps were enriched for glycosaminoglycan (GAG) chondroitin sulfate (CS)/dermatan sulfate (DS) metabolism. Transcriptomic analyses prioritized synergic gene expression patterns in this pathway, which may lead to an increased CS/DS content in the resistant family. Further experimental evidence showed that carbohydrate sulfotransferases 12 (Chst12), a key enzyme for CS/DS biosynthesis, has a direct antibacterial activity. To the best of our knowledge, this is the first report that the chst12 gene has a bactericidal effect. In addition, CS/DS is a major component of the extracellular matrix (ECM) and the selection signatures and fine-tuned gene expressions of ECM-receptor interaction genes indicated a modification in the ECM structure with an enhancement of the barrier function. Furthermore, functional studies conducted on Col6a2, encoding a collagen gene which constitutes the ECM, pointed to that it may act as a cellular receptor for Vibrio pathogens, thus plays an important role for the Vibrio invasion. Taken together, these findings provide new insights into the molecular protective mechanism underlying vibriosis resistance in fish, which offers crucial genomic resources for the resistant germplasm breeding and infectious disease control in fish culturing.
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Affiliation(s)
- Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
| | - Yadong Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Zhangfan Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Xinran Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Jie Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Qihao Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
- College of Life Science, Qingdao University, Qingdao, China
- *Correspondence: Songlin Chen,
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Zhou Q, Zhu X, Li Y, Yang P, Wang S, Ning K, Chen S. Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis. MICROBIOME 2022; 10:153. [PMID: 36138436 PMCID: PMC9503257 DOI: 10.1186/s40168-022-01346-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/10/2022] [Indexed: 06/06/2023]
Abstract
BACKGROUND Infectious diseases have caused huge economic loss and food security issues in fish aquaculture. Current management and breeding strategies heavily rely on the knowledge of regulative mechanisms underlying disease resistance. Though the intestinal microbial community was linked with disease infection, there is little knowledge about the roles of intestinal microbes in fish disease resistance. Cynoglossus semilaevis is an economically important and widely cultivated flatfish species in China. However, it suffers from outbreaks of vibriosis, which results in huge mortalities and economic loss. RESULTS Here, we used C. semilaevis as a research model to investigate the host-microbiome interactions in regulating vibriosis resistance. The resistance to vibriosis was reflected in intestinal microbiome on both taxonomic and functional levels. Such differences also influenced the host gene expressions in the resistant family. Moreover, the intestinal microbiome might control the host immunological homeostasis and inflammation to enhance vibriosis resistance through the microbe-intestine-immunity axis. For example, Phaeobacter regulated its hdhA gene and host cyp27a1 gene up-expressed in bile acid biosynthesis pathways, but regulated its trxA gene and host akt gene down-expressed in proinflammatory cytokines biosynthesis pathways, to reduce inflammation and resist disease infection in the resistant family. Furthermore, the combination of intestinal microbes and host genes as biomarkers could accurately differentiate resistant family from susceptible family. CONCLUSION Our study uncovered the regulatory patterns of the microbe-intestine-immunity axis that may contribute to vibriosis resistance in C. semilaevis. These findings could facilitate the disease control and selective breeding of superior germplasm with high disease resistance in fish aquaculture. Video Abstract.
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Affiliation(s)
- Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture; Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, Shandong, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture; Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, Shandong, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Shengpeng Wang
- Dezhou Key Laboratory for Applied Bile Acid Research, Shandong Longchang Animal Health Product Co., Ltd., Qihe, Shandong Lachance Co., Ltd., Jinan, 251100, Shandong, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture; Shandong Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, Shandong, China.
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Wang R, Lin X, Zha G, Wang J, Huang W, Wang J, Hou Y, Mou H, Zhang T, Zhu H, Wang J. Mechanism of enrofloxacin-induced multidrug resistance in the pathogenic Vibrio harveyi from diseased abalones. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154738. [PMID: 35331762 DOI: 10.1016/j.scitotenv.2022.154738] [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: 01/05/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Vibrio harveyi infection had caused severe economic losses in aquaculture. A pathogenic V. harveyi strain had been successfully induced to be a multiple-resistant strain by enrofloxacin (EFX), then the mechanism of multidrug resistance was analyzed. It suggested that the minimum inhibitory concentration of EFX increased by 32-folds. Results of the Kirby-Bauer test showed that the inhibitory zone diameter was 25.3 mm for the sensitive strain (labeled as HL-S) and 8.5 mm for the resistant strain (labeled as HL-R). After 20 serial passages, even when the stress of EFX was removed, the resistance persisted. After induction of EFX, HL-R resisted to other fluoroquinolones, it even resisted to furazolidone and streptomycin, although it was sensitive to these antibiotics initially. Its sensitivity to rifampicin and doxycycline also decreased obviously. Results showed that 3522 differentially expressed genes were identified. Expression of the multidrugs efflux resistance-nodulation-cell division was significantly upregulated (164.61-folds) in HL-R. Other key genes connected with drug efflux were also upregulated significantly (p<0.05). Notably, recA encoded for recombination protein was upregulated significantly, lexA was downregulated significantly in HL-R. Research results showed that the efflux system and the save our souls system have played crucial roles during the development of multidrug resistance of V. harveyi.
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Affiliation(s)
- Ruixuan Wang
- Hanshan Normal University, Chaozhou 521041, China
| | - Xiaozhi Lin
- Hanshan Normal University, Chaozhou 521041, China
| | - Guangcai Zha
- Hanshan Normal University, Chaozhou 521041, China
| | - Juan Wang
- Hanshan Normal University, Chaozhou 521041, China
| | - Wei Huang
- Hanshan Normal University, Chaozhou 521041, China
| | | | - Yuee Hou
- Zhuhai Kerric Testing Co., Ltd., Zhuhai 519000, China
| | - Hongli Mou
- South China Sea Fisheries Research Institute, Guangzhou 510300, China
| | - Ting Zhang
- Hanshan Normal University, Chaozhou 521041, China
| | - Hui Zhu
- Hanshan Normal University, Chaozhou 521041, China
| | - Jun Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
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Zhang X, Hao X, Ma W, Zhu T, Zhang Z, Wang Q, Liu K, Shao C, Wang HY. Transcriptome Analysis Indicates Immune Responses against Vibrio harveyi in Chinese Tongue Sole (Cynoglossus semilaevis). Animals (Basel) 2022; 12:ani12091144. [PMID: 35565570 PMCID: PMC9104532 DOI: 10.3390/ani12091144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Limited understanding of molecular mechanisms of immune response constrains marine fish farming. Analyzing the dynamic gene expression profile of fish in response to pathogen infection is gaining interest. We analyzed the expression changes of the Chinese tongue sole kidney after Vibrio harveyi infection with a series of transcriptome data. Notably, we observed rapid up-regulation of IL-17, TNF and TLR signaling pathways, indicating treatment measures should be taken in the early stage after infection. We also found a close connection between the immune system and neuroendocrine system, which may be the new strategy to improve immune function. Our research provides insights into disease prevention and treatment in fish farming. Abstract Pathogenic infection of fishes is an important constraining factor affecting marine aquaculture. Insufficient understanding of the molecular mechanisms has affected the diagnosis and corresponding treatment. Here, we reported the dynamic changes of gene expression patterns in the Chinese tongue sole kidney at 16 h, 48 h, 72 h and 96 h after Vibrio harveyi infection. In total, 366, 214, 115 and 238 differentially expressed genes were obtained from the 16 h−vs. −C, 48 h−vs. −C, 72 h−vs. −C and 96 h−vs. −C group comparisons, respectively. KEGG enrichment analysis revealed rapid up-regulation of several immune-related pathways, including IL-17, TNF and TLR signaling pathway. More importantly, time-series analyses of transcriptome showed that immune genes were specifically up-regulated in a short period of time and then decreased. The expression levels of chemokines increased after infection and reached a peak at 16 h. Specifically, Jak-STAT signaling pathway played a crucial role in the regulation during Vibrio harveyi infection. In the later stages of infection, genes in the neuroendocrine pathway, such as glucocorticoid-related genes, were activated in the kidney, indicating a close connection between the immune system and neuroendocrine system. Our dynamic transcriptome analyses provided profound insight into the gene expression profile and investigation of immunogenetic mechanisms of Chinese tongue sole.
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Affiliation(s)
- Xianghui Zhang
- College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China;
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
| | - Xiancai Hao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
| | - Wenxiu Ma
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
| | - Tengfei Zhu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
| | - Zhihua Zhang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
| | - Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Hong-Yan Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266072, China; (X.H.); (W.M.); (T.Z.); (Z.Z.); (Q.W.); (K.L.); (C.S.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Correspondence:
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Shi R, Li X, Cheng P, Yang Q, Chen Z, Chen S, Wang N. Characterization of growth differentiation factor 9 and bone morphogenetic factor 15 in Chinese tongue sole (Cynoglossus semilaevis): Sex-biased expression pattern and promoter regulation. Theriogenology 2022; 182:119-128. [DOI: 10.1016/j.theriogenology.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
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9
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Li Y, Hu Y, Yang Y, Zheng W. Insights into the genetic covariation between harvest survival and growth rate in olive flounder (Paralichthys olivaceus) under commercial production environment. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Li Y, Wang S, Hu Y, Cheng J, Cheng X, Cheng P, Cui Z. Dietary bile acid supplementation reveals beneficial effects on intestinal healthy status of tongue sole (Cynoglossus semiliaevis). FISH & SHELLFISH IMMUNOLOGY 2021; 116:52-60. [PMID: 34216786 DOI: 10.1016/j.fsi.2021.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/27/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The aim of this study was to investigate the effects of dietary bile acids (BAs) on intestinal healthy status of tongue sole in terms of immunity, antioxidant status, digestive ability, mucosal barrier-related genes expression and microbiota. Three experimental diets were prepared with BA levels at 0 mg/kg (CT), 300 mg/kg (BA1) and 900 mg/kg (BA2) in a commercial basal diet. Each diet was fed to three replicates with 120 fish (10.87 ± 0.32 g) in each tank. After an 8-week feeding trial, growth parameters were significantly enhanced in both BAs supplementary groups (P < 0.05), and compared with CT group, survival rate in BA2 group was significantly improved (P < 0.05). Intestinal lysozyme activity and contents of immunoglobulin M and complement 3 were significantly increased in both BAs supplementary groups (P < 0.05), suggesting an enhancement effect on the non-specific immune response. BAs inclusion also significantly improved intestinal antioxidant capabilities by increasing antioxidase activities and decreasing malondialdehyde levels. In addition, compared with CT group, intestinal digestive ability was substantially enhanced as indicated by the significantly increased lipase activity in BA2 group (P < 0.05) and significantly increased amylase activity in BA1 and BA2 groups (P < 0.05). Coincidentally, BAs inclusion significantly upregulated the relative expression of intestinal mucosal barrier-related genes (P < 0.05). Further, dietary BAs distinctly remodeled intestinal microbiota by decreased the abundance of some potential pathogenic bacteria. In conclusion, dietary BAs supplementation is an effective way to improve the intestinal healthy status of tongue sole.
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Affiliation(s)
- Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Shengpeng Wang
- Dezhou Key Laboratory for Applied Bile Acid Research, Shandong Longchang Animal Health Product CO., Ltd., Dezhou 251100, China.
| | - Yuanri Hu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Jiayu Cheng
- Engineering and Technology Center for Flatfish Aquaculture of Tangshan, Tangshan Weizhuo Aquaculture Co., Ltd., Tangshan 063202, China
| | - Xiangming Cheng
- Engineering and Technology Center for Flatfish Aquaculture of Tangshan, Tangshan Weizhuo Aquaculture Co., Ltd., Tangshan 063202, China
| | - Peng Cheng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhongkai Cui
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
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11
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Fu X, Chen Y, Wang L, Zhou Q, Li M, Song Y, Li Y, Zhao F, Chen S. Identification and functional analysis of the perforin-1 like gene in disease resistance in half smooth tongue sole (Cynoglossus semilaevis). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 122:104135. [PMID: 34004267 DOI: 10.1016/j.dci.2021.104135] [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: 03/01/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
The pore-forming protein perforin is one of the effectors of cell-mediated killing via the granule exocytosis pathway. In this study, a genome-wide association study was conducted in Vibrio harveyi disease-resistant and disease-susceptible families of half smooth tongue sole (Cynoglossus semilaevis) to determine the genes accounting for host resistance, and a perforin homologue was identified, designated perforin-1 like (CsPRF1l). The full-length cDNA of CsPRF1l is 1835 bp, and encodes 514 amino acids. The CsPRF1l gene consists of 10 exons and 9 introns, spanning approximately 7 kb. The amino acid sequence of CsPRF1l shows 60.35, 54.03, 41.92, and 34.17% identities to Morone saxatilis PRF1l, Oryzias melastigma PRF1l, Danio rerio PRF1.5 and Homo sapiens PRF, respectively. Sequence analysis revealed the presence of membrane attack complex/perforin (MACPF) and C2 domains in CsPRF1l. Quantitative real-time PCR showed that CsPRF1l presented a higher intestinal expression level in disease-resistant families than in susceptible families. Tissue expression pattern analysis showed that CsPRF1l is present in most of the tested tissues and highly expressed in the intestine, brain, stomach and gills. After challenge with V. harveyi, CsPRF1l mRNA was markedly upregulated in the liver, spleen, kidney, intestine, gills and skin. In addition, the recombinant CsPRF1l protein exhibited obvious antimicrobial activity against V. harveyi in vitro and in a zebrafish model. Collectively, these data indicate that CsPRF1l modulates host immune defense against V. harveyi invasion and provide clues about the efficacy of rCsPRF1l in fish that will give rise to useful therapeutic applications for V. harveyi infection in C. semilaevis.
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Affiliation(s)
- Xiaoqin Fu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yadong Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Ming Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yu Song
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Fazhen Zhao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
| | - Songlin Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology(Qingdao), Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
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12
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Chen Z, Wang L, Xu X, Zhou Q, Wang J, Chen Y, Wang N, Gong Z, Chen S. Molecular cloning and immune characterization of CIITA in artificially challenged Chinese tongue sole (Cynoglossus semilaevis) with Vibrio harveyi. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 121:104091. [PMID: 33819543 DOI: 10.1016/j.dci.2021.104091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
In mammals, Class II, major histocompatibility complex (MHC II) transactivator (CIITA) recognizes microbial pathogens and triggers immune responses. In Chinese tongue sole Cynoglossus semilaevis, Cs-CIITA was prevalently expressed in various tissues. Cs-CIITA, Cs-MHC IIA and Cs-MHC IIB were expressed significantly higher in skin in susceptible families infected with Vibrio harveyi, while higher expression of Cs-CIITA and Cs-MHC IIB was examined in liver in resistant families. In addition, the three genes were up-regulated in gill, skin, intestine, liver, spleen and kidney at 48 h or 72 h after V. harveyi infection. Furthermore, the three genes were co-expressed in the epithelial mucous cells of gill, skin, and intestine. Knockdown of Cs-CIITA regulates the expression of other inflammation-related genes, including CD40, IL-1β, IL-8, RelB, NFκB, and Myd88. These results suggest that CIITA functions in the inflammatory responses of C. semilaevis against V. harveyi, via MHC II transcriptional regulation.
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Affiliation(s)
- Zhangfan Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Xiwen Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Jie Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yadong Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Na Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Zhihong Gong
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (CAFS), Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Qingdao, 266071,China.
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13
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Griot R, Allal F, Phocas F, Brard-Fudulea S, Morvezen R, Haffray P, François Y, Morin T, Bestin A, Bruant JS, Cariou S, Peyrou B, Brunier J, Vandeputte M. Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass ( Dicentrarchus labrax) and the Gilthead Sea Bream ( Sparus aurata). Front Genet 2021; 12:665920. [PMID: 34335683 PMCID: PMC8317601 DOI: 10.3389/fgene.2021.665920] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K-60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51-0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream.
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Affiliation(s)
- Ronan Griot
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Romain Morvezen
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France
| | | | | | - Thierry Morin
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Viral Fish Diseases Unit, National Reference Laboratory for Regulated Fish Diseases, Technopôle Brest-Iroise, Plouzané, France
| | | | | | | | - Bruno Peyrou
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Joseph Brunier
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Marc Vandeputte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
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14
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Lu S, Zhou Q, Chen Y, Liu Y, Li Y, Wang L, Yang Y, Chen S. Development of a 38 K single nucleotide polymorphism array and application in genomic selection for resistance against Vibrio harveyi in Chinese tongue sole, Cynoglossus semilaevis. Genomics 2021; 113:1838-1844. [PMID: 33819565 DOI: 10.1016/j.ygeno.2021.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/20/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022]
Abstract
Based on 1572 re-sequenced Chinese tongue sole (Cynoglossus semilaevis), we investigated the accuracy of four genomic methods at predicting genomic estimated breeding values (GEBVs) of Vibrio harveyi resistance in C. semilaevis when SNPs varying from 500 to 500 k. All methods outperformed the pedigree-based best linear unbiased prediction when SNPs reached 50 k or more. Then, we developed an SNP array "Solechip No.1" for C. semilaevis breeding using the Affymetrix Axiom technology. This array contains 38,295 SNPs with an average of 10.5 kb inter-spacing between two adjacent SNPs. We selected 44 candidates as the parents of 23 families and genotyped them by the array. The challenge survival rates of offspring families had a correlation of 0.706 with the mid-parental GEBVs. This SNP array is a convenient and reliable tool in genotyping, which could be used for improving V. harveyi resistance in C. semilaevis coupled with the genomic selection methods.
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Affiliation(s)
- Sheng Lu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Wuxi Fisheries College, Nanjing Agricultural University, 214081 Wuxi, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Yadong Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Yang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Yingming Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, 266071 Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266373, China; Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 266071 Qingdao, China.
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15
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Transcriptome analysis and candidate gene identification reveals insights into the molecular mechanisms of hypermelanosis in Chinese tongue sole (Cynoglossus semilaevis). AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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16
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Dinh Pham K, Ødegård J, Van Nguyen S, Magnus Gjøen H, Klemetsdal G. Genetic analysis of resistance in Mekong striped catfish (Pangasianodon hypophthalmus) to bacillary necrosis caused by Edwardsiella ictaluri. JOURNAL OF FISH DISEASES 2021; 44:201-210. [PMID: 33217014 DOI: 10.1111/jfd.13279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study was to analyse four cohabitation challenge-test experiments with Mekong striped catfish (Pangasianodon hypophthalmus) against the bacterium Edwardsiella ictaluri. The data were genetically analysed per experiment by three models: 1) a cross-sectional linear model; 2) a cross-sectional threshold model; and 3) a linear survival model, at both 50% mortality (for models 1 and 2) and at the end of the test (for all three models). In two of the experiments (3 and 4) that were carried out in two replicated tanks, the predicted family effects (sum of sire, dam and common environmental effects) in each tank were correlated with the family survival in the other replicated tank (cross-validation). The heritability estimates of resistance to E. ictaluri infection were ≤ 0.012 with the survival model, and up to 0.135 - 0.220 (50% survival) and 0.085 and 0.174 (endpoint survival) for the cross-sectional linear and threshold models, respectively. The challenge test should aim for an endpoint survival that ceases naturally at 50%. Then, genetic analysis should be carried out for survival at the endpoint (reflecting susceptibility) with a simple cross-sectional linear model.
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Affiliation(s)
- Khoi Dinh Pham
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
- Research Institute for Aquaculture No. 2 (RIA2), Ho Chi Minh City, Vietnam
| | - Jørgen Ødegård
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
- AquaGen AS, Trondheim, Norway
| | - Sang Van Nguyen
- Research Institute for Aquaculture No. 2 (RIA2), Ho Chi Minh City, Vietnam
| | - Hans Magnus Gjøen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Gunnar Klemetsdal
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway
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17
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Li M, Yang Y, Zheng W, Li Z, Cheng J, Li Y. Estimation of heritabilities of disease resistance to Edwardsiella tarda and genetic correlations between resistance and growth traits in Chinese tongue sole (Cynoglossus semilaevis). AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2019.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Prediction of genomic breeding values based on pre-selected SNPs using ssGBLUP, WssGBLUP and BayesB for Edwardsiellosis resistance in Japanese flounder. Genet Sel Evol 2020; 52:49. [PMID: 32811444 PMCID: PMC7437005 DOI: 10.1186/s12711-020-00566-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/03/2020] [Indexed: 02/06/2023] Open
Abstract
Background Edwardsiella tarda causes acute symptoms with ascites in Japanese flounder (Paralichthys olivaceus) and is a major problem for China’s aquaculture sector. Genomic selection (GS) has been widely adopted in breeding industries because it shortens generation intervals and results in the selection of individuals that have great breeding potential with high accuracy. Based on an artificial challenge test and re-sequenced data of 1099 flounders, the aims of this study were to estimate the genetic parameters of resistance to E. tarda in Japanese flounder and to evaluate the accuracy of single-step GBLUP (ssGBLUP), weighted ssGBLUP (WssGBLUP), and BayesB for improving resistance to E. tarda by using three subsets of pre-selected single nucleotide polymorphisms (SNPs). In addition, SNPs that are associated with this trait were identified using a single-SNP genome-wide association study (GWAS) and WssGBLUP. Results We estimated a heritability of 0.13 ± 0.02 for resistance to E. tarda in Japanese flounder. One million SNPs at fixed intervals were selected from 4,978,724 SNPs that passed quality controls. GWAS identified significant SNPs on chromosomes 14 and 24. WssGBLUP revealed that the putative quantitative trait loci on chromosomes 1 and 14 contained SNPs that explained more than 1% of the genetic variance. Three 50 k-SNP subsets were pre-selected based on different criteria. Compared with pedigree-based prediction (ABLUP), the three genomic methods evaluated resulted in at least 7.7% greater accuracy of predictions. The accuracy of these genomic prediction methods was almost unchanged when pre-selected trait-related SNPs were used for prediction. Conclusions Resistance to E. tarda in Japanese flounder has a low heritability. GWAS and WssGBLUP revealed that the genetic architecture of this trait is polygenic. Genomic prediction of breeding values performed better than ABLUP. It is feasible to implement genomic selection to increase resistance to E. tarda in Japanese flounder with 50 k SNPs. Based on the criteria used here, pre-selection of SNPs was not beneficial and other criteria for pre-selection should be considered.
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Zhou Q, Su Z, Li Y, Liu Y, Wang L, Lu S, Wang S, Gan T, Liu F, Zhou X, Wei M, Liu G, Chen S. Genome-Wide Association Mapping and Gene Expression Analyses Reveal Genetic Mechanisms of Disease Resistance Variations in Cynoglossus semilaevis. Front Genet 2019; 10:1167. [PMID: 31824570 PMCID: PMC6880758 DOI: 10.3389/fgene.2019.01167] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/23/2019] [Indexed: 12/15/2022] Open
Abstract
The sustainable development of aquaculture has been impeded by infectious diseases worldwide. However, the genomic architecture and the genetic basis underlying the disease resistance remain poorly understood, which severely hampers both the understanding of the evolution of fish disease resistance traits and the prevention of these diseases in the aquaculture community. Cynoglossus semilaevis is a representative and commercially-important flatfish species. Here we combined genome-wide association study and Fst and nucleotide diversity filtration to identify loci important for the disease resistance. Based on 1,016,774 single-nucleotide polymorphisms (SNPs) identified from 650 Gb genome resequencing data of 505 individuals, we detected 33 SNPs significantly associated with disease resistance and 79 candidate regions after filtration steps. Both the allele frequencies and genotype frequencies of the associated loci were significantly different between the resistant and susceptible fish, suggesting a role in the genetic basis of disease resistance. The SNP with strongest association with disease resistance was located in Chr 17, at 145 bp upstream of fblx19 gene, and overlapped with the major quantitative trait locus previously identified. Several genes, such as plekha7, nucb2, and fgfr2, were also identified to potentially play roles in the disease resistance. Furthermore, the expression of some associating genes were likely under epigenetic regulations between the bacterial resistant and susceptible families. These results provide insights into the mechanism that enable variation of disease resistance to bacterial pathogen infection. The identified polymorphisms and genes are valuable targets and molecular resources for disease resistance and other traits, and for advanced breeding practice for superior germplasm in fish aquaculture.
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Affiliation(s)
- Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
| | - Zhencheng Su
- Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Yang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Sheng Lu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Shuanyan Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Tian Gan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Feng Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Xun Zhou
- Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Min Wei
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Guangjian Liu
- Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
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