1
|
Niu M, Whang H, Wu Z, Jiang S, Chen L. Deletion of Asb15b gene can lead to a significant decrease in zebrafish intermuscular bone. Gene 2024; 923:148561. [PMID: 38754570 DOI: 10.1016/j.gene.2024.148561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Intermuscular bones, which are present in numerous economically significant fish species, have a negative impact on the development of aquaculture. The Asb15b gene, primarily expressed in skeletal muscle, plays a crucial role in regulating protein turnover and the development of muscle fibers. It stimulates protein synthesis and controls the differentiation of muscle fibers. In this study, we employed CRISPR/Cas9 technology to generate homozygous zebrafish strains with 7 bp and 49 bp deletions in the Asb15b gene. Subsequent analyses using skeleton staining demonstrated a substantial reduction in the number of intermuscular bones in adult Asb15b-/- -7 bp and Asb15b-/- -49 bp mutants compared to the wild-type zebrafish, with decreases of 30 % (P < 0.001) and 40 % (P < 0.0001), respectively. Histological experiments further revealed that the diameter and number of muscle fibers in adult Asb15b-/- mutants did not exhibit significant changes when compared to wild-type zebrafish. Moreover, qRT-PCR experiments demonstrated significant differences in the expression of bmp6 and runx2b genes, which are key regulators of intermuscular bone development, during different stages of intermuscular bone development in Asb15b-/- mutants. This study strongly suggests that the Asb15b gene plays a crucial role in regulating intermuscular bone development in fish and lays the groundwork for further exploration of the role of the Asb15b gene in zebrafish intermuscular bone development.
Collapse
Affiliation(s)
- Minghui Niu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Huamin Whang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Zhichao Wu
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Shouwen Jiang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China
| | - Liangbiao Chen
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Fishery Germplasm Resources Exploration and Utilization, Ministry of Education, Shanghai 201306, China.
| |
Collapse
|
2
|
Torsabo D, Ishak SD, Noordin NM, Waiho K, Koh ICC, Yazed MA, Abol-Munafi AB. Optimizing reproductive performance in pangasius catfish broodstock: A review of dietary and molecular strategies. Vet Anim Sci 2024; 25:100375. [PMID: 39005967 PMCID: PMC11245938 DOI: 10.1016/j.vas.2024.100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Pangasius catfish, a significant player in the global whitefish market, encounters challenges in aquaculture production sustainability. Quality broodstock maintenance and seed production are impeded by growth, maturation, and fecundity issues. This review investigates the efficacy of strategic nutrient composition and molecular strategies in enhancing broodstock conditions and reproductive performance across various fish species. A notable knowledge gap for Pangasius catfish hampers aquaculture progress. The review assesses nutrient manipulation's impact on reproductive physiology, emphasizing pangasius broodstock. A systematic review analysis following PRISMA guidelines was conducted to identify research trends and hotspots quantitatively, revealing a focus on P. bocourti and fertilization techniques. Addressing this gap, the review offers insights into dietary nutrients manipulation and genetic tool utilization for improved seed production, contributing to pangasius catfish aquaculture sustainability.
Collapse
Affiliation(s)
- Donald Torsabo
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Department of Fisheries and Aquaculture, Joseph Sarwuan Tarka University, Makurdi, Makurdi, Benue State, Nigeria
| | - Sairatul Dahlianis Ishak
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Noordiyana Mat Noordin
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity and Conservation, College of Marine Sciences, Beibu Gulf University, Guangxi, China
- Center for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Ivan Chong Chu Koh
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Muhammad Abduh Yazed
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Ambok Bolong Abol-Munafi
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| |
Collapse
|
3
|
Wang Z, Akimoto T, Yue T, Hatakeyama Y, Maruo C, Pascual G, Fujibayashi M, Sakamaki T. Testing combined effects of environmental trace metals/arsenic and marine trophic status on the bioaccumulation in Pacific oysters: Insights from 22-site field samplings. MARINE POLLUTION BULLETIN 2024; 207:116827. [PMID: 39168088 DOI: 10.1016/j.marpolbul.2024.116827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/04/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Pacific oysters were sampled from 22 human-impacted sites in northeastern Japan to measure Cr, Cu, Zn, Pb, Cd, and As. The hazard quotient was slightly >1 for Cu and/or As at two sites, but <1 for all metal species and As at the other sites, indicating low human health risks. Oysters' Cu, Zn, and Pb contents were positively related to their concentrations in the sediment, while Cr and As were not. Oysters' Cu and Zn were negatively related to the inorganic nitrogen in seawater, while oysters' Pb and As showed positive relationships with the particulate organic carbon. These findings suggest that marine trophic status affects oysters' metal uptake differently among the metal species. Furthermore, oysters' Cr, Cu, Zn, and Pb contents were negatively related to their eicosapentaenoic acid content and condition index. Therefore, the nutritional conditions of oysters may influence their elimination or accumulation of these metals.
Collapse
Affiliation(s)
- Zhongcheng Wang
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki-Aza-Aoba, Sendai 980-8579, Japan
| | - Takeshi Akimoto
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki-Aza-Aoba, Sendai 980-8579, Japan
| | - Tingting Yue
- School of Life Sciences, Technical University of Munich, Emil-Ramann-Str. 2, Building 4217, 85354 Freising, Germany
| | - Yuji Hatakeyama
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki-Aza-Aoba, Sendai 980-8579, Japan
| | - Chikako Maruo
- Technical Division, School of Engineering, Tohoku University, 6-6-06 Aramaki-Aza-Aoba, Sendai 980-8579, Japan
| | - Gissela Pascual
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki-Aza-Aoba, Sendai 980-8579, Japan
| | - Megumu Fujibayashi
- Faculty of Engineering, Kyushu University, 744, Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Takashi Sakamaki
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aramaki-Aza-Aoba, Sendai 980-8579, Japan; Advanced Institute for Marine Ecosystem Change (Tohoku University & JAMSTEC WPI-AIMEC), 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan.
| |
Collapse
|
4
|
Zhou Q, Wang J, Li J, Chen Z, Wang N, Li M, Wang L, Si Y, Lu S, Cui Z, Liu X, Chen S. Decoding the fish genome opens a new era in important trait research and molecular breeding in China. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2670-5. [PMID: 39145867 DOI: 10.1007/s11427-023-2670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/01/2024] [Indexed: 08/16/2024]
Abstract
Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.
Collapse
Affiliation(s)
- 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
| | - Jialin Wang
- 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
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100041, 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
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Na Wang
- 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
| | - Ming Li
- 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
| | - Lei Wang
- 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
| | - Yufeng Si
- 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
| | - Sheng Lu
- 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
| | - Zhongkai Cui
- 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
| | - Xuhui Liu
- 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
| | - 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.
| |
Collapse
|
5
|
Rao H, Tian H, Wang X, Huo C, Zhu L, Li Z, Li Y. Diversification of Toll-like receptor 1 in swamp eel (Monopterus albus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 157:105190. [PMID: 38697378 DOI: 10.1016/j.dci.2024.105190] [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: 01/16/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Toll-like receptor 1 (TLR1) is a pattern recognition receptor that plays critical roles in triggering immune activation via detecting bacterial lipoproteins and lipopeptides. In this study, the genetic characteristic of TLR1 was studied for an important aquaculture fish, swamp eel Monopterus albus. The eel has been seriously threatened by infectious diseases. However, a low level of genetic heterogeneity in the fish that has resulted from a demographic bottleneck presents further challenges in breeding for disease resistance. A comparison with the homologue of closely related species M. javanensis revealed that amino acid replacement (nonsynonymous) but not silent (synonymous) differences have accumulated nonrandomly over the coding sequences of the receptors at the early stage of their phylogenetic split. The combined results from comparative analyses of nonsynonymous-to-synonymous polymorphisms showed that the receptor has undergone significant diversification in M. albus driven by adaptive selection likely after the genetic bottleneck. Some of the changes reported here have taken place in the structures mediating heterodimerization with co-receptor TLR2, ligand recognition, and/or formation of active signaling complex with adaptor, which highlighted key structural elements and strategies of TLR1 in arms race against exogenous challenges. The findings of this study will add to the knowledge base of genetic engineering and breeding for disease resistance in the eel.
Collapse
Affiliation(s)
- Han Rao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, PR China
| | - Xueting Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, PR China
| | - Caifei Huo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China
| | - Lilan Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, PR China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, PR China.
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, PR China.
| |
Collapse
|
6
|
Dorant Y, Quillien V, Le Luyer J, Ky CL. Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera. BMC Genomics 2024; 25:717. [PMID: 39049022 PMCID: PMC11270918 DOI: 10.1186/s12864-024-10636-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In bivalves, the rate at which organisms grow is a major functional trait underlying many aspects of their commercial production. Growth is a highly polygenic trait, which is typically regulated by many genes with small to moderate effects. Due to its complexity, growth variability in such shellfish remains poorly understood. In this study, we aimed to investigate differential gene expression among spat of the pearl oyster Pinctada margaritifera with distinct growth phenotypes. RESULTS We selected two groups of P. margaritifera spat belonging to the same F2 cohort based on their growth performance at 5.5 months old. Transcriptome profile analysis identified a total of 394 differentially expressed genes between these Fast-growing (F) and Slow-growing (S) phenotypes. According to functional enrichment analysis, S oysters overexpressed genes associated with stress-pathways and regulation of innate immune responses. In contrast, F oysters up-regulated genes associated with cytoskeleton activity, cell proliferation, and apoptosis. Analysis of genome polymorphism identified 16 single nucleotide polymorphisms (SNPs) significantly associated with the growth phenotypes. SNP effect categorization revealed one SNP identified for high effect and annotated for a stop codon gained mutation. Interestingly, this SNP is located within a gene annotated for scavenger receptor class F member 1 (SRF1), which is known to modulate apoptosis. Our analyses also revealed that all F oysters showed up-regulation for this gene and were homozygous for the stop-codon mutation. Conversely, S oysters had a heterozygous genotype and a reduced expression of this gene. CONCLUSIONS Altogether, our findings suggest that differences in growth among the same oyster cohort may be explained by contrasted metabolic allocation between regulatory pathways for growth and the immune system. This study provides a valuable contribution towards our understanding of the molecular components associated with growth performance in the pearl oyster P. margaritifera and bivalves in general.
Collapse
Affiliation(s)
- Y Dorant
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France.
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France.
| | - V Quillien
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - J Le Luyer
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- Ifremer, Univ Brest, CNRS, IRD, UMR 6539, LEMAR, Plouzane, F-29280, France
| | - C L Ky
- Ifremer, ILM, IRD, UPF, UMR 241 SECOPOL, Polynésie française, Taravao, Tahiti, France
- IHPE, UMR 5244, Université de Montpellier, CNRS, Université de Perpignan Via Domitia, Ifremer, Montpellier, France
| |
Collapse
|
7
|
Song H, Dong T, Wang W, Jiang B, Yan X, Geng C, Bai S, Xu S, Hu H. Cost-effective genomic prediction of critical economic traits in sturgeons through low-coverage sequencing. Genomics 2024; 116:110874. [PMID: 38839024 DOI: 10.1016/j.ygeno.2024.110874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/27/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024]
Abstract
Low-coverage whole-genome sequencing (LCS) offers a cost-effective alternative for sturgeon breeding, especially given the lack of SNP chips and the high costs associated with whole-genome sequencing. In this study, the efficiency of LCS for genotype imputation and genomic prediction was assessed in 643 sequenced Russian sturgeons (∼13.68×). The results showed that using BaseVar+STITCH at a sequencing depth of 2× with a sample size larger than 300 resulted in the highest genotyping accuracy. In addition, when the sequencing depth reached 0.5× and SNP density was reduced to 50 K through linkage disequilibrium pruning, the prediction accuracy was comparable to that of whole sequencing depth. Furthermore, an incremental feature selection method has the potential to improve prediction accuracy. This study suggests that the combination of LCS and imputation can be a cost-effective strategy, contributing to the genetic improvement of economic traits and promoting genetic gains in aquaculture species.
Collapse
Affiliation(s)
- Hailiang Song
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Tian Dong
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Wei Wang
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Boyun Jiang
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; Hangzhou Qiandaohu Xunlong Sci-tech Co., Ltd., Hangzhou 311799, China.
| | - Xiaoyu Yan
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Chenfan Geng
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Song Bai
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China
| | - Shijian Xu
- Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; Hangzhou Qiandaohu Xunlong Sci-tech Co., Ltd., Hangzhou 311799, China.
| | - Hongxia Hu
- Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; Key Laboratory of Sturgeon Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hangzhou 311799, China; National Innovation Center for Digital Seed Industry, Beijing 100097, China.
| |
Collapse
|
8
|
Qu ZL, Zhang YB. Protocol for linking enhanced interferon immunity to virus resistance in gene-knockout zebrafish. STAR Protoc 2024; 5:103156. [PMID: 38941183 PMCID: PMC11260832 DOI: 10.1016/j.xpro.2024.103156] [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: 04/15/2024] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/30/2024] Open
Abstract
A gene-rescue experiment under a mutant background is essential to clarify gene function and the resulting biological potential in vivo. Here, we present a protocol for determining the change in interferon response by microinjecting plasmids into one-cell-stage zebrafish embryos. We describe steps for comparing the resistance potential to virus infection in wild-type and knockout zebrafish larvae following plasmid microinjection. We then detail how to link the enhanced interferon immunity to the improved resistance in knockout zebrafish larvae by gene-rescue experiments. For complete details on the use and execution of this protocol, please refer to Qu et al.1.
Collapse
Affiliation(s)
- Zi-Ling Qu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Yi-Bing Zhang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| |
Collapse
|
9
|
Orlova SY, Ruzina MN, Emelianova OR, Sergeev AA, Chikurova EA, Orlov AM, Mugue NS. In Search of a Target Gene for a Desirable Phenotype in Aquaculture: Genome Editing of Cyprinidae and Salmonidae Species. Genes (Basel) 2024; 15:726. [PMID: 38927661 PMCID: PMC11202958 DOI: 10.3390/genes15060726] [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: 04/24/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Aquaculture supplies the world food market with a significant amount of valuable protein. Highly productive aquaculture fishes can be derived by utilizing genome-editing methods, and the main problem is to choose a target gene to obtain the desirable phenotype. This paper presents a review of the studies of genome editing for genes controlling body development, growth, pigmentation and sex determination in five key aquaculture Salmonidae and Cyprinidae species, such as rainbow trout (Onchorhynchus mykiss), Atlantic salmon (Salmo salar), common carp (Cyprinus carpio), goldfish (Carassius auratus), Gibel carp (Carassius gibelio) and the model fish zebrafish (Danio rerio). Among the genes studied, the most applicable for aquaculture are mstnba, pomc, and acvr2, the knockout of which leads to enhanced muscle growth; runx2b, mutants of which do not form bones in myoseptae; lepr, whose lack of function makes fish fast-growing; fads2, Δ6abc/5Mt, and Δ6bcMt, affecting the composition of fatty acids in fish meat; dnd mettl3, and wnt4a, mutants of which are sterile; and disease-susceptibility genes prmt7, gab3, gcJAM-A, and cxcr3.2. Schemes for obtaining common carp populations consisting of only large females are promising for use in aquaculture. The immobilized and uncolored zebrafish line is of interest for laboratory use.
Collapse
Affiliation(s)
- Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Maria N. Ruzina
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Olga R. Emelianova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey A. Sergeev
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Evgeniya A. Chikurova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology, Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Laboratory of Genome Evolution and Speciation, Institute of Developmental Biology Russian Academy of Sciences, 117808 Moscow, Russia
| |
Collapse
|
10
|
Tchonkouang RD, Onyeaka H, Nkoutchou H. Assessing the vulnerability of food supply chains to climate change-induced disruptions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:171047. [PMID: 38373458 DOI: 10.1016/j.scitotenv.2024.171047] [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: 09/15/2023] [Revised: 01/19/2024] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
Climate change is one of the most significant challenges worldwide. There is strong evidence from research that climate change will impact several food chain-related elements such as agricultural output, incomes, prices, food access, food quality, and food safety. This scoping review seeks to outline the state of knowledge of the food supply chain's vulnerability to climate change and to identify existing literature that may guide future research, policy, and decision-making aimed at enhancing the resilience of the food supply chain. A total of 1526 publications were identified using the SCOPUS database, of which 67 were selected for the present study. The vulnerability assessment methods as well as the adaptation and resilience measures that have been employed to alleviate the impact of climate change in the food supply chain were discussed. The results revealed a growing number of publications providing evidence of the weakening of the food supply chain due to climate change and extreme weather events. Our assessment demonstrated the need to broaden research into the entire food supply chain and various forms of climatic variability because most studies have concentrated on the relationships between climatic fluctuations (especially extreme rainfall, temperatures, and drought) and production. A lack of knowledge about the effects of climate change on the food supply chain and the underlying socio-economic consequences could result in underperformance or failure of the food supply chain.
Collapse
Affiliation(s)
- Rose Daphnee Tchonkouang
- MED-Mediterranean Institute for Agriculture, Environment and Development & Change-Global Change and Sustainability Institute, Faculty of Sciences and Technology, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
| | - Hugue Nkoutchou
- Public Policy in Africa Initiative (PPiAI), Douala, Cameroon
| |
Collapse
|
11
|
Brown MS, Carvalheiro R, Taylor RS, Mekkawy W, Luke TDW, Rands L, Nieuwesteeg D, Evans BS, Wade NM, Lind CE, Hilder PE. Probabilistic reaction norm reveals family-related variation in the association between size, condition, and sexual maturation onset in Atlantic salmon (Salmo salar). JOURNAL OF FISH BIOLOGY 2024; 104:939-949. [PMID: 37996984 DOI: 10.1111/jfb.15626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
This study investigated the relationship between the size, condition, year class, family, and sexual maturity of Atlantic salmon (Salmo salar) using data collected in an aquaculture selective breeding programme. Males that were sexually mature at 2 years of age (maiden spawn) have, on average, greater fork length and condition factor (K) at 1 year of age than their immature counterparts. For every 10-mm increase in fork length or 0.1 increase in K at 1 year of age, the odds of sexual maturity at 2 years of age increased by 1.48 or 1.22 times, respectively. Females that were sexually mature at 3 years of age (maiden spawn) have, on average, greater fork length and K at 2 years of age than their immature counterparts. For every 10-mm increase in fork length or 0.1 increase in K at 2 years of age, the odds of sexual maturity at 3 years of age increased by 1.06 or 1.44 times, respectively. The family explained 34.93% of the variation in sexual maturity among 2-year-old males that was not attributable to the average effects of fork length and K at 1 year of age and year class. The proportion of variation in sexual maturity among 3-year-old females explained by the family could not be investigated. These findings suggest that the onset of sexual maturation in Atlantic salmon is conditional on performance (with respect to energy availability) surpassing a threshold, the magnitude of which can vary between families and is determined by a genetic component. This could support the application of genetic selection to promote or inhibit the onset of sexual maturation in farmed stocks.
Collapse
Affiliation(s)
| | | | | | - Wagdy Mekkawy
- CSIRO Agriculture and Food, Hobart, Tasmania, Australia
| | | | - Lewis Rands
- Salmon Enterprises of Tasmania Pty. Ltd., Wayatinah, Tasmania, Australia
| | - Damien Nieuwesteeg
- Salmon Enterprises of Tasmania Pty. Ltd., Wayatinah, Tasmania, Australia
| | - Brad S Evans
- CSIRO Agriculture and Food, Hobart, Tasmania, Australia
| | - Nicholas M Wade
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, UK
| | - Curtis E Lind
- CSIRO Agriculture and Food, Hobart, Tasmania, Australia
| | | |
Collapse
|
12
|
Raza A, Chen H, Zhang C, Zhuang Y, Sharif Y, Cai T, Yang Q, Soni P, Pandey MK, Varshney RK, Zhuang W. Designing future peanut: the power of genomics-assisted breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:66. [PMID: 38438591 DOI: 10.1007/s00122-024-04575-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 02/03/2024] [Indexed: 03/06/2024]
Abstract
KEY MESSAGE Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.
Collapse
Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yasir Sharif
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Pooja Soni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Manish K Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.
| |
Collapse
|
13
|
Wang J, Torres IM, Shang M, Al-Armanazi J, Dilawar H, Hettiarachchi DU, Paladines-Parrales A, Chambers B, Pottle K, Soman M, Su B, Dunham RA. One-step knock-in of two antimicrobial peptide transgenes at multiple loci of catfish by CRISPR/Cas9-mediated multiplex genome engineering. Int J Biol Macromol 2024; 260:129384. [PMID: 38224812 DOI: 10.1016/j.ijbiomac.2024.129384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/23/2023] [Accepted: 01/01/2024] [Indexed: 01/17/2024]
Abstract
CRISPR/Cas9-mediated multiplex genome editing (MGE) conventionally uses multiple single-guide RNAs (sgRNAs) for gene-targeted mutagenesis via the non-homologous end joining (NHEJ) pathway. MGE has been proven to be highly efficient for functional gene disruption/knockout (KO) at multiple loci in mammalian cells or organisms. However, in the absence of a DNA donor, this approach is limited to small indels without transgene integration. Here, we establish the linear double-stranded DNA (dsDNA) and double-cut plasmid (dcPlasmid) combination-assisted MGE in channel catfish (Ictalurus punctatus), allowing combinational deletion mutagenesis and transgene knock-in (KI) at multiple sites through NHEJ/homology-directed repair (HDR) pathway in parallel. In this study, we used single-sgRNA-based genome editing (ssGE) and multi-sgRNA-based MGE (msMGE) to replace the luteinizing hormone (lh) and melanocortin-4 receptor (mc4r) genes with the cathelicidin (As-Cath) transgene and the myostatin (two target sites: mstn1, mstn2) gene with the cecropin (Cec) transgene, respectively. A total of 9000 embryos were microinjected from three families, and 1004 live fingerlings were generated and analyzed. There was no significant difference in hatchability (all P > 0.05) and fry survival (all P > 0.05) between ssGE and msMGE. Compared to ssGE, CRISPR/Cas9-mediated msMGE assisted by the mixture of dsDNA and dcPlasmid donors yielded a higher knock-in (KI) efficiency of As-Cath (19.93 %, [59/296] vs. 12.96 %, [45/347]; P = 0.018) and Cec (22.97 %, [68/296] vs. 10.80 %, [39/361]; P = 0.003) transgenes, respectively. The msMGE strategy can be used to generate transgenic fish carrying two transgenes at multiple loci. In addition, double and quadruple mutant individuals can be produced with high efficiency (36.3 % ∼ 71.1 %) in one-step microinjection. In conclusion, we demonstrated that the CRISPR/Cas9-mediated msMGE allows the one-step generation of simultaneous insertion of the As-Cath and Cec transgenes at four sites, and the simultaneous disruption of the lh, mc4r, mstn1 and mstn2 alleles. This msMGE system, aided by the mixture donors, promises to pioneer a new dimension in the drive and selection of multiple designated traits in other non-model organisms.
Collapse
Affiliation(s)
- Jinhai Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Indira Medina Torres
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Jacob Al-Armanazi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Hamza Dilawar
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Darshika U Hettiarachchi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Abel Paladines-Parrales
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Barrett Chambers
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Kate Pottle
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Misha Soman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America.
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, United States of America
| |
Collapse
|
14
|
Bouza C, Losada AP, Fernández C, Álvarez-Dios JA, de Azevedo AM, Barreiro A, Costas D, Quiroga MI, Martínez P, Vázquez S. A comprehensive coding and microRNA transcriptome of vertebral bone in postlarvae and juveniles of Senegalese sole (Solea senegalensis). Genomics 2024; 116:110802. [PMID: 38290593 DOI: 10.1016/j.ygeno.2024.110802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Understanding vertebral bone development is essential to prevent skeletal malformations in farmed fish related to genetic and environmental factors. This is an important issue in Solea senegalensis, with special impact of spinal anomalies in postlarval and juvenile stages. Vertebral bone transcriptomics in farmed fish mainly comes from coding genes, and barely on miRNA expression. Here, we used RNA-seq of spinal samples to obtain the first comprehensive coding and miRNA transcriptomic repertoire for postlarval and juvenile vertebral bone, covering different vertebral phenotypes and egg-incubation temperatures related to skeleton health in S. senegalensis. Coding genes, miRNA and pathways regulating bone development and growth were identified. Differential transcriptomic profiles and suggestive mRNA-miRNA interactions were found between postlarvae and juveniles. Bone-related genes and functions were associated with the extracellular matrix, development and regulatory processes, calcium binding, retinol and lipid metabolism or response to stimulus, including those revealed by the miRNA targets related to signaling, cellular and metabolic processes, growth, cell proliferation and biological adhesion. Pathway enrichment associated with fish skeleton were identified when comparing postlarvae and juveniles: growth and bone development functions in postlarvae, while actin cytoskeleton, focal adhesion and proteasome related to bone remodeling in juveniles. The transcriptome data disclosed candidate coding and miRNA gene markers related to bone cell processes, references for functional studies of the anosteocytic bone of S. senegalensis. This study establishes a broad transcriptomic foundation to study healthy and anomalous spines under early thermal conditions across life-stages in S. senegalensis, and for comparative analysis of skeleton homeostasis and pathology in fish and vertebrates.
Collapse
Affiliation(s)
- Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
| | - Ana P Losada
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - José A Álvarez-Dios
- Department of Applied Mathematics, Faculty of Mathematics, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - Ana Manuela de Azevedo
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Andrés Barreiro
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Damián Costas
- Centro de Investigación Mariña, Universidade de Vigo, ECIMAT, Vigo 36331, Spain
| | - María Isabel Quiroga
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Sonia Vázquez
- Department of Anatomy, Animal Production and Veterinary Clinical Sciences, Faculty of Veterinary, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| |
Collapse
|
15
|
Gao S, Chen W, Cao S, Sun P, Gao X. Microalgae as fishmeal alternatives in aquaculture: current status, existing problems, and possible solutions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16113-16130. [PMID: 38315337 DOI: 10.1007/s11356-024-32143-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Fishmeal is an indispensable ingredient for most aquatic animals. However, the finite supply and escalating price of fishmeal seriously limit its use in aquaculture. Thus the development of new, sustainable protein ingredients has been a research focus. Microalgae are potential fishmeal alternatives owing to their high protein content and balanced amino acid profile. Studies suggest that suitable replacement of fishmeal with microalgae is beneficial for fish growth performance, but excessive replacement would induce poor growth and feed utilization. Therefore, this paper aims to review research on the maximum substitutional level of fishmeal by microalgae and propose the main issues and possible solutions for fishmeal replacement by microalgae. The maximum replacement level is affected by microalgal species, fish feeding habits, quality of fishmeal and microalgal meals, and supplemental levels of fishmeal in the control group. Microalgae could generally replace 100%, 95%, 95%, 64.1%, 25.6%, and 18.6% fishmeal protein in diets of carp, shrimp, catfish, tilapia, marine fish, and salmon and trout, respectively. The main issues with fishmeal replacement using microalgae include low production and high production cost, poor digestibility, and anti-nutritional factors. Possible solutions to these problems are recommended in this paper. Overall, microalgae are promising fishmeal alternatives in aquaculture.
Collapse
Affiliation(s)
- Shiyang Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471000, China
| | - Weijun Chen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471000, China.
| | - Shenping Cao
- Hunan Provincial Key Laboratory of Nutrition and Quality Control of Aquatic Animals, Department of Biological and Environmental Engineering, Changsha University, Changsha, 410022, China
| | - Ping Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471000, China
| | - Xiaochan Gao
- College of Agricultural Equipment Engineering, Henan University of Science and Technology, Luoyang, China
| |
Collapse
|
16
|
Olymon K, Yadav M, Teronpi V, Kumar A. Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability. Mol Biol Rep 2024; 51:364. [PMID: 38407655 DOI: 10.1007/s11033-024-09331-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.
Collapse
Affiliation(s)
- Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Valentina Teronpi
- Department, of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
| |
Collapse
|
17
|
Miranda J, Veneza I, Ferreira C, Santana P, Lutz I, Furtado C, Pereira P, Rabelo L, Guerreiro-Diniz C, Melo M, Sampaio I, Vallinoto M, Evangelista-Gomes G. First neurotranscriptome of adults Tambaquis (Colossoma macropomum) with characterization and differential expression between males and females. Sci Rep 2024; 14:3130. [PMID: 38326509 PMCID: PMC10850070 DOI: 10.1038/s41598-024-53734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/04/2024] [Indexed: 02/09/2024] Open
Abstract
The Tambaqui is one of the most representative Amazon fish species, being highly exploited in fisheries, aquaculture and as a research model. Nonetheless, data about functional genome are still required to evaluate reproductive and nutrition parameters as well as resistance to pathogens. The of next-generation sequencing has allows assessing the transcriptional processes in non-model species by providing comprehensive gene collections to be used as a database in further genomic applications and increased performance of captive populations. In this study, we relied on RNAseq approach to generate the first transcriptome of the telencephalon from adult males and females of Colossoma macropomum, resulting in a reference dataset for future functional studies. We retrieved 896,238 transcripts, including the identification of 267,785 contigs and 203,790 genes. From this total, 91 transcripts were differentially expressed, being 63 and 28 of them positively regulated for females and males, respectively. The functional annotation resulted in a library of 40 candidate genes for females and 20 for males. The functional enrichment classes comprised reproductive processes (GO:0,048,609; GO:0,003,006; GO:0,044,703; GO:0,032,504; GO:0,019,953) being related to sex differentiation (e.g., SAFB) and immune response (e.g., SLC2A6, AHNAK, NLRC3, NLRP3 and IgC MHC I alpha3), thus indicating that the genes in the neurotranscriptome of Tambaqui participate in sex differentiation and homeostasis of captive specimens. These data are useful to design the selection of genes related to sex determination and animal welfare in raising systems of Tambaqui.
Collapse
Affiliation(s)
- Josy Miranda
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Ivana Veneza
- Universidade Federal do Oeste do Pará, Campus Monte Alegre, Av. Major Francisco Mariano - Bairro Cidade Alta, Monte Alegre, Pará, ZIP Code 68220-000, Brazil
| | - Charles Ferreira
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Paula Santana
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Italo Lutz
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Carolina Furtado
- Divisão de Genética, Instituto Nacional de Câncer José de Alencar Gomes da Silva (INCA), Pr. da Cruz Vermelha, 23 - Bairro Centro, Rio de Janeiro, ZIP Code: 20230-130, Brazil
| | - Patrick Pereira
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência E Tecnologia Do Pará, - Campus Bragança, Rua da Escola Agrícola S/N - Bairro Vila Sinhá - Caixa Postal 72, Bragança, PA, ZIP Code: 68600-000, Brazil
| | - Luan Rabelo
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Cristovam Guerreiro-Diniz
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência E Tecnologia Do Pará, - Campus Bragança, Rua da Escola Agrícola S/N - Bairro Vila Sinhá - Caixa Postal 72, Bragança, PA, ZIP Code: 68600-000, Brazil
| | - Mauro Melo
- Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Ciência E Tecnologia Do Pará, - Campus Bragança, Rua da Escola Agrícola S/N - Bairro Vila Sinhá - Caixa Postal 72, Bragança, PA, ZIP Code: 68600-000, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil
| | - Grazielle Evangelista-Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal Do Pará, Al. Leandro Ribeiro S/N - Bairro Aldeia, Bragança, Pará, ZIP Code: 68600-000, Brazil.
| |
Collapse
|
18
|
Puthumana J, Chandrababu A, Sarasan M, Joseph V, Singh ISB. Genetic improvement in edible fish: status, constraints, and prospects on CRISPR-based genome engineering. 3 Biotech 2024; 14:44. [PMID: 38249355 PMCID: PMC10796887 DOI: 10.1007/s13205-023-03891-7] [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: 05/13/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024] Open
Abstract
Conventional selective breeding in aquaculture has been effective in genetically enhancing economic traits like growth and disease resistance. However, its advances are restricted by heritability, the extended period required to produce a strain with desirable traits, and the necessity to target multiple characteristics simultaneously in the breeding programs. Genome editing tools like zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) are promising for faster genetic improvement in fishes. CRISPR/Cas9 technology is the least expensive, most precise, and well compatible with multiplexing of all genome editing approaches, making it a productive and highly targeted approach for developing customized fish strains with specified characteristics. As a result, the use of CRISPR/Cas9 technology in aquaculture is rapidly growing, with the main traits researched being reproduction and development, growth, pigmentation, disease resistance, trans-GFP utilization, and omega-3 metabolism. However, technological obstacles, such as off-target effects, ancestral genome duplication, and mosaicism in founder population, need to be addressed to achieve sustainable fish production. Furthermore, present regulatory and risk assessment frameworks are inadequate to address the technical hurdles of CRISPR/Cas9, even though public and regulatory approval is critical to commercializing novel technology products. In this review, we examine the potential of CRISPR/Cas9 technology for the genetic improvement of edible fish, the technical, ethical, and socio-economic challenges to using it in fish species, and its future scope for sustainable fish production.
Collapse
Affiliation(s)
- Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Aswathy Chandrababu
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - I. S. Bright Singh
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| |
Collapse
|
19
|
Angelakopoulos R, Tsipourlianos A, Giannoulis T, Mamuris Z, Moutou KA. MassArray Genotyping as a Selection Tool for Extending the Shelf-Life of Fresh Gilthead Sea Bream and European Seabass. Animals (Basel) 2024; 14:205. [PMID: 38254374 PMCID: PMC10812826 DOI: 10.3390/ani14020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs.
Collapse
Affiliation(s)
- Rafael Angelakopoulos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Science, University of Thessaly, Greece Gaiopolis, 41334 Larissa, Greece;
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| |
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
| |
Collapse
|
21
|
Wang X, Zhu J, Wang H, Deng W, Jiao S, Wang Y, He M, Zhang F, Liu T, Hao Y, Ye D, Sun Y. Induced formation of primordial germ cells from zebrafish blastomeres by germplasm factors. Nat Commun 2023; 14:7918. [PMID: 38097571 PMCID: PMC10721796 DOI: 10.1038/s41467-023-43587-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
The combination of genome editing and primordial germ cell (PGC) transplantation has enormous significance in the study of developmental biology and genetic breeding, despite its low efficiency due to limited number of donor PGCs. Here, we employ a combination of germplasm factors to convert blastoderm cells into induced PGCs (iPGCs) in zebrafish and obtain functional gametes either through iPGC transplantation or via the single blastomere overexpression of germplasm factors. Zebrafish-derived germplasm factors convert blastula cells of Gobiocypris rarus into iPGCs, and Gobiocypris rarus spermatozoa can be produced by iPGC-transplanted zebrafish. Moreover, the combination of genome knock-in and iPGC transplantation perfectly resolves the contradiction between high knock-in efficiency and early lethality during embryonic stages and greatly improves the efficiency of genome knock-in. Together, we present an efficient method for generating PGCs in a teleost, a technique that will have a strong impact in basic research and aquaculture.
Collapse
Affiliation(s)
- Xiaosi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Junwen Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Houpeng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Wenqi Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shengbo Jiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaqing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Mudan He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Fenghua Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongkang Hao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ding Ye
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| |
Collapse
|
22
|
Delomas TA, Willis SC. Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data. BMC Bioinformatics 2023; 24:415. [PMID: 37923981 PMCID: PMC10623847 DOI: 10.1186/s12859-023-05554-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: 07/25/2022] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-coverage whole genome sequencing or pooled sequencing (pool-seq) data. RESULTS We developed new methods for estimating microhaplotype allele frequency from low-coverage whole genome sequence and pool-seq data. We validated these methods using datasets from three non-model organisms. These methods allowed estimation of allele frequency and expected heterozygosity at depths routinely achieved from pooled sequencing. CONCLUSIONS These new methods will allow microhaplotype panels to be designed using low-coverage WGS and pool-seq data to discover and evaluate candidate loci. The python script implementing the two methods and documentation are available at https://www.github.com/delomast/mhFromLowDepSeq .
Collapse
Affiliation(s)
- Thomas A Delomas
- Agricultural Research Service, United States Department of Agriculture, National Cold Water Marine Aquaculture Center, 483 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
| | - Stuart C Willis
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| |
Collapse
|
23
|
Gutierrez AP, Selly SLC, Pountney SM, Taggart JB, Kokkinias P, Cavrois-Rogacki T, Fernandez EJ, Migaud H, Lein I, Davie A, Bekaert M. Development of genomic markers associated to growth-related traits and sex determination in lumpfish (Cyclopterus lumpus). Genomics 2023; 115:110721. [PMID: 37769819 DOI: 10.1016/j.ygeno.2023.110721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 high Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animal's phenotype by machine learning. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programmes in lumpfish.
Collapse
Affiliation(s)
- Alejandro P Gutierrez
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Sarah-Louise Counter Selly
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Samuel M Pountney
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK; University of Victoria, Victoria, BC V8P 5C2, Canada
| | - John B Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Panagiotis Kokkinias
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | | | | | - Herve Migaud
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Ingrid Lein
- Nofima AS, Sjølsengvegen 22, Sunndalsøra 6600, Norway
| | - Andrew Davie
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| |
Collapse
|
24
|
Wiens GD, Marancik DP, Chadwick CC, Osbourn K, Reid RM, Leeds TD. Plasma proteomic profiling of bacterial cold water disease-resistant and -susceptible rainbow trout lines and biomarker discovery. Front Immunol 2023; 14:1265386. [PMID: 37928534 PMCID: PMC10623068 DOI: 10.3389/fimmu.2023.1265386] [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: 07/24/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Genetic variation for disease resistance is present in salmonid fish; however, the molecular basis is poorly understood, and biomarkers of disease susceptibility/resistance are unavailable. Previously, we selected a line of rainbow trout for high survival following standardized challenge with Flavobacterium psychrophilum (Fp), the causative agent of bacterial cold water disease. The resistant line (ARS-Fp-R) exhibits over 60 percentage points higher survival compared to a reference susceptible line (ARS-Fp-S). To gain insight into the differential host response between genetic lines, we compared the plasma proteomes from day 6 after intramuscular challenge. Pooled plasma from unhandled, PBS-injected, and Fp-injected groups were simultaneously analyzed using a TMT 6-plex label, and the relative abundance of 513 proteins was determined. Data are available via ProteomeXchange, with identifier PXD041308, and the relative protein abundance values were compared to mRNA measured from a prior, whole-body RNA-seq dataset. Our results identified a subset of differentially abundant intracellular proteins was identified, including troponin and myosin, which were not transcriptionally regulated, suggesting that these proteins were released into plasma following pathogen-induced tissue damage. A separate subset of high-abundance, secreted proteins were transcriptionally regulated in infected fish. The highest differentially expressed protein was a C1q family member (designated complement C1q-like protein 3; C1q-LP3) that was upregulated over 20-fold in the infected susceptible line while only modestly upregulated, 1.8-fold, in the infected resistant line. Validation of biomarkers was performed using immunoassays and C1q-LP3, skeletal muscle troponin C, cathelcidin 2, haptoglobin, leptin, and growth and differentiation factor 15 exhibited elevated concentration in susceptible line plasma. Complement factor H-like 1 exhibited higher abundance in the resistant line compared to the susceptible line in both control and challenged fish and thus was a baseline differentiator between lines. C1q-LP3 and STNC were elevated in Atlantic salmon plasma following experimental challenge with Fp. In summary, these findings further the understanding of the differential host response to Fp and identifies salmonid biomarkers that may have use for genetic line evaluation and on-farm health monitoring.
Collapse
Affiliation(s)
- Gregory D. Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, U.S. Department of Agriculture (USDA), Kearneysville, WV, United States
| | - David P. Marancik
- Department of Pathobiology, School of Veterinary Medicine, St. George’s University, True Blue, Grenada
| | | | - Keira Osbourn
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, U.S. Department of Agriculture (USDA), Kearneysville, WV, United States
| | - Ross M. Reid
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, U.S. Department of Agriculture (USDA), Kearneysville, WV, United States
| | - Timothy D. Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, U.S. Department of Agriculture (USDA), Kearneysville, WV, United States
| |
Collapse
|
25
|
Nielsen SS, Alvarez J, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin MS, Michel V, Miranda Chueca MÁ, Padalino B, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Bron J, Olesen NJ, Sindre H, Stone D, Vendramin N, Antoniou SE, Karagianni AE, Broglia A, Papanikolaou A, Bicout DJ. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) 2016/429): Spring Viraemia of Carp (SVC). EFSA J 2023; 21:e08324. [PMID: 37908451 PMCID: PMC10613943 DOI: 10.2903/j.efsa.2023.8324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Spring Viraemia of Carp (SVC) was assessed according to the criteria of the Animal Health Law (AHL), in particular the criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to SVC. The assessment was performed following the ad hoc method for data collection and assessment previously developed by the AHAW panel and already published. The outcome reported is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with an uncertain outcome. According to the assessment performed here, it is uncertain whether SVC can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (45-90% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that SVC does not meet the criteria in Section 1 (Category A; 5-33% probability of meeting the criteria) and it is uncertain whether it meets the criteria in Sections 2, 3, 4 and 5 (Categories B, C, D and E; 33-66%, 10-66%, 45-90% and 45-90% probability of meeting the criteria, respectively). The animal species to be listed for SVC according to Article 8 criteria are provided.
Collapse
|
26
|
Venegas L, López P, Derome N, Yáñez JM. Leveraging microbiome information for animal genetic improvement. Trends Genet 2023; 39:721-723. [PMID: 37516623 DOI: 10.1016/j.tig.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/31/2023]
Abstract
There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.
Collapse
Affiliation(s)
- Lucas Venegas
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Paulina López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - José M Yáñez
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Millennium Nucleus of Austral Invasive Salmonids, INVASAL, Concepción, Chile.
| |
Collapse
|
27
|
Li Y, Mokrani A, Fu H, Shi C, Li Q, Liu S. Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas. Genomics 2023; 115:110697. [PMID: 37567397 DOI: 10.1016/j.ygeno.2023.110697] [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: 05/08/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The Pacific oyster (Crassostrea gigas) is a widely cultivated shellfish in the world, while its transcriptome diversity remains less unexplored due to the limitation of short reads. In this study, we used Oxford Nanopore sequencing to develop the full-length transcriptome database of C. gigas. We identified 77,920 full-length transcripts from 21,523 genes, and uncovered 9668 alternative splicing events and 87,468 alternative polyadenylation sites. Notably, a total of 16,721 novel transcripts were annotated in this work. Furthermore, integrative analysis of 25 publicly available RNA-seq datasets revealed the transcriptome diversity involved in post-transcriptional regulation in C. gigas. We further developed a Drupal based webserver, Cgtdb, which can be used for transcriptome visualization, sequence alignment, and functional genome annotation analyses. This work provides valuable resources and a useful tool for integrative analysis of various transcriptome datasets in C. gigas, which will serve as an essential reference for functional annotation of the oyster genome.
Collapse
Affiliation(s)
- Yin Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Ahmed Mokrani
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Huiru Fu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Chenyu Shi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
28
|
Fraslin C, Robledo D, Kause A, Houston RD. Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss). Genet Sel Evol 2023; 55:59. [PMID: 37580697 PMCID: PMC10424455 DOI: 10.1186/s12711-023-00832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that affects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of the host resistance. However, genomic selection is expensive partly because of the cost of genotyping large numbers of animals using high-density single nucleotide polymorphism (SNP) arrays. The objective of this study was to assess the efficiency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2874 challenged fish and 469 fish from the parental generation (n = 81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD panels was assessed for 10 panels of different densities, which were created in silico using two sampling methods, random and equally spaced. All LD panels were also imputed to the full 28K HD panel using the parental generation as the reference population, and genomic predictions were re-evaluated. The potential of prioritizing SNPs that are associated with resistance to F. columnare was also tested for the six lower-density panels. RESULTS The accuracies of both imputation and genomic predictions were similar with random and equally-spaced sampling of SNPs. Using LD panels of at least 3000 SNPs or lower-density panels (as low as 300 SNPs) combined with imputation resulted in accuracies that were comparable to those of the 28K HD panel and were 11% higher than the pedigree-based predictions. CONCLUSIONS Compared to using the commercial HD panel, LD panels combined with imputation may provide a more affordable approach to genomic prediction of breeding values, which supports a more widespread adoption of genomic selection in aquaculture breeding programmes.
Collapse
Affiliation(s)
- Clémence Fraslin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Antti Kause
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Ross D Houston
- Benchmark Genetics, Edinburgh Technopole, 1 Pioneer Building, Penicuik, EH26 0GB, UK
| |
Collapse
|
29
|
Wang J, Bai Y, Zou X, Li C, Yang J, Ke Q, Zhao J, Zhou T, Xu P. First Genomic Prediction of Single-Step Models in Large Yellow Croaker. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:603-611. [PMID: 37410311 DOI: 10.1007/s10126-023-10229-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
Genome selection is mainly used in disease-resistant traits of aquatic species; however, its implementation is hindered by a high cost of genotype and phenotype data collection. Single-step genomic best linear unbiased prediction (SSGBLUP) can integrate phenotypes, genetic markers, and pedigree records into simultaneous prediction without increasing genotyping costs. The objective of this study is to investigate the performance of SSGBLUP in large yellow croaker and to evaluate the effects of the number of phenotypic records and genotyping per family on the predictive ability of SSGBLUP. A large yellow croaker population consists of 6898 individuals from 14 families with survival time resistant against Cryptocaryon irritans (C. irritans), body weight (BW), and body length (BL) traits were collected, of which 669 individuals were genotyped. Results showed that the mean predictive ability of all traits in the individuals randomly sampling for SSGBLUP, GBLUP, and BLUP was 0.738, 0.738, and 0.736, respectively. Moreover, the predictive ability of SSGBLUP and BLUP models did not increase with the extra phenotypic records per family, in which the predictive ability of SSGBLUP and BLUP in survival time was 0.853 and 0.851 for only genotyped data (N = 0) used, and 0.852, 0.845 for all phenotypic records (N = 600) used, respectively. However, with the increase in the genotype number of training set, the prediction ability of SSGBLUP and GBLUP model was increased and the highest predictive ability was gained when the genotype number per family was 40 or 45. In addition, the prediction ability of SSGBLUP model was higher than that of GBLUP. Our study showed that the SSGBLUP model still has great potential and advantages in genomic breeding of large yellow croakers. It is recommended that each family provide 100 phenotypic individuals, of which 40 individuals with genotyping data for SSGBLUP model prediction and family resistance evaluation.
Collapse
Affiliation(s)
- Jiaying Wang
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yulin Bai
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
| | - Xiaoqing Zou
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
| | - Chengyu Li
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
| | - Junyi Yang
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
| | - QiaoZhen Ke
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ji Zhao
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
| | - Tao Zhou
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Peng Xu
- State Key Laboratory of Mariculture Breeding, Xiamen University, Xiamen, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| |
Collapse
|
30
|
Kim C, Cnaani A, Kültz D. Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system. Sci Rep 2023; 13:12086. [PMID: 37495710 PMCID: PMC10371998 DOI: 10.1038/s41598-023-37928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia (Oreochromis mossambicus) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line and an optimized vector-based CRISPR/Cas9 system to functionally disrupt MYC in the tilapia genome and to establish causal links between MYC and cell functions, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal myca (a gene encoding MYC) knockout (ko) cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2%). Subsequent isolation and dilution of cells from these pools produced a myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.
Collapse
Affiliation(s)
- Chanhee Kim
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, 7528809, Rishon LeZion, Israel
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
31
|
Lorgen-Ritchie M, Uren Webster T, McMurtrie J, Bass D, Tyler CR, Rowley A, Martin SAM. Microbiomes in the context of developing sustainable intensified aquaculture. Front Microbiol 2023; 14:1200997. [PMID: 37426003 PMCID: PMC10327644 DOI: 10.3389/fmicb.2023.1200997] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023] Open
Abstract
With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.
Collapse
Affiliation(s)
| | - Tamsyn Uren Webster
- Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - David Bass
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
| | - Charles R. Tyler
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andrew Rowley
- Department of Biosciences, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Samuel A. M. Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
32
|
Kriaridou C, Tsairidou S, Fraslin C, Gorjanc G, Looseley ME, Johnston IA, Houston RD, Robledo D. Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species. Front Genet 2023; 14:1194266. [PMID: 37252666 PMCID: PMC10213886 DOI: 10.3389/fgene.2023.1194266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Genomic selection can accelerate genetic progress in aquaculture breeding programmes, particularly for traits measured on siblings of selection candidates. However, it is not widely implemented in most aquaculture species, and remains expensive due to high genotyping costs. Genotype imputation is a promising strategy that can reduce genotyping costs and facilitate the broader uptake of genomic selection in aquaculture breeding programmes. Genotype imputation can predict ungenotyped SNPs in populations genotyped at a low-density (LD), using a reference population genotyped at a high-density (HD). In this study, we used datasets of four aquaculture species (Atlantic salmon, turbot, common carp and Pacific oyster), phenotyped for different traits, to investigate the efficacy of genotype imputation for cost-effective genomic selection. The four datasets had been genotyped at HD, and eight LD panels (300-6,000 SNPs) were generated in silico. SNPs were selected to be: i) evenly distributed according to physical position ii) selected to minimise the linkage disequilibrium between adjacent SNPs or iii) randomly selected. Imputation was performed with three different software packages (AlphaImpute2, FImpute v.3 and findhap v.4). The results revealed that FImpute v.3 was faster and achieved higher imputation accuracies. Imputation accuracy increased with increasing panel density for both SNP selection methods, reaching correlations greater than 0.95 in the three fish species and 0.80 in Pacific oyster. In terms of genomic prediction accuracy, the LD and the imputed panels performed similarly, reaching values very close to the HD panels, except in the pacific oyster dataset, where the LD panel performed better than the imputed panel. In the fish species, when LD panels were used for genomic prediction without imputation, selection of markers based on either physical or genetic distance (instead of randomly) resulted in a high prediction accuracy, whereas imputation achieved near maximal prediction accuracy independently of the LD panel, showing higher reliability. Our results suggests that, in fish species, well-selected LD panels may achieve near maximal genomic selection prediction accuracy, and that the addition of imputation will result in maximal accuracy independently of the LD panel. These strategies represent effective and affordable methods to incorporate genomic selection into most aquaculture settings.
Collapse
Affiliation(s)
- Christina Kriaridou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Smaragda Tsairidou
- Global Academy of Agriculture and Food Systems, University of Edinburgh, Edinburgh, United Kingdom
| | - Clémence Fraslin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Benchmark Genetics, Penicuik, United Kingdom
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
33
|
Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
Collapse
Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
| |
Collapse
|
34
|
O'Neill EA, Rowan NJ. Potential disruptive effects of zoosporic parasites on peatland-based organic freshwater aquaculture: Case study from the Republic of Ireland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161495. [PMID: 36634789 DOI: 10.1016/j.scitotenv.2023.161495] [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: 10/21/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Irish freshwater aquaculture holds great potential for aiding food security. However, its necessary expansion has been hampered by the adoption of important environmental EU directives. A novel peatland-based recirculating aquaculture multi-trophic pond system (RAMPS) was developed to assess its potential to assist in the sustainable development of industry whilst remaining aligned with environmental protection by adhering to organic aquaculture practices. Microalgae play a pivotal role in the farms' wastewater bioremediation. However, a collapse of the algal population within the system towards the end of the pilot study was observed. No relationship between physicochemical fluctuations and the collapse were indicated. Further investigations into the potential presence of biological agents were then conducted and fourteen species of zoosporic parasites from five different genera (Labyrinthula, Vampyrella, Amoeboaphelidium, Paraphelidium and Aphelidium) were identified after conducting next-generation sequencing (MinION). The presence of these species indicated the potential cause of algal collapse. Additionally, changes in weather conditions may have also contributed to the issue. Given the lack of data available on zoosporic parasites and their potential impact on organic aquaculture practices, additional research needs to be conducted. Developing a means to monitor and mitigate against these complex zoosporic parasites will inform food security, it will particularly help safeguard "organic" freshwater aquaculture where there is a reliance on using natural-based approaches to address disease mitigation. This information will in turn inform the replication of this RAMPs system in peatlands internationally creating local employment in green technologies, as communities' transition away from burning peat as fossil fuel. Also, zoosporic parasites may reduce important microalgae in peatland-based culture ponds that serve as exceptional sequesters of carbon. Findings of this study will inform related research that focus on the emergence of microbial pathogens in local aquatic ecosystems brought on by variances in climate.
Collapse
Affiliation(s)
- Emer A O'Neill
- Centre for Sustainable Disinfection and Sustainability, Bioscience Research Institute, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland; Faculty of Science & Health, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland.
| | - Neil J Rowan
- Centre for Sustainable Disinfection and Sustainability, Bioscience Research Institute, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland; Faculty of Science & Health, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland
| |
Collapse
|
35
|
Coleman RR, Kraft DW, Hoban ML, Toonen RJ, Bowen BW. Genomic assessment of larval odyssey: self-recruitment and biased settlement in the Hawaiian surgeonfish Acanthurus triostegus sandvicensis. JOURNAL OF FISH BIOLOGY 2023; 102:581-595. [PMID: 36564830 DOI: 10.1111/jfb.15294] [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: 06/23/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54-77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of O'ahu, Hawai'i. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi-enclosed Kāne'ohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāne'ohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self-recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.
Collapse
Affiliation(s)
- Richard R Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, Florida, USA
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
| | - Derek W Kraft
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Mykle L Hoban
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kāne'ohe, Hawai'i, USA
| |
Collapse
|
36
|
Coimbra MRM, Farias RDS, da Silva BC, Blanco A, Hermida M, Caballero A, Bekaert M, Martinez P. A genetic linkage map of the threatened catfish Lophiosilurus alexandri: Inferences on effective population size. AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
|
37
|
Li X, Bai Y, Dong Z, Xu C, Liu S, Yu H, Kong L, Li Q. Chromosome-level genome assembly of the European flat oyster (Ostrea edulis) provides insights into its evolution and adaptation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101045. [PMID: 36470107 DOI: 10.1016/j.cbd.2022.101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
The European flat oyster (Ostrea edulis) is an endangered and economically important marine bivalve species that plays a critical role in the coastal ecosystem. Here, we report a high-quality chromosome-level genome assembly of O. edulis, generated using PacBio HiFi-CCS long reads and annotated with Nanopore full-length transcriptome. The O. edulis genome covers 946.06 Mb (scaffold N50 94.82 Mb) containing 34,495 protein-coding genes and a high proportion of repeat sequences (58.49 %). The reconstructed demographic histories show that O. edulis population might be shaped by breeding habit (embryo brooding) and historical climatic change. Comparative genomic analysis indicates that transposable elements may drive lineage-specific evolution in oysters. Notably, the O. edulis genome has a Hox gene cluster rearrangement that has never been reported in bivalves, making this species valuable for evolutionary studies of molluscan diversification. Moreover, genome expansion of O. edulis is probably central to its adaptation to filter-feeding and sessile lifestyles, as well as embryo brooding and pathogen resistance, in coastal ecosystems. This chromosome-level genome assembly provides new insights into the genome feature of oysters, and presents an important resource for genetic research, evolutionary studies, and biological conservation of O. edulis.
Collapse
Affiliation(s)
- Xinchun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhen Dong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| |
Collapse
|
38
|
Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
Collapse
Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | | | | |
Collapse
|
39
|
Pappas F, Kurta K, Vanhala T, Jeuthe H, Hagen Ø, Beirão J, Palaiokostas C. Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (
Salvelinus alpinus
) populations of anadromous and landlocked origin from Scandinavia. Evol Appl 2023; 16:797-813. [PMID: 37124091 PMCID: PMC10130564 DOI: 10.1111/eva.13537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/05/2022] [Accepted: 02/12/2023] [Indexed: 03/03/2023] Open
Abstract
Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.
Collapse
Affiliation(s)
- Fotis Pappas
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Khrystyna Kurta
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tytti Vanhala
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
- Aquaculture Center North Kälarne Sweden
| | - Ørjan Hagen
- Faculty of Bioscience and Aquaculture Nord University Bodø Norway
| | - José Beirão
- Faculty of Bioscience and Aquaculture Nord University Bodø Norway
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| |
Collapse
|
40
|
Host Hybridization Dominates over Cohabitation in Affecting Gut Microbiota of Intrageneric Hybrid Takifugu Pufferfish. mSystems 2023; 8:e0118122. [PMID: 36815841 PMCID: PMC10134855 DOI: 10.1128/msystems.01181-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Microbial symbionts are of great importance for macroscopic life, including fish, and both collectively comprise an integrated biological entity known as the holobiont. Yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to biotic and/or abiotic influences. Here, through amplicon profiling, the genealogical relationship between artificial F1 hybrid pufferfish with growth heterosis, produced from crossing female Takifugu obscurus with male Takifugu rubripes and its maternal halfsibling purebred, was well recapitulated by their gut microbial community similarities, indicating an evident parallelism between host phylogeny (hybridity) and microbiota relationships therein. Interestingly, modest yet significant fish growth promotion and gut microbiota alteration mediated by hybrid-purebred cohabitation were observed, in comparison with their respective monoculture cohorts that share common genetic makeups, implying a certain degree of environmental influences. Moreover, the underlying assemblage patterns of gut microbial communities were found associated with a trade-off between variable selection and dispersal limitation, which are plausibly driven by the augmented social interactions between hybrid and purebred cohabitants differing in behaviors. Results from this study not only can enrich, from a microbial perspective, the sophisticated understanding of complex and dynamic assemblage of the fish holobiont, but will also provide deeper insights into the ecophysiological factors imposed on the diversity-function relationships thereof. Our findings emphasize the intimate associations of gut microbiota in host genetics-environmental interactions and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve the production of farmed fishes. IMPORTANCE Microbial symbionts are of great importance for macroscopic life, including fish, and yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to the biotic and/or abiotic influences. Through gut microbiota profiling, we show that host intrageneric hybridization and cohabitation can impose a strong disturbance upon pufferfish gut microbiota. Moreover, marked alterations in the composition and function of gut microbiota in both hybrid and purebred pufferfish cohabitants were observed, which are potentially correlated with different metabolic priorities and behaviors between host genealogy. These results can enrich, from a microbial perspective, the sophisticated understanding of the complex and dynamic assemblage of the fish holobiont and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve farmed fish production.
Collapse
|
41
|
Vu NT, Phuc TH, Nguyen NH, Van Sang N. Effects of common full-sib families on accuracy of genomic prediction for tagging weight in striped catfish Pangasianodon hypophthalmus. Front Genet 2023; 13:1081246. [PMID: 36685869 PMCID: PMC9845282 DOI: 10.3389/fgene.2022.1081246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
Common full-sib families (c 2 ) make up a substantial proportion of total phenotypic variation in traits of commercial importance in aquaculture species and omission or inclusion of the c 2 resulted in possible changes in genetic parameter estimates and re-ranking of estimated breeding values. However, the impacts of common full-sib families on accuracy of genomic prediction for commercial traits of economic importance are not well known in many species, including aquatic animals. This research explored the impacts of common full-sib families on accuracy of genomic prediction for tagging weight in a population of striped catfish comprising 11,918 fish traced back to the base population (four generations), in which 560 individuals had genotype records of 14,154 SNPs. Our single step genomic best linear unbiased prediction (ssGLBUP) showed that the accuracy of genomic prediction for tagging weight was reduced by 96.5%-130.3% when the common full-sib families were included in statistical models. The reduction in the prediction accuracy was to a smaller extent in multivariate analysis than in univariate models. Imputation of missing genotypes somewhat reduced the upward biases in the prediction accuracy for tagging weight. It is therefore suggested that genomic evaluation models for traits recorded during the early phase of growth development should account for the common full-sib families to minimise possible biases in the accuracy of genomic prediction and hence, selection response.
Collapse
Affiliation(s)
- Nguyen Thanh Vu
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia,Center for Bio-Innovation, University of the Sunshine Coast, Maroochydore, QLD, Australia,Research Institute for Aquaculture No. 2, Ho Chi Minh City, Vietnam
| | - Tran Huu Phuc
- Research Institute for Aquaculture No. 2, Ho Chi Minh City, Vietnam
| | - Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia,Center for Bio-Innovation, University of the Sunshine Coast, Maroochydore, QLD, Australia,*Correspondence: Nguyen Hong Nguyen, ; Nguyen Van Sang,
| | - Nguyen Van Sang
- Research Institute for Aquaculture No. 2, Ho Chi Minh City, Vietnam,*Correspondence: Nguyen Hong Nguyen, ; Nguyen Van Sang,
| |
Collapse
|
42
|
Calboli FCF, Iso-Touru T, Bitz O, Fischer D, Nousiainen A, Koskinen H, Tapio M, Tapio I, Kause A. Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus. J Anim Sci 2023; 101:skad333. [PMID: 37777972 PMCID: PMC10583997 DOI: 10.1093/jas/skad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023] Open
Abstract
Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.
Collapse
Affiliation(s)
| | - Terhi Iso-Touru
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Oliver Bitz
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Daniel Fischer
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Antti Nousiainen
- Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland
| | - Heikki Koskinen
- Natural Resources Institute Finland (LUKE), FI-70210 Kuopio, Finland
| | - Miika Tapio
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Ilma Tapio
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| | - Antti Kause
- Natural Resources Institute Finland (LUKE), FI-31600 Jokioinen, Finland
| |
Collapse
|
43
|
Prentice PM, Houslay TM, Wilson AJ. Exploiting animal personality to reduce chronic stress in captive fish populations. Front Vet Sci 2022; 9:1046205. [PMID: 36590805 PMCID: PMC9794626 DOI: 10.3389/fvets.2022.1046205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/22/2022] [Indexed: 12/16/2022] Open
Abstract
Chronic stress is a major source of welfare problems in many captive populations, including fishes. While we have long known that chronic stress effects arise from maladaptive expression of acute stress response pathways, predicting where and when problems will arise is difficult. Here we highlight how insights from animal personality research could be useful in this regard. Since behavior is the first line of organismal defense when challenged by a stressor, assays of shy-bold type personality variation can provide information about individual stress response that is expected to predict susceptibility to chronic stress. Moreover, recent demonstrations that among-individual differences in stress-related physiology and behaviors are underpinned by genetic factors means that selection on behavioral biomarkers could offer a route to genetic improvement of welfare outcomes in captive fish stocks. Here we review the evidence in support of this proposition, identify remaining empirical gaps in our understanding, and set out appropriate criteria to guide development of biomarkers. The article is largely prospective: fundamental research into fish personality shows how behavioral biomarkers could be used to achieve welfare gains in captive fish populations. However, translating potential to actual gains will require an interdisciplinary approach that integrates the expertise and viewpoints of researchers working across animal behavior, genetics, and welfare science.
Collapse
Affiliation(s)
- Pamela M. Prentice
- Centre for Ecology and Conservation, University of Exeter, Exeter, United Kingdom,Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Thomas M. Houslay
- Centre for Ecology and Conservation, University of Exeter, Exeter, United Kingdom,Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Alastair J. Wilson
- Centre for Ecology and Conservation, University of Exeter, Exeter, United Kingdom,*Correspondence: Alastair J. Wilson
| |
Collapse
|
44
|
Jones HE, Wilson PB. Progress and opportunities through use of genomics in animal production. Trends Genet 2022; 38:1228-1252. [PMID: 35945076 DOI: 10.1016/j.tig.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
Abstract
The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.
Collapse
Affiliation(s)
- Huw E Jones
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK.
| | - Philippe B Wilson
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK
| |
Collapse
|
45
|
Wang W, Pan C, Lv M, Ruan Q, Chen W, Shafique L, Parveen S, Liang Z, Ma H, Luo X. Effect of hemoglobin on Nile tilapia (Oreochromis niloticus) kidney (NTK) cell line damage. FISH & SHELLFISH IMMUNOLOGY 2022; 131:637-645. [PMID: 36272521 DOI: 10.1016/j.fsi.2022.10.029] [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: 06/07/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Bacteria or viral outbreaks can cause tilapia hemorrhage, ensuring considerable volume of hemoglobin (Hb) into the tissue. However, the hemoglobin toxicity on tissue and high doses also effect on tissue this phenomena is still under consideration. Therefore, current study exploited Nile tilapia kidney (NTK) cells to deeply expose the toxic effect of Hb on NTK cells. Toxicity of Hb on NTK cells was determined in terms of cells growth, expression of iron metabolism and inflammation-related genes, consequently examined antioxidant-related enzymes genes expression, intracellular iron and reactive oxygen species (ROS) contents, and apoptosis-related genes expression. The results showed that Hb and heme significantly inhibited NTK cells growth and up-regulated iron metabolism-related genes expression in different degrees. The Hb and heme activated the expression of pro-inflammatory cytokines (TNF-α, tumor necrosis factor-α; IL-1β, interleukin 1β; IL-6, interleukin 6), the anti-inflammatory factor (IL-10, interleukin 10) and the chemotactic factors (IL-4, interleukin 4; IL-8, interleukin 8) through NF-κB pathway, meanwhile activated the expression of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px). Moreover, the Hb significantly increased intracellular iron and ROS contents while the expression of apoptosis-related genes was significantly activated by both Hb and heme. Current investigation suggested that high oxidative activity of Hb could activate iron metabolism- and inflammation-related genes expression, and increase intracellular iron and ROS levels, lead to up-regulated the expression of apoptosis genes in NTK cells.
Collapse
Affiliation(s)
- Weisheng Wang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Chuanyan Pan
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| | - Min Lv
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China; The Food Engineering and Technology Center, Guangxi Xiaoyanren Biotechnology Co., Ltd, Nanning, 530017, Guangxi, China
| | - Qiufeng Ruan
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| | - Weijie Chen
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| | - Laiba Shafique
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Shakeela Parveen
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, Pakistan
| | - Zheng Liang
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| | - Huawei Ma
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| | - Xu Luo
- Center of Aquaculture and Processing Technology, Guangxi Academy of Fishery Science, Nanning, 530021, Guangxi, China
| |
Collapse
|
46
|
Gervais O, Papadopoulou A, Gratacap R, Hillestad B, Tinch AE, Martin SAM, Houston RD, Robledo D. Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon. BMC Genomics 2022; 23:775. [PMID: 36443659 PMCID: PMC9703674 DOI: 10.1186/s12864-022-09007-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Infectious Salmon Anaemia virus (ISAV) is an orthomyxovirus responsible for large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus. RESULTS Three different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post challenge) and RNA sequenced. The transcriptomes of infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes, our results suggest that other processes such as ubiquitination and ribosomal processing are important during early infection with ISAV. Moreover, the comparison between resistant and susceptible fish has also highlighted some interesting genes related to ubiquitination, intracellular transport and the inflammasome. CONCLUSIONS Atlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An immune response was observed in the head kidney in these early timepoints, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.
Collapse
Affiliation(s)
- Ophélie Gervais
- grid.4305.20000 0004 1936 7988The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Athina Papadopoulou
- grid.4305.20000 0004 1936 7988The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Remi Gratacap
- grid.4305.20000 0004 1936 7988The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Alan E. Tinch
- Benchmark Genetics, Penicuik, UK ,The Center for Aquaculture Technologies, San Diego, USA
| | - Samuel A. M. Martin
- grid.7107.10000 0004 1936 7291School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Ross D. Houston
- grid.4305.20000 0004 1936 7988The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Diego Robledo
- grid.4305.20000 0004 1936 7988The Roslin Institute, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
47
|
Virulence Genes and In Vitro Antibiotic Profile of Photobacterium damselae Strains, Isolated from Fish Reared in Greek Aquaculture Facilities. Animals (Basel) 2022; 12:ani12223133. [PMID: 36428362 PMCID: PMC9687077 DOI: 10.3390/ani12223133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteria belonging to the species Photobacterium damselae are pathogens of cultured marine fish, causing diseases of high importance, such as Pasteurellosis. Thus, they are considered a major threat to the aquaculture sector. Despite the great importance of fish mariculture for the Greek economy, the distribution and abundance of these bacteria are not well documented in aquaculture units in Greece. Keeping this in mind, the scope of the present study was to investigate the presence, antibiotic profile, and virulence of Photobacterium bacteria originating from a representative sample of mariculture units throughout Greece. Samples were collected from diseased fish belonging to three different cultured fish species, namely Sparus aurata, Dicentrarchus labrax, and Pagrus pagrus, from both the Aegean and the Ionian Sea. Tissue samples were cultured in agar media, and bacteria were molecularly identified using both bacterial universal and species-specific primer pairs for Photobacterium spp. Additionally, the identified strains were characterized for the presence of virulence genes as well as antibiotic profiles. According to the results, the aforementioned bacteria are distributed in the Greek aquaculture units and are characterized by high pathogenicity based on the abundance of virulence genes. Furthermore, the majority of the detected strains exhibit some level of antibiotic resistance. In summary, our results indicate the need for systematic surveillance and study of their antibiotic profiles in Greek aquaculture since these bacteria constitute a major threat to the sector.
Collapse
|
48
|
Yu P, Wang Y, Li Z, Jin H, Li LL, Han X, Wang ZW, Yang XL, Li XY, Zhang XJ, Zhou L, Gui JF. Causal gene identification and desirable trait recreation in goldfish. SCIENCE CHINA LIFE SCIENCES 2022; 65:2341-2353. [DOI: 10.1007/s11427-022-2194-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022]
|
49
|
Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
Collapse
Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
| |
Collapse
|
50
|
Ou J, Liu Q, Bian Y, Luan X, Meng Y, Dong H, Cao M, Zhang B, Wang Z, Zhao W. Integrated analysis of mRNA and microRNA transcriptome related to immunity and autophagy in shrimp hemocytes infected with Spiroplasma eriocheiris. FISH & SHELLFISH IMMUNOLOGY 2022; 130:436-452. [PMID: 36184970 DOI: 10.1016/j.fsi.2022.09.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
In recent years, the industry in charge of the cultivation of Macrobrachium nipponense (M.nipponense) has suffered significant economic losses due to an infectious pathogen called Spiroplasma eriocheiris (S.eriocheiris). There has therefore been a need to identify the key immune and autophagy genes that respond to M.nipponense's infection with S. eriocheiris to analyze its immune response mechanism and the regulation of related microRNAs (miRNAs). In this study, the mRNA and miRNA transcriptome of M.nipponense's hemocytes were analyzed at different stages of infection. This analysis employed the second and third-generation sequencing technologies. In the mRNA transcriptome, 1656 genes were expressed in healthy and susceptible M.nipponense. 892 of these were significantly up-regulated, while 764 were down-regulated. 118 genes with significant differences in autophagy, endocytosis, lysosome, Toll, IMD, and VEGF pathways were obtained from the transcriptome. In the miRNA transcriptome, 312 miRNAs (Conserved: 112, PN-type: 18, PC-type: 182) were sequenced. 74 were significantly up-regulated, and 57 were down-regulated. There were 25 miRNAs involved in regulating the Toll and IMD pathways, 41 in endocytosis, 30 in lysosome, and 12 in the VEGF pathway. An integrated analysis of immune-related miRNAs and mRNAs showed that miRNAs with significant differences (P < 0.05) such as ame-miR-29b-3p, dpu-miR-1and PC-3p-945_4074, had corresponding regulatory relationships with 118 important immune genes such as Relish, Dorsal, Caspase-3, and NF-κB. This study obtained the key immune and autophagy-related genes and corresponding regulatory miRNAs in M. nipponense's hemocytes in response to an infection by S.eriocheiris. The results can provide vital data that further reveals the defense mechanism of M.nipponense's immune system against S.eriocheiris. It can also help further comprehension and interpretation of M.nipponense's resistance mechanism to the invading S.eriocheiris, and provide molecular research information for the realization of host-directed therapies (HDT) for M.nipponense.
Collapse
Affiliation(s)
- Jiangtao Ou
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China.
| | - Qiao Liu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China; The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Province Jiangsu, China
| | - Yunxia Bian
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Xiaoqi Luan
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China; Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Yusuo Meng
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Huizi Dong
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Miao Cao
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Benhou Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Zisheng Wang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| | - Weihong Zhao
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, School of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng, 224051, Province Jiangsu, China
| |
Collapse
|