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Liu Q, Duan L, Li B, Zhang X, Liu F, Yu J, Shu Y, Hu F, Lin J, Xiong X, Liu S. The key role of myostatin b in somatic growth in fishes derived from distant hybridization. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1441-1454. [PMID: 38561484 DOI: 10.1007/s11427-023-2487-8] [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: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 04/04/2024]
Abstract
The basic mechanism of heterosis has not been systematically and completely characterized. In previous studies, we obtained three economically important fishes that exhibit rapid growth, WR (WCC ♀ × RCC ♂), WR-II (WR ♀ × WCC ♂), and WR-III (WR-II ♀ × 4nAU ♂), through distant hybridization. However, the mechanism underlying this rapid growth remains unclear. In this study, we found that WR, WR-II, and WR-III showed muscle hypertrophy and higher muscle protein and fat contents compared with their parent species (RCC and WCC). Candidate genes responsible for this rapid growth were then obtained through an analysis of 12 muscle transcriptomes. Notably, the mRNA level of mstnb (myostatin b), which is a negative regulator of myogenesis, was significantly reduced in WR, WR-II, and WR-III compared with the parent species. To verify the function of mstnb, a mstnb-deficient mutant RCC line was generated using the CRISPR-Cas9 technique. The average body weight of mstnb-deficient RCC at 12 months of age was significantly increased by 29.57% compared with that in wild-type siblings. Moreover, the area and number of muscle fibers were significantly increased in mstnb-deficient RCC, indicating hypertrophy and hyperplasia. Furthermore, the muscle protein and fat contents were significantly increased in mstnb-deficient RCC. The molecular regulatory mechanism of mstnb was then revealed by transcription profiling, which showed that genes related to myogenesis (myod, myog, and myf5), protein synthesis (PI3K-AKT-mTOR), and lipogenesis (pparγ and fabp3) were highly activated in hybrid fishes and mstnb-deficient RCC. This study revealed that low expression or deficiency of mstnb regulates somatic growth by promoting myogenesis, protein synthesis, and lipogenesis in hybrid fishes and mstnb-deficient RCC, which provides evidence for the molecular mechanism of heterosis via distant hybridization.
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Affiliation(s)
- Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lujiao Duan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Bei Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xuanyi Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fanglei Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jianming Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuqin Shu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Jingjing Lin
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaoxia Xiong
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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He X, Wu F, Wang L, Li L, Zhang G. Integrated application of transcriptomics and metabolomics provides insights into condition index difference mechanisms in the Pacific oyster (Crassostrea gigas). Genomics 2022; 114:110413. [PMID: 35716821 DOI: 10.1016/j.ygeno.2022.110413] [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: 12/22/2021] [Revised: 05/04/2022] [Accepted: 06/12/2022] [Indexed: 11/25/2022]
Abstract
The condition index (CI) is an economically important tool for assessing the quality of oysters, such as the Pacific oyster Crassostrea gigas. However, little is known about the mechanisms that underlie differences in CI between different C. gigas populations. In this study, we integrated transcriptomic and metabolomic profiling to investigate the mechanisms that underlie the differences between high- and low-CI groups in one- and two-year-old populations of C. gigas. The results indicate that differences in CI were associated with the regulation of growth-related genes, the FoxO signaling pathway, and the complex regulation of carbohydrate, lipid, amino acid, and energy metabolism. Moreover, the mechanisms underlying these differences differed between the populations. This study is the first to elucidate the molecular and chemical mechanisms associated with CI, and the results will be helpful for breeding higher quality oysters.
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Affiliation(s)
- Xin He
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100039, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fucun Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Luping Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao 266071, China
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Wang L, Guo Y, Pan M, Li X, Huang D, Liu Y, Wu C, Zhang W, Mai K. Functions of Forkhead Box O on Glucose Metabolism in Abalone Haliotis discus hannai and Its Responses to High Levels of Dietary Lipid. Genes (Basel) 2021; 12:genes12020297. [PMID: 33672704 PMCID: PMC7924355 DOI: 10.3390/genes12020297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/05/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
The forkhead box O (FoxO) subfamily is a member of the forkhead transcription factor family. It has regulation functions in glucose metabolism in mammals and fish. In the present study, a gene of the foxo homolog in abalone Haliotis discus hannai was cloned. A conservative forkhead (FH) domain and a transactivation (FoxO-TAD) domain were identified. Abalone foxo-specific siRNA (small interfering RNA) was injected to investigate the functions of foxo on glucose metabolism. Knockdown of foxo inhibited expression of phosphoenolpyruvate carboxykinase (pepck) and significantly increased expressions of hexokinase (hk) and pyruvate kinase (pk), but it failed to inhibit the relative mRNA level of glucose-6-phosphatase (g6pase). Then, a 100-day feeding trial was conducted to investigate the response of foxo and glucose metabolism in abalone fed with 1.57% (LFD, low-fat diet), 3.82% (MFD, middle-fat diet) and 6.72% (HFD, high-fat diet) of dietary lipid, respectively. The insulin-signaling pathway (AKT) was depressed and FoxO was activated by the HFD, but it did not inhibit glycolysis (hk) or improved gluconeogenesis significantly (pepck and g6pase). At the same time, impaired hepatopancreas glycogen storage raised hemolymph glucose levels. In conclusion, abalone foxo can be regulated by dietary lipid and can regulate gluconeogenesis or glycolysis in response to changes of dietary lipid levels, in which glycogen metabolism plays an important role.
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Affiliation(s)
- Liu Wang
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
| | - Yanlin Guo
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
| | - Mingzhu Pan
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
| | - Xinxin Li
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
| | - Dong Huang
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
| | - Yue Liu
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
| | - Chenglong Wu
- School of Life Science, Huzhou University, 759 East 2nd Road, Huzhou 313000, China
- Correspondence: (C.W.); (W.Z.); Tel.: +86-532-8203-2145 (W.Z.)
| | - Wenbing Zhang
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
- Correspondence: (C.W.); (W.Z.); Tel.: +86-532-8203-2145 (W.Z.)
| | - Kangsen Mai
- The Key Laboratory of Aquaculture Nutrition and Feeds (Ministry of Agriculture and Rural Affairs), the Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; (L.W.); (Y.G.); (M.P.); (X.L.); (D.H.); (Y.L.); (K.M.)
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Cruz A, da Costa F, Fernández-Pérez J, Nantón A, Fernández-Boo S, Insua A, Méndez J. Genetic variability in Ruditapes decussatus clam combined with Perkinsus infection level to support founder population selection for a breeding program. PeerJ 2020; 8:e9728. [PMID: 33194343 PMCID: PMC7602687 DOI: 10.7717/peerj.9728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/24/2020] [Indexed: 11/20/2022] Open
Abstract
Clam farmers worldwide face several challenges, including irregular seed supply and high mortalities due to pathogenic organisms such as Perkinsus olseni. In Europe, there is a high unmet consumer demand for native clam species such as Ruditapes decussatus. The high market value of R. decussatus makes the culture of this species potentially more attractive than that culture of the alien species Ruditapes philippinarum. Thus, there is a market opportunity in breeding and producing R. decussatus at an industrial scale. A selective breeding program to improve R. decussatus performance will be carried out in Portugal; and the first critical step to develop such a breeding program is the establishment of a founder population. In this study, intra- and interpopulation genetic diversity was assessed using 13 microsatellite markers in eight natural beds located in Portugal, Spain and Italy. Also, allele and genotypic frequencies of each microsatellite locus were assessed discriminating between clams infected and non-infected by P. olseni. All locations showed similar values for several genetic diversity parameters. Analyses of population differentiation (FST, Bayesian clustering and AMOVAs) revealed five genetically differentiated regions: Rías Altas and Rías Baixas (NW Spain), North/Central Coast of Portugal, Gulf of Cadiz and Adriatic Sea. Significant differences in the allelic and genotypic frequency distribution between infected clams and non-infected ones at four microsatellite loci are reported suggesting that resistance to the disease could have a genetic basis. Moreover, a positive or negative relationship between the frequency of certain alleles and the parasite infection was inferred. Further studies should confirm the potential use of those alleles as genetic markers for P. olseni infection. Integrating results of genetic diversity within and between populations and Perkinsus infection levels, a founder population for a R. decussatus breeding program is proposed, composed by individuals from Barallobre (Rías Altas), Pontevedra or Cangas (Rías Baixas), Óbidos (North/Central Coast of Portugal), Algarve (Gulf of Cadiz) and Venice (Adriatic Sea).
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Affiliation(s)
| | | | - Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
| | - Sergio Fernández-Boo
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Matosinhos, Portugal
| | - Ana Insua
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
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Yang Z, Wang L, Wong SM, Yue GH. The HIF1αn gene and its association with hypoxia tolerance in the Asian seabass. Gene 2020; 731:144341. [PMID: 31935502 DOI: 10.1016/j.gene.2020.144341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 11/30/2022]
Abstract
Hypoxia is one of the major challenges in aquaculture industry. Breeding of fish tolerant to hypoxia is an important task in genetic improvement of aquaculture species. The Asian seabass, Lates calcarifer, is an important foodfish species. We identified and characterized the hypoxia-inducible factor inhibitor (HIF1αn) gene in the Asian seabass. The full-length cDNA sequence of the HIF1αn was 3425 bp, with an ORF of 1065 bp, encoding 354 amino acids. The genomic sequence of the gene was 8667 bp in length, and contained eight exons and seven introns. Phylogenetic analysis of the gene in fish and tetrapods revealed that the HIF1αn in the Asian seabass was closely related to that of tilapia (Oreochromis niloticus). The HIF1αn was highly up-regulated in the gill, spleen and heart after 3.5-hours hypoxia treatment. We identified three SNPs in the third and fourth introns of the HIF1αn gene. The SNP (i.e. SNP 9332241 (C/T)) in the fourth intron was significantly (P < 0.01) associated with hypoxia tolerance. This SNP might be useful in selecting Asian seabass for improved tolerance to hypoxia. Our data also provide useful information for further detailed analysis of the function of the HIF1αn gene in hypoxia tolerance.
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Affiliation(s)
- Zituo Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543, Singapore; Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
| | - Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
| | - Sek Man Wong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543, Singapore; National University of Singapore Suzhou Research Institute, Suzhou, Jiangsu 215123, China.
| | - Gen Hua Yue
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, 117543, Singapore; Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore; School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, 637551, Singapore.
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Hosseinpoor MJ, Parvin H, Nejatian S, Rezaie V. Gene Regulatory Elements Extraction in Breast Cancer by Hi-C Data Using a Meta-Heuristic Method. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419090072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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