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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.
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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.
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2
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Liu M, He C, Zhu T, Jia X, Zhang L, Jiang W, Chi C, Li X, Jiang G, Liu H, Zhang D. Characterizing and identifying of miRNAs involved in berberine modulating glucose metabolism of Megalobrama amblycephala. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1667-1682. [PMID: 38963582 DOI: 10.1007/s10695-024-01362-1] [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: 01/30/2024] [Accepted: 05/24/2024] [Indexed: 07/05/2024]
Abstract
The present study, as one part of a larger project that aimed to investigate the effects of dietary berberine (BBR) on fish growth and glucose regulation, mainly focused on whether miRNAs involve in BBR's modulation of glucose metabolism in fish. Blunt snout bream Megalobrama amblycephala (average weight of 20.36 ± 1.44 g) were exposed to the control diet (NCD, 30% carbohydrate), the high-carbohydrate diet (HCD, 43% carbohydrate) and the berberine diet (HCB, HCD supplemented with 50 mg/kg BBR). After 10 weeks' feeding trial, intraperitoneal injection of glucose was conducted, and then, the plasma and liver were sampled at 0 h, 1 h, 2 h, 6 h, and 12 h. The results showed the plasma glucose levels in all groups rose sharply and peaked at 1 h after glucose injection. Unlike the NCD and HCB groups, the plasma glucose in the HCD group did not decrease after 1 h, while remained high level until at 2 h. The NCD group significantly increased liver glycogen content at times 0-2 h compared to the other two groups and then liver glycogen decreased sharply until at times 6-12 h. To investigate the role of BBR that may cause the changes in plasma glucose and liver glycogen, miRNA high-throughput sequencing was performed on three groups of liver tissues at 2 h time point. Eventually, 20 and 12 differentially expressed miRNAs (DEMs) were obtained in HCD vs NCD and HCB vs HCD, respectively. Through function analyzing, we found that HCD may affect liver metabolism under glucose loading through the NF-κB pathway; and miRNAs regulated by BBR mainly play roles in adipocyte lipolysis, niacin and nicotinamide metabolism, and amino acid transmembrane transport. In the functional exploration of newly discovered novel:Chr12_18892, we found its target gene, adenylate cyclase 3 (adcy3), was widely involved in lipid decomposition, amino acid metabolism, and other pathways. Furthermore, a targeting relationship of novel:Chr12_18892 and adcy3 was confirmed by double luciferase assay. Thus, BBR may promote novel:Chr12_18892 to regulate the expression of adcy3 and participate in glucose metabolism.
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Affiliation(s)
- Mingyang Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Chang He
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Zhu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyan Jia
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibo Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cheng Chi
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hengtong Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Xu H, Tong G, Yan T, Dong L, Yang X, Dou D, Sun Z, Liu T, Zheng X, Yang J, Sun X, Zhou Y, Kuang Y. Transcriptomic Analysis Provides Insights to Reveal the bmp6 Function Related to the Development of Intermuscular Bones in Zebrafish. Front Cell Dev Biol 2022; 10:821471. [PMID: 35646941 PMCID: PMC9135397 DOI: 10.3389/fcell.2022.821471] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
Intermuscular bones (IBs) are small, hard-boned spicules located in the muscle tissue that mainly exist in the myosepta of lower teleosts, which hurt the edibleness and economic value of fish. The study of the development of IBs is very important for freshwater aquaculture fish, but the molecular mechanism of its formation and the key regulatory genes remain unclear. In this study, we first constructed two types of zebrafish mutants (the mutants losing IBs and the mutants with partial deletion of IBs) by knocking out bmp6. We then carried out a transcriptomic analysis to reveal the role of bmp6 in the developmental mechanism of IBs; we used the caudal musculoskeletal tissues of these mutants and wild-type zebrafish at three development stages (20, 45, and 60 dph) to perform transcriptomic analysis. The results showed that the deficiency of bmp6 upregulated sik1 and activated the TNF-A signaling via the NF-KB pathway, which inhibited the development of osteoblasts and promoted osteoclast formation, thereby inhibiting the formation of IBs. These results provided insights to understand the role of bmp6 in the development of IBs in zebrafish and are useful for selective breeding of IBs in cyprinids.
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Affiliation(s)
- Huan Xu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
- Heilongjiang Provincial Key Laboratory of Hard Tissue Development and Regeneration, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guangxiang Tong
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Ting Yan
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Le Dong
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xiaoxing Yang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Dongyu Dou
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Zhipeng Sun
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Tianqi Liu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Xianhu Zheng
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Jian Yang
- Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
| | - Xiaowen Sun
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
| | - Yi Zhou
- Stem Cell Program of Boston Children’s Hospital, Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Youyi Kuang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National and Local Joint Engineering Laboratory for Freshwater Fish Breeding, Harbin, China
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China
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Bulked Segregant Analysis and Association Analysis Identified the Polymorphisms Related to the Intermuscular Bones in Common Carp ( Cyprinus carpio). BIOLOGY 2022; 11:biology11030477. [PMID: 35336850 PMCID: PMC8945855 DOI: 10.3390/biology11030477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Many widely cultured freshwater fish species, such as common carp, belong to the Cyprinidae family. However, most cyprinids have numerous and complex intermuscular bones (IBs), resulting in an adverse effect on cyprinid fish meat processing and consumption. Numerous studies have been trying to understand the development mechanism of IBs and to identify the SNPs associated with the total IB number. However, the SNPs associated with different forms of IBs have been studied less thoroughly. The joint effects of the SNPs on IB development also remain poorly understood. The common carp has numerous geographical populations and domesticated strains, diversifying its phenotypes. The question of whether consensus IB-related SNPs or genes exist among multiple strains of common carp has also not yet been answered. Selective breeding of IB-reduced common carp has been hindered due to a lack of effective molecular markers. To answer these questions, we performed bulked segregant analysis (BSA) to detect the consensus SNPs in three strains. The consensus BSA-SNPs and the other SNPs in their flanking regions were validated in additional individuals. The SNPs associated with the frequency of different IB types were identified. We examined the joint effects of significant SNPs on the numbers of different types of IBs. The identified genetic markers may benefit future selective breeding and reduce the IB number in common carp. Abstract The allotetraploid common carp is one of the most important freshwater food fish. However, the IBs found in allotetraploid common carp increase the difficulty in fish meat processing and consumption. Although candidate genes associated with the total IB number have been identified, the SNPs associated with the numbers of the total IBs and different forms of IBs have not yet been identified, hindering the breeding of IB-reduced common carp. Herein, the numbers of different types of IBs in three common carp strains were measured. Using whole-genome resequencing and bulked segregant analysis in three pairs of IB-more and IB-less groups, we identified the consensus nonsynonymous SNPs in three strains of common carp. Screening the flanking regions of these SNPs led to the detection of other SNPs. Association study detected 21 SNPs significantly associated with the number of total IBs, epineural-IBs, and ten detailed types of IBs. We observed the joint effects of multiple SNPs on each associated IB number with an improved explained percentage of phenotypic variation. The resulting dataset provides a resource to understand the molecular mechanisms of IB development in different common carp strains. These SNPs are potential markers for future selection to generate IB-reduced common carp.
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Abstract
Intermuscular bones (IBs) are slender linear bones embedded in muscle, which ossify from tendons through a process of intramembranous ossification, and only exist in basal teleosts. IBs are essential for fish swimming, but they present a choking risk during human consumption, especially in children, which can lead to commercial risks that have a negative impact on the aquaculture of these fish. In this review, we discuss the morphogenesis and functions of IBs, including their underlying molecular mechanisms, as well as the advantages and disadvantages of different methods for IB studies and techniques for breeding and generating IB-free fish lines. This review reveals that the many key genes involved in tendon development, osteoblast differentiation, and bone formation, e.g., scxa, msxC, sost, twist, bmps, and osterix, also play roles in IB development. Thus, this paper provides useful information for the breeding of new fish strains without IBs via genome editing and artificial selection.
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Affiliation(s)
- Bo Li
- Cave Fish Development and Evolution Research Group, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yuan-Wei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiao Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Li Ma
- Cave Fish Development and Evolution Research Group, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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6
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Nie C, Wan S, Chen Y, Zhu D, Wang X, Dong X, Gao ZX. Loss of scleraxis leads to distinct reduction of mineralized intermuscular bone in zebrafish. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Chen Y, Wan S, Li Q, Dong X, Diao J, Liao Q, Wang GY, Gao ZX. Genome-Wide Integrated Analysis Revealed Functions of lncRNA-miRNA-mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala. Front Cell Dev Biol 2021; 8:603815. [PMID: 33614620 PMCID: PMC7891300 DOI: 10.3389/fcell.2020.603815] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Intermuscular bone (IB) occurs in the myosepta of teleosts. Its existence has an adverse influence on the edible and economic value of fish, especially for aquaculture species belonging to Cypriniformes. The growth mechanism of IBs is quite lacking. In this study, we firstly used single molecular real-time sequencing (SMRT) technology to improve the draft genome annotation and full characterization of the transcriptome for one typical aquaculture species, blunt snout bream (Megalobrama amblycephala). The long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles in two IB growth stages (1 and 3 years old) were compared through transcriptome and degradome analyses. A total of 126 miRNAs, 403 mRNAs, and 353 lncRNAs were found to be differentially expressed between the two stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the significantly upregulated map2k6 and cytc in the MAPK/p53 signaling pathway and the significantly downregulated lama3 and thbs4b in the extracellular matrix (ECM)–receptor pathway may play a key regulatory role in IB growth. Bioinformatics analysis subsequently revealed 14 competing endogenous RNA (ceRNA) pairs related to the growth of IBs, consisting of 10 lncRNAs, 7 miRNAs, and 10 mRNAs. Of these, dre-miR-24b-3p and dre-miR-193b-3p are core regulatory factors interacting with four lncRNAs and three mRNAs, the interaction mechanism of which was also revealed by subsequent experiments at the cellular level. In conclusion, our data showed that IBs had higher activity of cell apoptosis and lower mineralization activity in IB_III compared to IB_I via interaction of MAPK/p53 and ECM–receptor signaling pathways. The downregulated zip1 interacted with miR-24a-3p and lnc017705, decreased osteoblast differentiation and Ca2+ deposition in the IB_III stage. Our identified functional mRNAs, lncRNAs, and miRNAs provide a data basis for in-depth elucidation of the growth mechanism of teleost IB.
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Affiliation(s)
- Yulong Chen
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Shiming Wan
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Qing Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan, China
| | - Xiaoru Dong
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Jinghan Diao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Qing Liao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Gui-Ying Wang
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan Xianfeng Aquaculture Technology Co. Ltd, Wuhan, China
| | - Ze-Xia Gao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China.,Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, China
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Nunes JRS, Pértille F, Andrade SCS, Perazza CA, Villela PMS, Almeida-Val VMF, Gao ZX, Coutinho LL, Hilsdorf AWS. Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum). Anim Genet 2020; 51:899-909. [PMID: 33006182 DOI: 10.1111/age.13001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 01/21/2023]
Abstract
The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (Padj < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.
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Affiliation(s)
- J R S Nunes
- Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, 69630-000, Brazil.,Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.,Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, 58 183, Sweden
| | - S C S Andrade
- Genetics and Evolutionary Biology Department, University of São Paulo (USP)/Bioscience Institute (IB), São Paulo, São Paulo, 05508-090, Brazil
| | - C A Perazza
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
| | - P M S Villela
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - V M F Almeida-Val
- Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, 69067-375, Brazil
| | - Z-X Gao
- College of Fisheries, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Hongshan District, Wuhan, 430070, China
| | - L L Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - A W S Hilsdorf
- Unit of Biotechnology, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, 08780-911, Brazil
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9
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Yang K, Jiang W, Wang X, Zhang Y, Pan X, Yang J. Evolution of the intermuscular bones in the Cyprinidae (Pisces) from a phylogenetic perspective. Ecol Evol 2019; 9:8555-8566. [PMID: 31410261 PMCID: PMC6686301 DOI: 10.1002/ece3.5374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 01/15/2023] Open
Abstract
Intermuscular bones (IBs) are widely present in morphologically generalized teleost fishes and are commonly found in the Cyprinidae. Intermuscular bones are small, hard spicules of bone that are formed by ossification in the myosepta between neighboring myomeres. Why fish have IBs, and whether there is any evolutionary pattern to their occurrence, has been poorly understood. However, the presence of IBs does substantially affect the meat quality and commercial values of many cyprinid fishes in aquaculture. In this study, we sampled 592 individuals of cyprinid fishes to systematically investigate the evolution of IBs from a phylogenetic point of view. We found that the total number of IBs in the Cyprinidae ranged from 73 to 169, and we clarified that only two categories of IBs (epineural and epipleural) were present in all examined cyprinids. Most of the IBs were distributed in the posterior region of the fish, which might be an optimal target for selecting fewer IB strains in aquaculture. There was a positive correlation between IBs and the number of vertebrae, thus making it possible to predict the approximate number of IBs by counting the number of vertebrae. Although the IBs displayed some correlation with phylogenetic relationships in some lineages and to ecological factors such as diet (especially carnivore), in an overall view the variations of IBs in cyprinids were extremely diverse. The number and patterns of IBs in these fishes may reflect their phylogenetic history, but have been shaped by multiple environment factors. In this study, we also confirmed that X-ray photography remains an optimal and reliable method for the study of IBs.
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Affiliation(s)
- Kunfeng Yang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Wansheng Jiang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Xiaoai Wang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yuanwei Zhang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Xiaofu Pan
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Junxing Yang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
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10
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Gong W, Huang Y, Xie J, Wang G, Yu D, Sun X, Zhang K, Li Z, Ermeng Y, Tian J, Zhu Y. Identification and expression analysis of miRNA in hybrid snakehead by deep sequencing approach and their targets prediction. Genomics 2018; 111:1315-1324. [PMID: 30196078 DOI: 10.1016/j.ygeno.2018.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/04/2018] [Accepted: 08/15/2018] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) play important regulatory roles in numerous biological processes, but there is no report on miRNAs of hybrid snakehead. In this study, four independent small RNA libraries were constructed from the spleen, liver kidney and muscle of hybrid snakehead. These libraries were sequenced using deep sequencing technology, as result, a total of 1,067,172, 1,152,002, 1,653,941 and 970,866 clean reads from these four libraries were obtained. 252 known miRNAs and 63 putative novel miRNAs in these small RNA dataset were identified. The stem-loop RT-qPCR analysis indicated that eight known miRNAs and two novel miRNAs show different expression in eight different kinds of tissues. For better understanding the functions of miRNAs, 95,947 predicated target genes were analyzed by GO and their pathways, the results indicated that these targets of the identified miRNAs are involved in a broad range of physiological functions.
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Affiliation(s)
- Wangbao Gong
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China.
| | - Jun Xie
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Guangjun Wang
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Deguang Yu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xihong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471003, China
| | - Kai Zhang
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zhifei Li
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yu Ermeng
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jingjing Tian
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yun Zhu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
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11
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Huang Y, Gong W, Xiong J, Gao XC, Ren HT. Discovery and characterization of conserved and novel microRNAs from blunt snout bream (Megalobrama amblycephala) by deep sequencing. Gene 2018; 654:57-63. [PMID: 29466763 DOI: 10.1016/j.gene.2018.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/27/2018] [Accepted: 02/15/2018] [Indexed: 10/18/2022]
Abstract
MicroRNAs (miRNAs) are short, single stranded RNA molecules with approximately 22 nts in length, which regulate the stability and translation of messenger RNAs in several organisms. To increase the repertoire of miRNAs characterized in M. amblycephala, we used the deep sequencing technology to sequence a small RNA library using pooled RNA sample isolated from the 4 different tissues of M. amblycephala. A total of 309 conserved miRNAs that originated from 131 miRNA families were detected. 15 novel candidates miRNA were identified. Randomly selected 6 miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in 6 different tissues of M. amblycephala. Furthermore, the potential targets were predicted. GO analysis showed that most of the targets were involved in a broad range of physiological functions including fish growth, development, metabolism, stress responses and so on. Overall, our results significantly increased the number of novel miRNAs in M. amblycephala, which should be useful for further investigation into the role of miRNAs in regulating diverse biological processes.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jianli Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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12
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Zhang WZ, Lan T, Nie CH, Guan NN, Gao ZX. Characterization and spatiotemporal expression analysis of nine bone morphogenetic protein family genes during intermuscular bone development in blunt snout bream. Gene 2017; 642:116-124. [PMID: 29129809 DOI: 10.1016/j.gene.2017.11.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 01/24/2023]
Abstract
Intermuscular bones (IBs) only exist in the myosepta of lower teleosts and its molecular mechanism remains to be clarified. Bone morphogenetic proteins (BMPs) have been demonstrated to be involved in various physiological processes, including bone and cartilage formation. In this study, we firstly obtained and characterized nine bmp genes for Megalobrama amblycephala, which belongs to Cyprinidae and have a certain amount of IBs. Sequence alignment and phylogenetic analysis both documented that the mature proteins of M. amblycephala bmp genes were highly conserved with other corresponding homologs, respectively, indicating that the function of each bmp gene has been conserved throughout evolution. As a step to characterize potential involvement of bmp genes in IB formation and development, spatiotemporal expressions of nine bmp genes (bmp2a, bmp2b, bmp3, bmp4, bmp5, bmp7b, bmp8a, bmp14 and bmp16) were investigated during the key development stages of IBs. During the ossification process from stage I (the IBs haven't emerged) to stage IV (all of the IBs ossified in the tail with the mature morphology), the expression profiles revealed that bmp16 was the most abundant transcript while bmp4 had the lowest abundance. The mRNA levels of bmp3, bmp4, bmp5 and bmp8a increased significantly at stage II, suggesting their roles in stimulating IB formation. The expression of bmp7b reached the highest level at stage III (the rapid period of IB development), suggesting potential involvement of bmp7b in promoting osteoblast differentiation. With the exception of bmp7b and bmp16, most bmp genes appeared a significant increase at IB maturation phase (stage IV), which means that they may play important roles in maintenance of IB morphogenesis. Spatial tissue distribution of bmp genes showed that most bmp genes were observed at the highest level in developing IBs at one year old fish. Spatiotemporal expression patterns suggest the potential key roles of these bmp genes in IBs formation and maintenance in fish, being as possible promoters or inhibitors.
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Affiliation(s)
- Wei-Zhuo Zhang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Tian Lan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Chun-Hong Nie
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Ning-Nan Guan
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China; Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China.
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13
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Miao LH, Pan WJ, Lin Y, Ge XP, Liu B, Ren MC, Zhou QL. Bioinformatic prediction and analysis of glucolipid metabolic regulation by miR-34a in Megalobrama amblycephala. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0593-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Huang Y, Gao XC, Ren HT, Xiong JL, Sun XH. Characterization of conserved and novel miRNAs using deep sequencing and prediction of miRNA targets in Crucian carp (Carassius auratus). Gene 2017; 635:61-68. [PMID: 28890379 DOI: 10.1016/j.gene.2017.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/03/2017] [Accepted: 09/06/2017] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs of -22 nucleotides that can base pair with their target mRNAs, which represses their translation or induces their degradation in various biological processes. However, little is known about identification of miRNAs and their target genes in C. auratus. In the present study, a small RNA library from pooled tissue of C. auratus was constructed and sequenced using the deep sequencing. A total of 320 conserved miRNAs (belonging to 105 families) as well as 11 potentially novel miRNAs were identified. Stem-loop qRT-PCR analysis confirmed that both conserved and novel miRNAs were expressed in C. auratus, and some of them were preferentially expressed in certain tissues. Subsequently, a total of 1668 potential target genes were predicted for these identified miRNAs and GO analysis showed that most of the targets were involved in lots of physiological actions. This study represents a first large-scale identification and characterization of C. auratus miRNAs and their potential target genes. Taken together, our results add new information to existing data on C. auratus miRNAs and should be useful for investigating the biological functions of miRNAs in fishes and other aquatic species.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
| | - Xiao Chan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Hong Tao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Jian Li Xiong
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Xi Hong Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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15
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Wan SM, Liu H, Zhao BW, Nie CH, Wang WM, Gao ZX. Construction of a high-density linkage map and fine mapping of QTLs for growth and gonad related traits in blunt snout bream. Sci Rep 2017; 7:46509. [PMID: 28422147 PMCID: PMC5395971 DOI: 10.1038/srep46509] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/17/2017] [Indexed: 01/16/2023] Open
Abstract
High-density genetic maps based on SNPs are essential for fine mapping loci controlling specific traits for fish species. Using restriction-site associated DNA tag sequencing (RAD-Seq) technology, we identified 42,784 SNPs evenly distributed across the Megalobrama amblycephala genome. Based on 2 parents and 187 intra-specific hybridization progenies, a total of 14,648 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs) of maternal and paternal map. The total length of the integrated map was 3,258.38 cM with an average distance of 0.57 cM among 5676 effective loci, thereby representing the first high-density genetic map reported for M. amblycephala. A total of eight positive quantitative trait loci (QTLs) were detected in QTL analysis. Of that, five QTL explained ≥35% of phenotypic variation for growth traits and three QTL explained ≥16% phenotypic variation for gonad related traits. A total of 176 mapped markers had significant hits in the zebrafish genome and almost all of the 24 putative-chromosomes of M. amblycephala were in relatively conserved synteny with chromosomes of zebrafish. Almost all M. amblycephala and zebrafish chromosomes had a 1:1 correspondence except for putative-chromosome 4, which mapped to two chromosomes of zebrafish caused by the difference in chromosome numbers between two species.
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Affiliation(s)
- Shi-Ming Wan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Bo-Wen Zhao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Chun-Hong Nie
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Wei-Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
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16
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Nie CH, Wan SM, Tomljanovic T, Treer T, Hsiao CD, Wang WM, Gao ZX. Comparative proteomics analysis of teleost intermuscular bones and ribs provides insight into their development. BMC Genomics 2017; 18:147. [PMID: 28183283 PMCID: PMC5301324 DOI: 10.1186/s12864-017-3530-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/31/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Intermuscular bones (IBs) and ribs both are a part of skeletal system in teleosts, but with different developing process. The chemical composition of fish IBs and ribs as well as the underlying mechanism about their development have not been investigated. In the present study, histological structures showed that one bone cavity containing osteoclasts were existed in ribs, but not in IBs of Megalobrama amblycephala. We constructed the first proteomics map for fish bones including IBs and ribs, and identified the differentially expressed proteins between IBs and ribs through iTRAQ LC-MS/MS proteomic analysis. RESULTS The proteins extracted from IBs and ribs at 1- to 2-year old M. amblycephala were quantified 2,342 proteins, with 1,451 proteins annotated with GO annotation in biological processes, molecular function and cellular component. A number of bone related proteins as well as pathways were identified in the study. A total of 93 and 154 differently expressed proteins were identified in comparison groups of 1-IB-vs-1-Rib and 2-IB-vs-2-Rib, which indicated the obvious differences of chemical composition between these two bone tissues. The two proteins (vitronectin b precursor and matrix metalloproteinase-2) related to osteoclasts differentiation were significantly up-regulated in ribs compared with IBs (P < 0.05), which was in accordance with the results from histological structures. In comparison groups of 1-IB-vs-2-IB and 1-Rib-vs-2-Rib, 33 and 51 differently expressed proteins were identified and the function annotation results showed that these proteins were involved in regulating bone development and differentiation. Subsequently, 11 and 13 candidate proteins in comparison group of 1-IB-vs-1-Rib and 1-IB-vs-2-IB related to bone development were validated by MRM assays. CONCLUSIONS Our present study suggested the different key proteins involved in the composition of fish ribs and IBs as well as their growth development. These findings could provide important clues towards further understanding of fish skeletal system and the roles of proteins playing in regulating diverse biological processes in fish.
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Affiliation(s)
- Chun-Hong Nie
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan, 430070 China
| | - Shi-Ming Wan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan, 430070 China
| | - Tea Tomljanovic
- Department for Fisheries, Beekeeping, Game management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Tomislav Treer
- Department for Fisheries, Beekeeping, Game management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan
| | - Wei-Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070 China
- Collaborative Innovation Center for Healthy Freshwater Aquaculture of Hubei Province, Wuhan, 430070 China
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan, 430070 Hubei China
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17
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Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala) Infected by Aeromonas hydrophila. Int J Mol Sci 2016; 17:ijms17121972. [PMID: 27898025 PMCID: PMC5187772 DOI: 10.3390/ijms17121972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that play key roles in regulation of various biological processes. In order to better understand the biological significance of miRNAs in the context of Aeromonas hydrophila infection in Megalobrama amblycephala, small RNA libraries obtained from fish liver at 0 (non-infection), 4, and 24 h post infection (poi) were sequenced using Illumina deep sequencing technology. A total of 11,244,207, 9,212,958, and 7,939,157 clean reads were obtained from these three RNA libraries, respectively. Bioinformatics analysis identified 171 conserved miRNAs and 62 putative novel miRNAs. The existence of ten randomly selected novel miRNAs was validated by RT-PCR. Pairwise comparison suggested that 61 and 44 miRNAs were differentially expressed at 4 and 24 h poi, respectively. Furthermore, the expression profiles of nine randomly selected miRNAs were validated by qRT-PCR. MicroRNA target prediction, gene ontology (GO) annotation, and Kyoto Encylopedia of Genes and Genomes (KEGG) analysis indicated that a variety of biological pathways could be affected by A. hydrophila infection. Additionally, transferrin (TF) and transferrin receptor (TFR) genes were confirmed to be direct targets of miR-375. These results will expand our knowledge of the role of miRNAs in the immune response of M. amblycephala to A. hydrophila infection, and facilitate the development of effective strategies against A. hydrophila infection in M. amblycephala.
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18
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Burgos-Aceves MA, Cohen A, Smith Y, Faggio C. Estrogen regulation of gene expression in the teleost fish immune system. FISH & SHELLFISH IMMUNOLOGY 2016; 58:42-49. [PMID: 27633675 DOI: 10.1016/j.fsi.2016.09.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/01/2016] [Accepted: 09/10/2016] [Indexed: 05/02/2023]
Abstract
Elucidating the mechanisms of estrogens-induced immunomodulation in teleost fish is of great importance due to the observed worldwide continuing decrease in pristine environments. However, little is know about the immunotoxicological consequences of exposure to these chemicals in fish, or of the mechanisms through which these effects are mediated. In this review, we summarize the results showing estrogens (natural or synthetic) acting through estrogen receptors and regulating specific target genes, also through microRNAs (miRNAs), leading to modulation of the immune functioning. The identification and characterization of miRNAs will provide new opportunities for functional genome research on teleost immune system and can also be useful when screening for novel molecule biomarkers for environmental pollution.
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Affiliation(s)
- Mario Alberto Burgos-Aceves
- Centro de Investigaciones Biológicas de Noroeste, S.C., Mar Bermejo 195, Col. Playa Palo de Sta. Rita, La Paz BCS, 23090, México
| | - Amit Cohen
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy.
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19
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Wan SM, Yi SK, Zhong J, Nie CH, Guan NN, Zhang WZ, Gao ZX. Dynamic mRNA and miRNA expression analysis in response to intermuscular bone development of blunt snout bream (Megalobrama amblycephala). Sci Rep 2016; 6:31050. [PMID: 27486015 PMCID: PMC4971466 DOI: 10.1038/srep31050] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 07/13/2016] [Indexed: 12/21/2022] Open
Abstract
Intermuscular bone (IB), which occurs only in the myosepta of lower teleosts, is attracting more attention because they are difficult to remove and make the fish unpleasant to eat. By gaining a better understanding of the genetic regulation of IB development, an integrated analysis of miRNAs and mRNAs expression profiling was performed on Megalobrama amblycephala. Four key development stages were selected for transcriptome and small RNA sequencing. A number of significantly differentially expressed miRNAs/genes associated with bone formation and differentiation were identified and the functional characteristics of these miRNAs/genes were revealed by GO function and KEGG pathway analysis. These were involved in TGF-β, ERK and osteoclast differentiation pathways known in the literature to affect bone formation and differentiation. MiRNA-mRNA interaction pairs were detected from comparison of expression between different stages. The function annotation results also showed that many miRNA-mRNA interaction pairs were likely to be involved in regulating bone development and differentiation. A negative regulation effect of two miRNAs was verified through dual luciferase reporter assay. As a unique public resource for gene expression and regulation during the IB development, this study is expected to provide forwards ideas and resources for further biological researches to understand the IBs’ development.
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Affiliation(s)
- Shi-Ming Wan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Shao-Kui Yi
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Jia Zhong
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Chun-Hong Nie
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Ning-Nan Guan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Wei-Zhuo Zhang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China
| | - Ze-Xia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China.,Hubei Provincial Engineering Laboratory for Pond Aquaculture, Wuhan 430070, China
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20
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Yuhong J, Leilei T, Fuyun Z, Hongyang J, Xiaowen L, Liying Y, Lei Z, Jingrong M, Jinpeng Y. Identification and characterization of immune-related microRNAs in blunt snout bream, Megalobrama amblycephala. FISH & SHELLFISH IMMUNOLOGY 2016; 49:470-492. [PMID: 26773859 DOI: 10.1016/j.fsi.2015.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/03/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) play vital roles in diverse biological processes, including in immune response. Blunt snout bream (Megalobrama amblycephala) is a prevalent and important commercial endemic freshwater fish species in China's intensive polyculture systems. To identify immune-related miRNAs of M. amblycephala, two small RNA (sRNA) libraries from immune tissues with or without lipopolysaccharide (LPS) stimulation were constructed and sequenced using the high-throughput sequencing technology. Totally, 16,425,543 and 15,076,813 raw reads, corresponding to 14,156,755 and 13,445,869 clean reads, were obtained in the normal and infected libraries, respectively. A total of 324 miRNAs, including 218 known miRNAs and 106 putative novel miRNAs were identified by bioinformatic analysis. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. 113 (34.88%) miRNAs were found to be significantly differentially expressed between two libraries, with 63 (55.75%) exhibiting elevated expression in LPS stimulation sample. Thereinto, a number of known miRNAs were identified immune-related. Real-time quantitative PCR (RT-qPCR) were implemented for 12 miRNAs of two samples, and agreement was confirmed between the sequencing and RT-qPCR data. Target genes likely regulated by these differentially expressed miRNAs were predicted using computational prediction. The functional annotation of target genes by Gene Ontology enrichment (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis (KEGG) indicated that a majority of differential miRNAs might involved in immune response. To our knowledge, this is the first comprehensive study of miRNAs in response to LPS stimulation in M. amblycephala, even in fish. These results deepened our understanding of the role of miRNAs in the intricate host's immune system, and should be useful to develop new control strategies for host immune defense against various bacterial invasions in M. amblycephala.
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Affiliation(s)
- Jiang Yuhong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Tang Leilei
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Zhang Fuyun
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Jiang Hongyang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China
| | - Liu Xiaowen
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Yang Liying
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Zhang Lei
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Mao Jingrong
- Xiangya School of Medcine, Central South University, Changsha 410017, China
| | - Yan Jinpeng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410017, China.
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Analysis of MicroRNA Expression Profiles in Weaned Pig Skeletal Muscle after Lipopolysaccharide Challenge. Int J Mol Sci 2015; 16:22438-55. [PMID: 26389897 PMCID: PMC4613317 DOI: 10.3390/ijms160922438] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/03/2015] [Accepted: 09/07/2015] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs (miRNAs) constitute a class of non-coding RNAs that play a crucial regulatory role in skeletal muscle development and disease. Several acute inflammation conditions including sepsis and cancer are characterized by a loss of skeletal muscle due primarily to excessive muscle catabolism. As a well-known inducer of acute inflammation, a lipopolysaccharide (LPS) challenge can cause serious skeletal muscle wasting. However, knowledge of the role of miRNAs in the course of inflammatory muscle catabolism is still very limited. In this study, RNA extracted from the skeletal muscle of pigs injected with LPS or saline was subjected to small RNA deep sequencing. We identified 304 conserved and 114 novel candidate miRNAs in the pig. Of these, four were significantly increased in the LPS-challenged samples and five were decreased. The expression of five miRNAs (ssc-miR-146a-5p, ssc-miR-221-5p, ssc-miR-148b-3p, ssc-miR-215 and ssc-miR-192) were selected for validation by quantitative polymerase chain reaction (qPCR), which found that ssc-miR-146a-5p and ssc-miR-221-5p were significantly upregulated in LPS-challenged pig skeletal muscle. Moreover, we treated mouse C2C12 myotubes with 1000 ng/mL LPS as an acute inflammation cell model. Expression of TNF-α, IL-6, muscle atrophy F-box (MAFbx) and muscle RING finger 1 (MuRF1) mRNA was strongly induced by LPS. Importantly, miR-146a-5p and miR-221-5p also showed markedly increased expression in LPS-treated C2C12 myotubes, suggesting the two miRNAs may be involved in muscle catabolism systems in response to acute inflammation caused by a LPS challenge. To our knowledge, this study is the first to examine miRNA expression profiles in weaned pig skeletal muscle challenged with LPS, and furthers our understanding of miRNA function in the regulation of inflammatory muscle catabolism.
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