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Molecular Cloning, Screening of Single Nucleotide Polymorphisms, and Analysis of Growth-Associated Traits of igf2 in Spotted Sea Bass (Lateolabrax maculatus). Animals (Basel) 2023; 13:ani13060982. [PMID: 36978523 PMCID: PMC10044540 DOI: 10.3390/ani13060982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/27/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023] Open
Abstract
The insulin-like growth factor 2 gene (igf2) is thought to be a key factor that could regulate animal growth. In fish, few researchers have reported on the single nucleotide polymorphisms (SNPs) located in igf2 and their association with growth traits. We screened the SNPs of igf2 from the spotted sea bass (Lateolabrax maculatus) by Sanger sequencing and made an association between these SNPs with growth traits. The full-length complementary (c) DNA of igf2 was 1045 bp, including an open reading frame of 648 bp. The amino acid sequence of Igf2 contained a signal peptide, an IGF domain, and an IGF2_C domain. Multiple sequence alignment showed that the IGF domain and IGF2_C domain were conserved in vertebrates. The genome sequence of igf2 had a length of 6227 bp. Fourteen SNPs (13 in the introns and one in one of the exons) were found in the genome sequence of igf2. Four SNPs located in the intron were significantly associated with growth traits (p < 0.05). These results demonstrated that these SNPs could be candidate molecular markers for breeding programs in L. maculatus.
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Yang G, Qin Z, Kou H, Liang R, Zhao L, Jiang S, Lin L, Zhang K. A Comparative Genomic and Transcriptional Survey Providing Novel Insights into Bone Morphogenetic Protein 2 ( bmp2) in Fishes. Int J Mol Sci 2019; 20:E6137. [PMID: 31817477 PMCID: PMC6940749 DOI: 10.3390/ijms20246137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Intermuscular bones (IBs) are only found in the muscles of fish. Bone morphogenetic protein 2 (bmp2) is considered to be the most active single osteogenesis factor. It promotes cell proliferation and differentiation during bone repair, as well as inducing the formation of bones and cartilages in vivo. However, detailed investigations of this family in fish are incredibly limited. Here, we have used a variety of published and unpublished bmp2 sequences for teleosts and cartilage fish in order to explore and expand our understanding of bmp2 genes in fish. Our results confirmed that teleost genomes contain two or more bmp2 genes, and the diversity of bmp2 genes in vertebrates appears to be as a result of a combination of whole genome duplication (WGD) and gene loss. Differences were also observed in tissue distribution and relative transcription abundance of the bmp2s through a transcriptomic analysis. Our data also indicated that bmp2b may play an important role in the formation of IBs in teleosts. In addition, protein sequence alignments and 3D structural predictions of bmp2a and bmp2b supported their similar roles in fishes. To summarize, our existing work provided novel insights into the bmp2 family genes in fishes through a mixture of comparative genomic and transcriptomic analysis.
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Affiliation(s)
- Guang Yang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, College of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhendong Qin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Hongyan Kou
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Rishen Liang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Lijuan Zhao
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Shoujia Jiang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China;
| | - Li Lin
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
| | - Kai Zhang
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology, Research Center, Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (G.Y.); (Z.Q.); (R.L.); (L.Z.)
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong 93117, China
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Su S, Li H, Du F, Zhang C, Li X, Jing X, Liu L, Li Z, Yang X, Xu P, Yuan X, Zhu J, Bouzoualegh R. Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain. Front Genet 2018; 9:592. [PMID: 30581452 PMCID: PMC6293859 DOI: 10.3389/fgene.2018.00592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/15/2018] [Indexed: 11/17/2022] Open
Abstract
Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.
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Affiliation(s)
- Shengyan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Hengde Li
- Ministry of Agriculture Key Laboratory of Aquatic Genomics, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Fukuan Du
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Chengfeng Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xiaojun Jing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Liyue Liu
- China Zebrafish Resource Center, Wuhan, China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinhua Yuan
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Raouf Bouzoualegh
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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