1
|
Tang H, Liu J, Wang Z, Zhang L, Yang M, Huang J, Wen X, Luo J. Genome-wide association study (GWAS) analysis of black color trait in the leopard coral grouper (Plectropomus leopardus) using whole genome resequencing. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101138. [PMID: 37683359 DOI: 10.1016/j.cbd.2023.101138] [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: 05/28/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
The leopard coral grouper (Plectropomus leopardus) is a coral reef fish species that exhibits rapid and diverse color variation. However, the presence of melanoma and the high proportion of individuals displaying black color in artificial breeding have led to reduced economic and ornamental value. To pinpoint single nucleotide polymorphisms (SNPs) and potential genes linked to the black pigmentation characteristic in this particular species, This study gathered a cohort of 360 specimens from diverse origins and conducted a comprehensive genome-wide association analysis (GWAS) employing whole-genome resequencing. As a result, 57 SNPs related to the black skin trait were identified, and a grand total of 158 genes were annotated within 50 kb of these SNPs. Subsequently, GWAS was applied to three populations (LED, QHH, and QHL), and the corresponding results were compared with the analysis results of the total population. The results of the four GWAS models showed significant enrichment in Rap1 signaling pathway, melanin biosynthesis, metabolic pathways, tyrosine metabolism, cAMP signaling pathway, AMPK signaling pathway, PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, HIF-1 signaling pathway, Ras signaling pathway, MAPK signaling pathway, etc. (p < 0.05), which were mainly associated with eleven genes (POL4, MET, E2F2, COMT, ZBED1, TYRP2, FOXP2, THIKA, LORF2, MYH16 and SOX2). Significant differences (p < 0.05) were observed in the expression of all 11 genes in the dorsal skin tissue, in 10 genes except COMT in the ventral skin tissue, and in all 11 genes in the caudal fin tissue. These findings imply that the control of body color in the P. leopardus is the result of the joint action of multiple genes and signaling pathways. These findings will contribute to a more profound comprehension of the genetic attributes that underlie the development of black skin in the vibrant P. leopardus, thus furnishing a theoretical foundation for genetic enhancement.
Collapse
Affiliation(s)
- Haizhan Tang
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Junchi Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Zirui Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Lianjie Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Min Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jie Huang
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Xin Wen
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
| | - Jian Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
| |
Collapse
|
2
|
Guo J, Guo H, Chen C, Yu F, Liu B, Zhang N, Xian L, Luo Z, Liu W, Zhu K, Zhang D. Functional Characterization of the Almstn2 Gene and Its Association with Growth Traits in the Yellowfin Seabream Acanthopagrus latus (Hottuyn, 1782). Genes (Basel) 2023; 14:2142. [PMID: 38136962 PMCID: PMC10742913 DOI: 10.3390/genes14122142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Myostatin (mstn), also known as GDF8, is a growth and differentiation factor of the transforming growth factor-β (TGF-β) superfamily and plays a key inhibitory effect in the regulation of skeletal muscle development and growth in vertebrates. In the present study, to comprehend the role of the mstn2 gene of the yellowfin seabream Acanthopagrus latus (Almstn2b), the genomic sequence of Almstn2b is 2359 bp, which encodes 360 amino acids and is composed of three exons and two introns, was obtained. Two typical regions, a TGF-β propeptide and TGF-β domain, constitute Almstn2b. The topology indicated that Almstn2 was grouped together with other Perciformes, such as the gilthead seabream Sparus aurata. Moreover, Almstn2b was mainly expressed in the brain, fins, and spleen. Furthermore, five SNPs, one in the exons and four in the introns, were identified in the Almstn2b gene. The allele and genotype frequencies of SNP-Almstn2b +1885 A/G were significantly related to the total weight, interorbital distance, stem length, tail length, caudal length, caudal height, body length, and total length (p < 0.05). The allele and genotype frequencies of SNP-Almstn2b +1888 A/G were significantly related to the weight, interorbital distance, long head behind the eyes, body height, tail length, caudal length, and body length. Additionally, the relationship between the SNP-Almstn2b +1915 A/G locus and weight and long head behind the eyes was significant (p < 0.05). Furthermore, the other two SNPs were not significantly associated with any traits. Thus, the SNPs identified in this study could be utilized as candidate SNPs for breeding and marker-assisted selection in A. latus.
Collapse
Affiliation(s)
- Jianyi Guo
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China; (J.G.); (C.C.); (F.Y.); (Z.L.); (W.L.)
| | - Huayang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Guangzhou 510300, China; (H.G.); (B.L.); (N.Z.); (L.X.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Chuanghua Chen
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China; (J.G.); (C.C.); (F.Y.); (Z.L.); (W.L.)
| | - Fangzhao Yu
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China; (J.G.); (C.C.); (F.Y.); (Z.L.); (W.L.)
| | - Baosuo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Guangzhou 510300, China; (H.G.); (B.L.); (N.Z.); (L.X.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Guangzhou 510300, China; (H.G.); (B.L.); (N.Z.); (L.X.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Lin Xian
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Guangzhou 510300, China; (H.G.); (B.L.); (N.Z.); (L.X.)
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| | - Zhiping Luo
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China; (J.G.); (C.C.); (F.Y.); (Z.L.); (W.L.)
| | - Wen Liu
- Modern Agricultural Development Center of Zhuhai City, Zhuhai 519000, China; (J.G.); (C.C.); (F.Y.); (Z.L.); (W.L.)
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Guangzhou 510300, China; (H.G.); (B.L.); (N.Z.); (L.X.)
| | - Dianchang Zhang
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China
- Sanya Tropical Fisheries Research Institute, Sanya 572018, China
| |
Collapse
|
3
|
Özcan Gökçek E, Işık R, Karahan B, Gamsız K. Characterisation of Single Nucleotide Polymorphisms and Haplotypes of MSTN Associated with Growth Traits in European Sea Bass (Dicentrarchus labrax). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:347-357. [PMID: 37162623 DOI: 10.1007/s10126-023-10211-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
The myostatin (MSTN) gene, known as growth differentiation factor-8 (GDF-8), is a member of the transforming growth factor-β (TGF-β) superfamily and plays a specific inhibitory role during the critical phases of skeletal muscle mass development in vertebrates. This study was conducted to investigate MSTN polymorphisms in harvest size European sea bass reared in Turkey. Nine single nucleotide polymorphisms (SNPs) and two indels were identified in exons 1-3 of MSTN in the European sea bass population The associations between the g.16612A indel located in intron 1 and standard length were significant. The MSTN g.15252 T > A locus in intron 2 was significantly related to the total weight, fillet weight and standard length (P < 0.05). The relationship between the g.14873C > T locus in exon 3 of MSTN and standard height, head length, body length, pre-anal length, abdominal length, post-anal length and head width was significant (P < 0.05). According to the results of the haplotype analysis, two haplogroup and eight haplotype combinations were detected in the population. The haplogroup 2 had significant associations with all measured growth traits (P < 0.05). Thus, SNPs and haplotypes identified in this study could be useful for European sea bass breeding and marker-assisted selection.
Collapse
Affiliation(s)
- Emel Özcan Gökçek
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, 35100, Türkiye.
| | - Raziye Işık
- Faculty of Agriculture, Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, 59030, Türkiye
| | - Bilge Karahan
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, 35100, Türkiye
| | - Kutsal Gamsız
- Faculty of Fisheries, Department of Aquaculture, Ege University, İzmir, 35100, Türkiye
| |
Collapse
|
4
|
Luo W, Wang J, Zhou Y, Pang M, Yu X, Tong J. Dynamic mRNA and miRNA expression of the head during early development in bighead carp (Hypophthalmichthys nobilis). BMC Genomics 2022; 23:168. [PMID: 35232381 PMCID: PMC8887032 DOI: 10.1186/s12864-022-08387-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 02/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Head of fish species, an exquisitely complex anatomical system, is important not only for studying fish evolution and development, but also for economic values. Currently, although some studies have been made on fish growth and body shapes, very limited information is available on the molecular mechanism of head development. Results In this study, RNA sequencing (RNA–Seq) and small RNA sequencing (sRNA–Seq) technologies were used to conduct integrated analysis for the head of bighead carp at different development stages, including 1, 3, 5, 15 and 30 Dph (days post hatch). By RNA-Seq data, 26 pathways related to growth and bone formation were identified as the main physiological processes during early development. Coupling this to sRNA–Seq data, we picked out six key pathways that may be responsible for head development, namely ECM receptor interaction, TNF signaling pathway, osteoclast differentiation, PI3K–Akt signaling pathway, Neuroactive ligand–receptor interaction and Jak–STAT signaling pathway. Totally, 114 important candidate genes from the six pathways were obtained. Then we found the top 20 key genes according to the degree value by cytohubba, which regulated cell growth, skeletal formation and blood homeostasis, such as pik3ca, pik3r1, egfr, vegfa, igf1 and itga2b. Finally, we also acquired 19 key miRNAs playing multiple roles in the perfection of various tissues in the head (such as brain, eye and mouth) and mineralization of head bone system, such as let–7e, miR–142a–5p, miR–144–3p, miR–23a–3p and miR–223. Conclusions Results of this study will be informative for genetic mechanisms of head development and also provide potential candidate targets for the interaction regulation during early growth in bighead carp. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08387-x.
Collapse
Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|