1
|
Liaw YC, Matsuda K, Liaw YP. Identification of an novel genetic variant associated with osteoporosis: insights from the Taiwan Biobank Study. JBMR Plus 2024; 8:ziae028. [PMID: 38655459 PMCID: PMC11037432 DOI: 10.1093/jbmrpl/ziae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/18/2024] [Accepted: 03/01/2024] [Indexed: 04/26/2024] Open
Abstract
Purpose The purpose of this study was to identify new independent significant SNPs associated with osteoporosis using data from the Taiwan Biobank (TWBB). Material and Methods The dataset was divided into discovery (60%) and replication (40%) subsets. Following data quality control, genome-wide association study (GWAS) analysis was performed, adjusting for sex, age, and the top 5 principal components, employing the Scalable and Accurate Implementation of the Generalized mixed model approach. This was followed by a meta-analysis of TWBB1 and TWBB2. The Functional Mapping and Annotation (FUMA) platform was used to identify osteoporosis-associated loci. Manhattan and quantile-quantile plots were generated using the FUMA platform to visualize the results. Independent significant SNPs were selected based on genome-wide significance (P < 5 × 10-8) and independence from each other (r2 < 0.6) within a 1 Mb window. Positional, eQTL(expression quantitative trait locus), and Chromatin interaction mapping were used to map SNPs to genes. Results A total of 29 084 individuals (3154 osteoporosis cases and 25 930 controls) were used for GWAS analysis (TWBB1 data), and 18 918 individuals (1917 cases and 17 001 controls) were utilized for replication studies (TWBB2 data). We identified a new independent significant SNP for osteoporosis in TWBB1, with the lead SNP rs76140829 (minor allele frequency = 0.055, P-value = 1.15 × 10-08). Replication of the association was performed in TWBB2, yielding a P-value of 6.56 × 10-3. The meta-analysis of TWBB1 and TWBB2 data demonstrated a highly significant association for SNP rs76140829 (P-value = 7.52 × 10-10). In the positional mapping of rs76140829, 6 genes (HABP2, RP11-481H12.1, RNU7-165P, RP11-139 K1.2, RP11-57H14.3, and RP11-214 N15.5) were identified through chromatin interaction mapping in mesenchymal stem cells. Conclusions Our GWAS analysis using the Taiwan Biobank dataset unveils rs76140829 in the VTI1A gene as a key risk variant associated with osteoporosis. This finding expands our understanding of the genetic basis of osteoporosis and highlights the potential regulatory role of this SNP in mesenchymal stem cells.
Collapse
Affiliation(s)
- Yi-Ching Liaw
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung 40201, Taiwan
| | - Koichi Matsuda
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
- Institute of Medical Science, The University of Tokyo, Laboratory of Genome Technology, Human Genome Center, Tokyo 108-8639, Japan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung 40201, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
| |
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
|
Guo C, Zhang X, Li Y, Xie J, Gao P, Hao P, Han L, Zhang J, Wang W, Liu P, Ding J, Chang Y. Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus. BMC Genomics 2023; 24:25. [PMID: 36647018 PMCID: PMC9843871 DOI: 10.1186/s12864-023-09113-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown. RESULT In this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses. CONCLUSIONS This study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.
Collapse
Affiliation(s)
- Chao Guo
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Xianglei Zhang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Yuanxin Li
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Jiahui Xie
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Pingping Gao
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Pengfei Hao
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Lingshu Han
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China ,grid.203507.30000 0000 8950 5267Ningbo University, Ningbo, Zhejiang 315211 People’s Republic of China
| | - Jinyuan Zhang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Wenpei Wang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Peng Liu
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Jun Ding
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Yaqing Chang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| |
Collapse
|