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Li J, Li W, Peng X, Li X, Zhao S, Wang H, Ma Y. Genetic basis of phenotypic convergence in pig terminal sires using pathway-based selection signature detection methods. Anim Genet 2024. [PMID: 38830632 DOI: 10.1111/age.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024]
Abstract
The primary purpose of genetic improvement in lean pig breeds is to enhance production performance. Owing to their similar breeding directions, Duroc and Pietrain pigs are ideal models for investigating the phenotypic convergence underlying artificial selection. However, most important economic traits are controlled by a polygenic basis, so traditional strategies for detecting selection signatures may not fully reveal the genetic basis of complex traits. The pathway-based gene network analysis method utilizes each pathway as a unit, overcoming the limitations of traditional strategies for detecting selection signatures by revealing the selection of complex biological processes. Here, we utilized 13 122 398 high-quality SNPs from whole-genome sequencing data of 48 Pietrain pigs, 156 Duroc pigs and 36 European wild boars to detect selective signatures. After calculating FST and iHS scores, we integrated the pathway information and utilized the r/bioconductor graphite and signet packages to construct gene networks, identify subnets and uncover candidate genes underlying selection. Using the traditional strategy, a total of 47 genomic regions exhibiting parallel selection were identified. The enriched genes, including INO80, FZR1, LEPR and FAF1, may be associated with reproduction, fat deposition and skeletal development. Using the pathway-based selection signatures detection method, we identified two significant biological pathways and eight potential candidate genes underlying parallel selection, such as VTN, FN1 and ITGAV. This study presents a novel strategy for investigating the genetic basis of complex traits and elucidating the phenotypic convergence underlying artificial selection, by integrating traditional selection signature methods with pathway-based gene network analysis.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Wangjiao Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xia Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou, China
| | - Haiyan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou, China
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Xiao L, Qiao J, Huang Y, Tan B, Hong L, Li Z, Cai G, Wu Z, Zheng E, Wang S, Gu T. RASGRP1 targeted by H3K27me3 regulates myoblast proliferation and differentiation in mice and pigs. Acta Biochim Biophys Sin (Shanghai) 2024; 56:452-461. [PMID: 38419500 PMCID: PMC10984873 DOI: 10.3724/abbs.2024011] [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: 09/09/2023] [Accepted: 11/14/2023] [Indexed: 03/02/2024] Open
Abstract
Skeletal muscle is not only the largest organ in the body that is responsible for locomotion and exercise but also crucial for maintaining the body's energy metabolism and endocrine secretion. The trimethylation of histone H3 lysine 27 (H3K27me3) is one of the most important histone modifications that participates in muscle development regulation by repressing the transcription of genes. Previous studies indicate that the RASGRP1 gene is regulated by H3K27me3 in embryonic muscle development in pigs, but its function and regulatory role in myogenesis are still unclear. In this study, we verify the crucial role of H3K27me3 in RASGRP1 regulation. The gain/loss function of RASGRP1 in myogenesis regulation is performed using mouse myoblast C2C12 cells and primarily isolated porcine skeletal muscle satellite cells (PSCs). The results of qPCR, western blot analysis, EdU staining, CCK-8 assay and immunofluorescence staining show that overexpression of RASGRP1 promotes cell proliferation and differentiation in both skeletal muscle cell models, while knockdown of RASGRP1 leads to the opposite results. These findings indicate that RASGRP1 plays an important regulatory role in myogenesis in both mice and pigs.
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Affiliation(s)
- Liyao Xiao
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Jiaxin Qiao
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Yiyang Huang
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Baohua Tan
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangzhou510000China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and TechnologyGuangzhou510000China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingGuangzhou510000China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- Guangdong Wens Breeding Swine Technology Co.Ltd.Yunfu527400China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangzhou510000China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and TechnologyGuangzhou510000China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingGuangzhou510000China
- Guangdong Wens Breeding Swine Technology Co.Ltd.Yunfu527400China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Shanshan Wang
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- College of Life ScienceHubei UniversityWuhan430000China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
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ITGβ6 Facilitates Skeletal Muscle Development by Maintaining the Properties and Cytoskeleton Stability of Satellite Cells. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070926. [PMID: 35888016 PMCID: PMC9318838 DOI: 10.3390/life12070926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022]
Abstract
Integrin proteins are important receptors connecting the intracellular skeleton of satellite cells and the extracellular matrix (ECM), playing an important role in the process of skeletal muscle development. In this research, the function of ITGβ6 in regulating the differentiation of satellite cells was studied. Transcriptome and proteome analysis indicated that Itgβ6 is a key node connecting ECM-related proteins to the cytoskeleton, and it is necessary for the integrity of the membrane structure and stability of the cytoskeletal system, which are essential for satellite cell adhesion. Functional analysis revealed that the ITGβ6 protein could affect the myogenic differentiation potential of satellite cells by regulating the expression of PAX7 protein, thus regulating the formation of myotubes. Moreover, ITGβ6 is involved in muscle development by regulating cell-adhesion-related proteins, such as β-laminin, and cytoskeletal proteins such as PXN, DMD, and VCL. In conclusion, the effect of ITGβ6 on satellite cell differentiation mainly occurs before the initiation of differentiation, and it regulates terminal differentiation by affecting satellite cell characteristics, cell adhesion, and the stability of the cytoskeleton system.
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