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Lin Y, Sun L, Lv Y, Liao R, Zhang K, Zhou J, Zhang S, Xu J, He M, Wu C, Zhang D, Shen X, Dai J, Gao J. Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance. BMC Genomics 2024; 25:443. [PMID: 38704563 PMCID: PMC11069289 DOI: 10.1186/s12864-024-10304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The transcriptome and metabolome dissection of the skeletal muscle of high- and low- growing individuals from a crossbred population of the indigenous Chongming white goat and the Boer goat were performed to discover the potential functional differentially expressed genes (DEGs) and differential expression metabolites (DEMs). RESULTS A total of 2812 DEGs were detected in 6 groups at three time stages (3,6,12 Month) in skeletal muscle using the RNA-seq method. A DEGs set containing seven muscle function related genes (TNNT1, TNNC1, TNNI1, MYBPC2, MYL2, MHY7, and CSRP3) was discovered, and their expression tended to increase as goat muscle development progressed. Seven DEGs (TNNT1, FABP3, TPM3, DES, PPP1R27, RCAN1, LMOD2) in the skeletal muscle of goats in the fast-growing and slow-growing groups was verified their expression difference by reverse transcription-quantitative polymerase chain reaction. Further, through the Liquid chromatography-mass spectrometry (LC-MS) approach, a total of 183 DEMs in various groups of the muscle samples and these DEMs such as Queuine and Keto-PGF1α, which demonstrated different abundance between the goat fast-growing group and slow-growing group. Through weighted correlation network analysis (WGCNA), the study correlated the DEGs with the DEMs and identified 4 DEGs modules associated with 18 metabolites. CONCLUSION This study benefits to dissection candidate genes and regulatory networks related to goat meat production performance, and the joint analysis of transcriptomic and metabolomic data provided insights into the study of goat muscle development.
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Affiliation(s)
- Yuexia Lin
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Lingwei Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Yuhua Lv
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Rongrong Liao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Keqing Zhang
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Jinyong Zhou
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Shushan Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Jiehuan Xu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Mengqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Caifeng Wu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Defu Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Xiaohui Shen
- Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
| | - Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
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Rong M, Xing X, Zhang R. Muscle Transcriptome Analysis of Mink at Different Growth Stages Using RNA-Seq. BIOLOGY 2024; 13:283. [PMID: 38785766 PMCID: PMC11117779 DOI: 10.3390/biology13050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Mink is a kind of small and precious fur animal resource. In this study, we employed transcriptomics technology to analyze the gene expression profile of mink pectoral muscle tissue, thereby elucidating the regulatory mechanisms underlying mink growth and development. Consequently, a total of 25,954 gene expression profiles were acquired throughout the growth and development stages of mink at 45, 90, and 120 days. Among these profiles, 2607 genes exhibited significant differential expression (|log2(fold change)| ≥ 2 and p_adj < 0.05). GO and KEGG enrichment analyses revealed that the differentially expressed genes were primarily associated with the mitotic cell cycle process, response to growth factors, muscle organ development, and insulin resistance. Furthermore, GSEA enrichment analysis demonstrated a significant enrichment of differentially expressed genes in the p53 signaling pathway at 45 days of age. Subsequent analysis revealed that genes associated with embryonic development (e.g., PEG10, IGF2, NRK), cell cycle regulation (e.g., CDK6, CDC6, CDC27, CCNA2), and the FGF family (e.g., FGF2, FGF6, FGFR2) were all found to be upregulated at 45 days of age in mink, which suggested a potential role for these genes in governing early growth and developmental processes. Conversely, genes associated with skeletal muscle development (PRVA, TNNI1, TNNI2, MYL3, MUSTN1), a negative regulator of the cell cycle gene (CDKN2C), and IGFBP6 were found to be up-regulated at 90 days of age, suggesting their potential involvement in the rapid growth of mink. In summary, our experimental data provide robust support for elucidating the regulatory mechanisms underlying the growth and development of mink.
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Affiliation(s)
- Min Rong
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (M.R.); (X.X.)
- Dezhou Animal Husbandry and Veterinary Development Center, Dezhou 253000, China
| | - Xiumei Xing
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (M.R.); (X.X.)
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Changchun 130112, China
| | - Ranran Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; (M.R.); (X.X.)
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Changchun 130112, China
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Li X, Xie F, Li R, Li L, Ren M, Jin M, Zhou J, Wang C, Li S. Integrated 4D Analysis of Intramuscular Fat Deposition: Quantitative Proteomic and Transcriptomic Studies in Wannanhua Pig Longissimus Dorsi Muscle. Animals (Basel) 2024; 14:167. [PMID: 38200898 PMCID: PMC10778203 DOI: 10.3390/ani14010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Wannanhua (WH) is a pig breed indigenous to Anhui Province, China. This breed has a high intramuscular fat (IMF) content, making it an ideal model for investigating lipid deposition mechanisms in pigs. IMF content is one of the main indicators of meat quality in pigs and is regulated by multiple genes and metabolic pathways. Building upon our prior transcriptomic investigation, the present study focused on the longissimus dorsi muscle tissue of Wannanhua (WH) pigs in the rapid fat-deposition stages (120 and 240 days of age). Employing 4D label-free quantitative proteomic analysis, we identified 106 differentially expressed proteins (DEPs). Parallel reaction monitoring (PRM) technology was used to verify the DEPs, and the results showed that the 4D label-free results were reliable and valid. Functional enrichment and protein-protein interaction analyses showed that the DEPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria, energy metabolism, and fatty acid metabolism. By integrating transcriptomic data, we identified seven candidate genes including ACADL, ACADM, ANKRD2, MYOZ2, TNNI1, UCHL1, and ART3 that play a regulatory role in fat deposition and muscle development. These findings establish a theoretical foundation for future analyses of lipid deposition traits, contributing to potential enhancements in pig meat quality during breeding and advancing the selection process for Chinese indigenous breeds.
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Affiliation(s)
- Xiaojin Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Fei Xie
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ruidong Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Lei Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Man Ren
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Mengmeng Jin
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
| | - Ju Zhou
- Kunshan Animal Health Supervision Institute, Kunshan 215300, China;
| | - Chonglong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shenghe Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 239000, China; (X.L.); (F.X.); (R.L.); (L.L.); (M.R.); (M.J.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
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He Q, Gao L, Zhang F, Yao W, Wu J, Song N, Luo J, Zhang Y. The FoxO1-ATGL axis alters milk lipolysis homeostasis through PI3K/AKT signaling pathway in dairy goat mammary epithelial cells. J Anim Sci 2023; 101:skad286. [PMID: 37638641 PMCID: PMC10699848 DOI: 10.1093/jas/skad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023] Open
Abstract
Goat milk is enriched in fatty acids which are beneficial to human health. Previous research has revealed that 98% of milk fat is composed of triglycerides. However, the mechanisms regulating milk fat composition remain unclear. Forkhead box protein O1 (FoxO1) is a crucial regulatory factor involved in lipid metabolism across various cell types. Chromatin immunoprecipitation sequencing (ChIP)-seq data) and RNA sequencing (RNA-seq) data revealed that have indicated a close association between FoxO1 was closely related to lipid metabolism during lactation in dairy goats. The objective of this study was to investigate the mechanisms by which FoxO1 regulates lipid metabolism in goat mammary epithelial cells (GMECs). FoxO1 knockdown significantly downregulated the expression of adipose triglyceride lipase (ATGL) and suppressed the activity of the ATGL promoter. Consistently, the number of lipid droplets decreased significantly in FoxO1-overexpressing cells and increased in ATGL-knockdown cells. To further verify the effect of FoxO1 on ATGL promoter activity, cells were transfected with four promoter fragments of different lengths. We found that the core region of the ATGL promoter was located between -882 bp and -524 bp, encompassing two FoxO1 binding sites (FKH1 and FKH2). Mutations in the FoxO1 binding sites significantly downregulated ATGL promoter activity in GMECs. Luciferase reporter assays demonstrated that FoxO1 overexpression markedly enhanced ATGL promoter activity. Furthermore, site-directed mutation confirmed that FKH1 and FKH2 sites were simultaneously mutated significantly attenuated the stimulatory effect of FoxO1 on ATGL promoter activities simultaneous mutation of FKH1 and FKH2 sites significantly attenuated the stimulatory effect of FoxO1 on ATGL promoter activity. ChIP assays showed that FoxO1 directly binds to the FKH2 element located in the ATGL promoter in vivo. Finally, immunofluorescence staining revealed that insulin promotes the translocation of FoxO1 from the nucleus to the cytoplasm, thereby attenuating the FoxO1-induced activation of the ATGL promoter. Collectively, these findings uncover a novel pathway where by FoxO1 may regulate lipid metabolism in GMECs specifically by modulating the transcriptional activity of ATGL.
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Affiliation(s)
- Qiuya He
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Liangjiahui Gao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weiwei Yao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiao Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ning Song
- College of Animal Science and Technology, Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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