1
|
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.
Collapse
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
| |
Collapse
|
2
|
Fu Y, Li S, Nie J, Yan D, Zhang B, Hao X, Zhang H. Expression of PDLIM5 Spliceosomes and Regulatory Functions on Myogenesis in Pigs. Cells 2024; 13:720. [PMID: 38667334 PMCID: PMC11049100 DOI: 10.3390/cells13080720] [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: 03/14/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Meat yield, determined by muscle growth and development, is an important economic trait for the swine industry and a focus of research in animal genetics and breeding. PDZ and LIM domain 5 (PDLIM5) are cytoskeleton-related proteins that play key roles in various tissues and cells. These proteins have multiple isoforms, primarily categorized as short (PDLIM5-short) and long (PDLIM5-long) types, distinguished by the absence and presence of an LIM domain, respectively. However, the expression patterns of swine PDLIM5 isoforms and their regulation during porcine skeletal muscle development remain largely unexplored. We observed that PDLIM5-long was expressed at very low levels in pig muscles and that PDLIM5-short and total PDLIM5 were highly expressed in the muscles of slow-growing pigs, suggesting that PDLIM5-short, the dominant transcript in pigs, is associated with a slow rate of muscle growth. PDLIM5-short suppressed myoblast proliferation and myogenic differentiation in vitro. We also identified two single nucleotide polymorphisms (-258 A > T and -191 T > G) in the 5' flanking region of PDLIM5, which influenced the activity of the promoter and were associated with muscle growth rate in pigs. In summary, we demonstrated that PDLIM5-short negatively regulates myoblast proliferation and differentiation, providing a theoretical basis for improving pig breeding programs.
Collapse
Affiliation(s)
- Yu Fu
- National Engineering Laboratory for Livestock and Poultry Breeding, Beijing Key Laboratory of Animal Genetic Engineering, China Agricultural University, Beijing 100193, China; (Y.F.); (S.L.); (J.N.); (B.Z.)
| | - Shixin Li
- National Engineering Laboratory for Livestock and Poultry Breeding, Beijing Key Laboratory of Animal Genetic Engineering, China Agricultural University, Beijing 100193, China; (Y.F.); (S.L.); (J.N.); (B.Z.)
| | - Jingru Nie
- National Engineering Laboratory for Livestock and Poultry Breeding, Beijing Key Laboratory of Animal Genetic Engineering, China Agricultural University, Beijing 100193, China; (Y.F.); (S.L.); (J.N.); (B.Z.)
| | - Dawei Yan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China;
| | - Bo Zhang
- National Engineering Laboratory for Livestock and Poultry Breeding, Beijing Key Laboratory of Animal Genetic Engineering, China Agricultural University, Beijing 100193, China; (Y.F.); (S.L.); (J.N.); (B.Z.)
| | - Xin Hao
- National Engineering Laboratory for Livestock and Poultry Breeding, Beijing Key Laboratory of Animal Genetic Engineering, China Agricultural University, Beijing 100193, China; (Y.F.); (S.L.); (J.N.); (B.Z.)
| | - Hao Zhang
- National Engineering Laboratory for Livestock and Poultry Breeding, Beijing Key Laboratory of Animal Genetic Engineering, China Agricultural University, Beijing 100193, China; (Y.F.); (S.L.); (J.N.); (B.Z.)
| |
Collapse
|
3
|
Wang S, Shi M, Zhang Y, Niu J, Li W, Yuan J, Cai C, Yang Y, Gao P, Guo X, Li B, Lu C, Cao G. Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages. Curr Issues Mol Biol 2024; 46:340-354. [PMID: 38248324 PMCID: PMC10814722 DOI: 10.3390/cimb46010022] [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: 11/28/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
The development of skeletal muscle in pigs might determine the quality of pork. In recent years, long non-coding RNAs (lncRNAs) have been found to play an important role in skeletal muscle growth and development. In this study, we investigated the whole transcriptome of the longissimus dorsi muscle (LDM) of Jinfen White pigs at three developmental stages (1, 90, and 180 days) and performed a comprehensive analysis of lncRNAs, mRNAs, and micro-RNAs (miRNAs), aiming to find the key regulators and interaction networks in Jinfen White pigs. A total of 2638 differentially expressed mRNAs (DE mRNAs) and 982 differentially expressed lncRNAs (DE lncRNAs) were identified. Compared with JFW_1d, there were 497 up-regulated and 698 down-regulated DE mRNAs and 212 up-regulated and 286 down-regulated DE lncRNAs in JFW_90d, respectively. In JFW_180d, there were 613 up-regulated and 895 down-regulated DE mRNAs and 184 up-regulated and 131 down-regulated DE lncRNAs compared with JFW_1d. There were 615 up-regulated and 477 down-regulated DE mRNAs and 254 up-regulated and 355 down-regulated DE lncRNAs in JFW_180d compared with JFW_90d. Compared with mRNA, lncRNA has fewer exons, fewer ORFs, and a shorter length. We performed GO and KEGG pathway functional enrichment analysis for DE mRNAs and the potential target genes of DE lncRNAs. As a result, several pathways are involved in muscle growth and development, such as the PI3K-Akt, MAPK, hedgehog, and hippo signaling pathways. These are among the pathways through which mRNA and lncRNAs function. As part of this study, bioinformatic screening was used to identify miRNAs and DE lncRNAs that could act as ceRNAs. Finally, we constructed an lncRNA-miRNA-mRNA regulation network containing 26 mRNAs, 7 miRNAs, and 17 lncRNAs; qRT-PCR was used to verify the key genes in these networks. Among these, XLOC_022984/miR-127/ENAH and XLOC_016847/miR-486/NRF1 may function as key ceRNA networks. In this study, we obtained transcriptomic profiles from the LDM of Jinfen White pigs at three developmental stages and screened out lncRNA-miRNA-mRNA regulatory networks that may provide crucial information for the further exploration of the molecular mechanisms during skeletal muscle development.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, No. 1 Mingxian South Road, Taigu 030801, China; (S.W.); (M.S.); (Y.Z.); (J.N.); (W.L.); (J.Y.); (C.C.); (Y.Y.); (P.G.); (X.G.); (B.L.)
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, No. 1 Mingxian South Road, Taigu 030801, China; (S.W.); (M.S.); (Y.Z.); (J.N.); (W.L.); (J.Y.); (C.C.); (Y.Y.); (P.G.); (X.G.); (B.L.)
| |
Collapse
|
4
|
Zhao X, Jia W, Wang J, Wang S, Zheng Q, Shan T. Identification of a Candidate Gene Regulating Intramuscular Fat Content in Pigs through the Integrative Analysis of Transcriptomics and Proteomics Data. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19154-19164. [PMID: 37987700 DOI: 10.1021/acs.jafc.3c05806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Pork is a widely consumed source of animal protein worldwide, and the intramuscular fat (IMF) content in pork plays a crucial role in determining its quality. In this study, we sought to identify candidate genes that regulate IMF deposition in pigs. We performed tandem mass tags (TMT)-based quantitative proteomics analysis using Longissimus dorsi (LD) muscle samples obtained from eight pigs with extremely high and low IMF content among a group of 28 Duroc pigs and identified 50 differentially abundant proteins (DAPs). Additionally, we compared the proteomics data with RNA-sequencing data obtained in our previous study and identified TUSC5 as a differentially expressed gene corresponding to the relevant DAP. To investigate the potential role of TUSC5 in adipogenesis, we suppressed TUSC5 expression in mouse 3T3-L1 preadipocytes using short hairpin RNA (shRNA) and observed a significant reduction in the differentiation of 3T3-L1 cells into adipocytes, as indicated by Oil Red O staining and triglyceride content. Moreover, we observed a reduction in the expression of genes associated with adipogenesis (PPARG, CEBPA, FABP4, and FASN) following TUSC5 suppression. Through an integrative analysis of transcriptomics and proteomics data, our study identified TUSC5 as a crucial candidate gene associated with the regulation of IMF content in pigs.
Collapse
Affiliation(s)
- Xueyan Zhao
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Wanli Jia
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Jiying Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Shouwei Wang
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
| | - Qiankun Zheng
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
| | - Tizhong Shan
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
5
|
Zeng Q, Du ZQ. Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig. Anim Genet 2023; 54:709-720. [PMID: 37796678 DOI: 10.1111/age.13365] [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: 07/25/2022] [Revised: 07/08/2023] [Accepted: 07/08/2023] [Indexed: 10/07/2023]
Abstract
As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber-type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio-temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next-generation sequencing technology, the integration of quantitative trait loci mapping with genome-wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in-depth understanding and utilization remain, and the cost of large-scale sequencing, which requires integrated analyses of high-throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs.
Collapse
Affiliation(s)
- Qingjie Zeng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China
| |
Collapse
|
6
|
Li X, Lu L, Tong X, Li R, Jin E, Ren M, Gao Y, Gu Y, Li S. Transcriptomic Profiling of Meat Quality Traits of Skeletal Muscles of the Chinese Indigenous Huai Pig and Duroc Pig. Genes (Basel) 2023; 14:1548. [PMID: 37628600 PMCID: PMC10454112 DOI: 10.3390/genes14081548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The Huai pig is a well-known indigenous pig breed in China. The main advantages of Huai pigs over Western commercial pig breeds include a high intramuscular fat (IMF) content and good meat quality. There are significant differences in the meat quality traits of the same muscle part or different muscle parts of the same variety. To investigate the potential genetic mechanism underlying the meat quality differences in different pig breeds or muscle groups, longissimus dorsi (LD), psoas major (PM), and biceps femoris (BF) muscle tissues were collected from two pig breeds (Huai and Duroc). There were significant differences in meat quality traits and amino acid content. We assessed the muscle transcriptomic profiles using high-throughput RNA sequencing. The IMF content in the LD, PM, and BF muscles of Huai pigs was significantly higher than that in Duroc pigs (p < 0.05). Similarly, the content of flavor amino acids in the three muscle groups was significantly higher in Huai pigs than that in Duroc pigs (p < 0.05). We identified 175, 110, and 86 differentially expressed genes (DEGs) between the LD, PM, and BF muscles of the Huai and Duroc pigs, respectively. The DEGs of the different pig breeds and muscle regions were significantly enriched in the biological processes and signaling pathways related to muscle fiber type, IMF deposition, lipid metabolism, PPAR signaling, cAMP signaling, amino acid metabolism, and ECM-receptor interaction. Our findings might help improve pork yield by using the obtained DEGs for marker-assisted selection and providing a theoretical reference for evaluating and improving pork quality.
Collapse
Affiliation(s)
- Xiaojin Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Liangyue Lu
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Xinwei Tong
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Ruidong Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Erhui Jin
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Man Ren
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Yafei Gao
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Youfang Gu
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Chuzhou 233100, China
- Key Laboratory of Quality and Safety Control for Pork, Ministry of Agriculture and Rural, No. 9, Chuzhou 233100, China;
| | - Shenghe Li
- College of Animal Science, Anhui Science and Technology University, Chuzhou 233100, China; (X.L.); (L.L.); (X.T.); (R.L.); (E.J.); (M.R.)
| |
Collapse
|
7
|
Fu Y, Hao X, Shang P, Chamba Y, Zhang B, Zhang H. Functional Identification of Porcine DLK1 during Muscle Development. Animals (Basel) 2022; 12:ani12121523. [PMID: 35739860 PMCID: PMC9219491 DOI: 10.3390/ani12121523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Skeletal muscle is the largest tissue and serves as a protein reservoir and energy reservoir in the human and animal body. It also serves as the main metabolic activity site. The formation of skeletal muscle mainly depends on the differentiation and fusion of myocytes and other complex ordered processes; each step is regulated by various factors. In this study, we investigated the expression profiles, functional identification, and regulatory pathways of Delta-like 1 homolog (DLK1) in pigs and myocytes. We found that DLK1 was highly expressed in the muscle tissues of pigs. DLK1 promoted myocyte proliferation, migration, differentiation, fusion, and muscular hypertrophy, but suppressed muscle degradation. DLK1 also inhibited the Notch signaling pathway by regulating the expression of key factors in the pathway, thereby producing a phenotype in which DLK1 promotes muscle development. These findings provide valuable information to improve our understanding of the functional mechanisms of DLK1 that underly myogenesis to accelerate the process of animal genetic improvement. Abstract DLK1 is paternally expressed and is involved in metabolism switching, stem cell maintenance, cell proliferation, and differentiation. Porcine DLK1 was identified in our previous study as a candidate gene that regulates muscle development. In the present study, we characterized DLK1 expression in pigs, and the results showed that DLK1 was highly expressed in the muscles of pigs. In-vitro cellular tests showed that DLK1 promoted myoblast proliferation, migration, and muscular hypertrophy, and at the same time inhibited muscle degradation. The expression of myogenic and fusion markers and the formation of multinucleated myotubes were both upregulated in myoblasts with DLK1 overexpression. DLK1 levels in cultured myocytes were negatively correlated with the expression of key factors in the Notch pathway, suggesting that the suppression of Notch signaling pathways may mediate these processes. Collectively, our results suggest a biological function of DLK1 as an enhancer of muscle development by the inhibition of Notch pathways.
Collapse
Affiliation(s)
- Yu Fu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
| | - Xin Hao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Y.C.)
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Y.C.)
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
- Correspondence: (B.Z.); (H.Z.); Tel.: +86-010-62734852 (H.Z.)
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Y.F.); (X.H.)
- Correspondence: (B.Z.); (H.Z.); Tel.: +86-010-62734852 (H.Z.)
| |
Collapse
|
8
|
Zhao Y, Wang Y, Guo F, Lu B, Sun J, Wang J, Ren Z. iTRAQ-based proteomic analysis of sperm reveals candidate proteins that affect the quality of spermatozoa from boars on plateaus. Proteome Sci 2021; 19:9. [PMID: 34330296 PMCID: PMC8323236 DOI: 10.1186/s12953-021-00177-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/09/2021] [Indexed: 01/19/2023] Open
Abstract
Background Tibetan pigs (TP) exhibit heritable adaptations to their hypoxic environments as a result of natural selection. However, candidate proteins that affect the sperm quality of boars on plateaus have not yet been clearly investigated. Methods In this study, to reveal the candidate proteins that affect the quality of spermatozoa of boars on plateaus, we analyzed the sperm quality using computer-assisted semen analysis (CASA) system and reactive oxygen species (ROS) levels. We also compared the proteomes of sperm proteomes between TP and Yorkshire pigs (YP) raised at high altitudes using the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC–MS/MS) proteomic method, and confirmed the relative expression levels of the four proteins by western blotting. Results The sperm quality of the TP was superior to that of the YP on plateaus. Of the 1,555 quantified proteins, 318 differentially expressed proteins (DEPs) were identified. Gene ontology (GO) analysis revealed that the DEPs were predominantly associated with the sorbitol metabolic process, removal of superoxide radicals, cellular response to superoxide, response to superoxide and regulation of the mitotic spindle assembly. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mainly enriched in pathways involved in the regulation of the actin cytoskeleton, glutathione metabolism, oxidative phosphorylation, and estrogen signaling. Based on the protein–protein interaction (PPI) network analysis, we identified 8 candidate proteins (FN1, EGF, HSP90B1, CFL1, GPX4, NDUFA6, VDAC2, and CP) that might play important roles and affect the sperm quality of boars on plateaus. Moreover, the relative expression levels of four proteins (CFL1, EGF, FN1, and GPX4) were confirmed by western blot analysis. Conclusions Our study revealed 8 candidate proteins (FN1, EGF, HSP90B1, CFL1, GPX4, NDUFA6, VDAC2, and CP) that affect the sperm quality of boar on plateaus and provide a reference for further studies on improving sperm quality and the molecular breeding of boars on plateaus. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-021-00177-9.
Collapse
Affiliation(s)
- Yanling Zhao
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Yaomei Wang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Feipeng Guo
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Bo Lu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Jiale Sun
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Jianzhou Wang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Zili Ren
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China.
| |
Collapse
|
9
|
Wang L, Zhang Y, Zhang B, Zhong H, Lu Y, Zhang H. Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs. BMC Genomics 2021; 22:441. [PMID: 34118873 PMCID: PMC8201413 DOI: 10.1186/s12864-021-07764-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Background Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation. Results A large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR). Conclusions This multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07764-2.
Collapse
Affiliation(s)
- Liyuan Wang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.,National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Yunfeng Lu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.
| |
Collapse
|
10
|
Fang C, Guo F, Zhao X, Zhang Z, Lu J, Pan H, Xu T, Li W, Yang M, Huang Y, Zhao Y, Zhao S. Biological mechanisms of growth performance and meat quality in porcine muscle tissue. Anim Biotechnol 2021; 33:1246-1254. [PMID: 33704018 DOI: 10.1080/10495398.2021.1886939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Growth performance and meat quality are important traits for pig production. The aim of the present study was to investigate the molecular mechanisms underlying growth performance and meat quality, and to identify novel target molecules for predicting the growth performance and meat quality. The differentially expressed genes (DEGs) in Diannan small ears pigs (DSP) and Landrace pigs (LP) were assessed by RNA-sequencing analyzing technology. A total of 339 DEGs were obtained between DSP and LP. 146 DEGs were upregulated in LP compared with DSP and 193 DEGs were upregulated in DSP compared with LP. The DEGs were significantly enriched in 26 GO and 3 KEGG pathways. The protein-protein interaction (PPI) network with 201 nodes and 382 edges was constructed and 5 modules were extracted from the entire network. The identified upregulated expression of genes involved in glycolysis and myogenesis as well as extracellular matrix may be associated with fast body and muscle deposition rates in LP. Increased expression of genes involved in PPAR signaling pathway and fatty acid metabolism as well as oxidative phosphate processes could be related to the intramuscular fat deposition and meat quality in DSP. The present study may provide an improved understanding of the growth performance and meat quality.
Collapse
Affiliation(s)
- Chen Fang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Fei Guo
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Xiaoqi Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China.,Institute of Herbivorous Livestock, Yunnan Academy of Animal Sciences, Kunming, China
| | - Zining Zhang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Junlan Lu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Hongbin Pan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Taojie Xu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Minghua Yang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Ying Huang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Yanguang Zhao
- Research Institute of Pig and Animal Nutrition, Yunnan Academy of Animal Sciences, Kunming, China
| | - Sumei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
11
|
Tandem mass tag-labeled quantitative proteomic analysis of tenderloins between Tibetan and Yorkshire pigs. Meat Sci 2021; 172:108343. [DOI: 10.1016/j.meatsci.2020.108343] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/12/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
|
12
|
Huang Z, Li Q, Li M, Li C. Transcriptome analysis reveals the long intergenic noncoding RNAs contributed to skeletal muscle differences between Yorkshire and Tibetan pig. Sci Rep 2021; 11:2622. [PMID: 33514792 PMCID: PMC7846844 DOI: 10.1038/s41598-021-82126-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
The difference between the skeletal muscle growth rates of Western and domestic breeds is remarkable, but the potential regulatory mechanism involved is still unclear. Numerous studies have pointed out that long intergenic noncoding RNA (lincRNA) plays a key role in skeletal muscle development. This study used published Yorkshire (LW) and Tibetan pig (TP) transcriptome data to explore the possible role of lincRNA in the difference in skeletal muscle development between the two breeds. 138 differentially expressed lincRNAs (DELs) were obtained between the two breeds, and their potential target genes (PTGs) were predicted. The results of GO and KEGG analysis revealed that PTGs are involved in multiple biological processes and pathways related to muscle development. The quantitative trait loci (QTLs) of DELs were predicted, and the results showed that most QTLs are related to muscle development. Finally, we constructed a co-expression network between muscle development related PTGs (MDRPTGs) and their corresponding DELs on the basis of their expression levels. The expression of DELs was significantly correlated with the corresponding MDRPTGs. Also, multiple MDRPTGs are involved in the key regulatory pathway of muscle fiber hypertrophy, which is the IGF-1-AKT-mTOR pathway. In summary, multiple lincRNAs that may cause differences in skeletal muscle development between the two breeds were identified, and their possible regulatory roles were explored. The findings of this study may provide a valuable reference for further research on the role of lincRNA in skeletal muscle development.
Collapse
Affiliation(s)
- Ziying Huang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianqian Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China. .,Guangxi Yangxiang Co., Ltd. Production Center, Guigang, 537131, China.
| |
Collapse
|
13
|
Fu Y, Shang P, Zhang B, Tian X, Nie R, Zhang R, Zhang H. Function of the Porcine TRPC1 Gene in Myogenesis and Muscle Growth. Cells 2021; 10:cells10010147. [PMID: 33450983 PMCID: PMC7828378 DOI: 10.3390/cells10010147] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 12/19/2022] Open
Abstract
In animals, muscle growth is a quantitative trait controlled by multiple genes. Previously, we showed that the transient receptor potential channel 1 (TRPC1) gene was differentially expressed in muscle tissues between pig breeds with divergent growth traits base on RNA-seq. Here, we characterized TRPC1 expression profiles in different tissues and pig breeds and showed that TRPC1 was highly expressed in the muscle. We found two single nucleotide polymorphisms (SNPs) (C-1763T and C-1604T) in TRPC1 that could affect the promoter region activity and regulate pig growth rate. Functionally, we used RNAi and overexpression to illustrate that TRPC1 promotes myoblast proliferation, migration, differentiation, fusion, and muscle hypertrophy while inhibiting muscle degradation. These processes may be mediated by the activation of Wnt signaling pathways. Altogether, our results revealed that TRPC1 might promote muscle growth and development and plays a key role in Wnt-mediated myogenesis.
Collapse
Affiliation(s)
- Yu Fu
- National Engineering Laboratory for Livestock and Poultry Breeding, Plateau Animal Genetic Resources Center, China Agriculture University, Beijing 100193, China; (Y.F.); (B.Z.); (X.T.); (R.N.); (R.Z.)
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China;
| | - Bo Zhang
- National Engineering Laboratory for Livestock and Poultry Breeding, Plateau Animal Genetic Resources Center, China Agriculture University, Beijing 100193, China; (Y.F.); (B.Z.); (X.T.); (R.N.); (R.Z.)
| | - Xiaolong Tian
- National Engineering Laboratory for Livestock and Poultry Breeding, Plateau Animal Genetic Resources Center, China Agriculture University, Beijing 100193, China; (Y.F.); (B.Z.); (X.T.); (R.N.); (R.Z.)
| | - Ruixue Nie
- National Engineering Laboratory for Livestock and Poultry Breeding, Plateau Animal Genetic Resources Center, China Agriculture University, Beijing 100193, China; (Y.F.); (B.Z.); (X.T.); (R.N.); (R.Z.)
| | - Ran Zhang
- National Engineering Laboratory for Livestock and Poultry Breeding, Plateau Animal Genetic Resources Center, China Agriculture University, Beijing 100193, China; (Y.F.); (B.Z.); (X.T.); (R.N.); (R.Z.)
| | - Hao Zhang
- National Engineering Laboratory for Livestock and Poultry Breeding, Plateau Animal Genetic Resources Center, China Agriculture University, Beijing 100193, China; (Y.F.); (B.Z.); (X.T.); (R.N.); (R.Z.)
- Correspondence:
| |
Collapse
|
14
|
Ayuso M, Buyssens L, Stroe M, Valenzuela A, Allegaert K, Smits A, Annaert P, Mulder A, Carpentier S, Van Ginneken C, Van Cruchten S. The Neonatal and Juvenile Pig in Pediatric Drug Discovery and Development. Pharmaceutics 2020; 13:44. [PMID: 33396805 PMCID: PMC7823749 DOI: 10.3390/pharmaceutics13010044] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
Pharmacotherapy in pediatric patients is challenging in view of the maturation of organ systems and processes that affect pharmacokinetics and pharmacodynamics. Especially for the youngest age groups and for pediatric-only indications, neonatal and juvenile animal models can be useful to assess drug safety and to better understand the mechanisms of diseases or conditions. In this respect, the use of neonatal and juvenile pigs in the field of pediatric drug discovery and development is promising, although still limited at this point. This review summarizes the comparative postnatal development of pigs and humans and discusses the advantages of the juvenile pig in view of developmental pharmacology, pediatric diseases, drug discovery and drug safety testing. Furthermore, limitations and unexplored aspects of this large animal model are covered. At this point in time, the potential of the neonatal and juvenile pig as nonclinical safety models for pediatric drug development is underexplored.
Collapse
Affiliation(s)
- Miriam Ayuso
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (M.S.); (A.V.); (C.V.G.)
| | - Laura Buyssens
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (M.S.); (A.V.); (C.V.G.)
| | - Marina Stroe
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (M.S.); (A.V.); (C.V.G.)
| | - Allan Valenzuela
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (M.S.); (A.V.); (C.V.G.)
| | - Karel Allegaert
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; (K.A.); (P.A.)
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
- Department of Hospital Pharmacy, Erasmus MC Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Anne Smits
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
- Neonatal Intensive Care Unit, University Hospitals UZ Leuven, 3000 Leuven, Belgium
| | - Pieter Annaert
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; (K.A.); (P.A.)
| | - Antonius Mulder
- Department of Neonatology, University Hospital Antwerp, 2650 Edegem, Belgium;
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, 2610 Wilrijk, Belgium
| | | | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (M.S.); (A.V.); (C.V.G.)
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (L.B.); (M.S.); (A.V.); (C.V.G.)
| |
Collapse
|
15
|
Duan M, Wang Z, Guo X, Wang K, Liu S, Zhang B, Shang P. Integrated analysis of transcriptomic and proteomic analyses reveals different metabolic patterns in the livers of Tibetan and Yorkshire pigs. Anim Biosci 2020; 34:922-930. [PMID: 33152227 PMCID: PMC8100475 DOI: 10.5713/ajas.20.0342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/13/2020] [Indexed: 11/27/2022] Open
Abstract
Objective Tibetan pigs, predominantly originating from the Tibetan Plateau, have been subjected to long-term natural selection in an extreme environment. To characterize the metabolic adaptations to hypoxic conditions, transcriptomic and proteomic expression patterns in the livers of Tibetan and Yorkshire pigs were compared. Methods RNA and protein were extracted from liver tissue of Tibetan and Yorkshire pigs (n = 3, each). Differentially expressed genes and proteins were subjected to gene ontology and Kyoto encyclopedia of genes and genomes functional enrichment analyses. Results In the RNA-Seq and isobaric tags for relative and absolute quantitation analyses, a total of 18,791 genes and 3,390 proteins were detected and compared. Of these, 273 and 257 differentially expressed genes and proteins were identified. Evidence from functional enrichment analysis showed that many genes were involved in metabolic processes. The combined transcriptomic and proteomic analyses revealed that small molecular biosynthesis, metabolic processes, and organic hydroxyl compound metabolic processes were the major processes operating differently in the two breeds. The important genes include retinol dehydrogenase 16, adenine phosphoribosyltransferase, prenylcysteine oxidase 1, sorbin and SH3 domain containing 2, ENSSSCG00000036224, perilipin 2, ladinin 1, kynurenine aminotransferase 1, and dimethylarginine dimethylaminohydrolase 1. Conclusion The findings of this study provide novel insight into the high-altitude metabolic adaptation of Tibetan pigs.
Collapse
Affiliation(s)
- Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Zhenmei Wang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Xinying Guo
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Siyuan Liu
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, Xizang 86000, China
| |
Collapse
|
16
|
Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages. Animals (Basel) 2020; 10:ani10071198. [PMID: 32679676 PMCID: PMC7401622 DOI: 10.3390/ani10071198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/18/2020] [Accepted: 07/11/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The pigs is the most popular agricultural animal in the world. Muscle growth—which has the highest economic value in pigs—can be regulated by multiple genes and involves complex regulatory mechanisms. It is necessary to understand the dynamics of muscle transcriptome during development to understand the muscle development mechanism. However, the genes and miRNAs that play regulatory roles underlying differences in the meat quality of pigs remain unclear. In the current study, qRT-PCR, miRNA-Seq, and RNA-Seq were applied to analyze and verify muscle tissues of pigs from three different developmental stages and screened genes, miRNAs and pathways related to pig muscle development. This study focused on analyzing the mechanisms of muscle development and uncover the development differences in muscle from embryo to adult. Abstract The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.
Collapse
|
17
|
Gu X, Gao Y, Luo Z, Yang L, Chi F, Xiao J, Wang W, Geng F. In-depth mapping of the proteome of Tibetan pig tenderloin (longissimus dorsi) using offline high-pH reversed-phase fractionation and LC-MS/MS. J Food Biochem 2019; 43:e13015. [PMID: 31429109 DOI: 10.1111/jfbc.13015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/29/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022]
Abstract
In recent years, Tibetan pig breeding and meat processing have developed rapidly. However, the basic physiological and biochemical characteristics of Tibetan pork have not been systematically explored. The present study conducted a high-throughput analysis of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs and performed a functional annotation and bioinformatics analysis of the identified proteins. Based on offline two-dimensional liquid chromatography fractionation and MS/MS identification, a total of 1,723 proteins were identified in the tenderloin of Tibetan pigs. Gene ontology analysis and pathway enrichment analysis revealed that the proteins involved in respiration (oxidative phosphorylation, glycolysis/gluconeogenesis, citric acid cycle, and pyruvate metabolism) and protein synthesis and metabolism (proteasome, amino acid biosynthesis, endoplasmic reticulum protein processing, and ribosomes) were significantly enriched, indicating that the energy production and protein metabolism are the most important physiological processes in Tibetan pig tenderloin. Practical applications The in-depth mapping of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs gives a panoramic perspective at the protein molecular level and provides important information on the mechanisms of postmortem muscle physiology and meat quality formation. Furthermore, the development of Tibetan pork storage and processing technologies would also benefit from the characterization of the biochemical properties of Tibetan pork.
Collapse
Affiliation(s)
- Xuedong Gu
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Yuling Gao
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Zhang Luo
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Lin Yang
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Fumin Chi
- College of Food Science, Tibet Agriculture and Animal Husbandry University, Linzhi, China
| | - Jing Xiao
- Meat Processing Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Wei Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| | - Fang Geng
- Meat Processing Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, China
| |
Collapse
|