1
|
Li Q, Hao M, Zhu J, Yi L, Cheng W, Xie Y, Zhao S. Comparison of differentially expressed genes in longissimus dorsi muscle of Diannan small ears, Wujin and landrace pigs using RNA-seq. Front Vet Sci 2024; 10:1296208. [PMID: 38249550 PMCID: PMC10796741 DOI: 10.3389/fvets.2023.1296208] [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: 09/18/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Pig growth is an important economic trait that involves the co-regulation of multiple genes and related signaling pathways. High-throughput sequencing has become a powerful technology for establishing the transcriptome profiles and can be used to screen genome-wide differentially expressed genes (DEGs). In order to elucidate the molecular mechanism underlying muscle growth, this study adopted RNA sequencing (RNA-seq) to identify and compare DEGs at the genetic level in the longissimus dorsi muscle (LDM) between two indigenous Chinese pig breeds (Diannan small ears [DSE] pig and Wujin pig [WJ]) and one introduced pig breed (Landrace pig [LP]). Methods Animals under study were from two Chinese indigenous pig breeds (DSE pig, n = 3; WJ pig, n = 3) and one introduced pig breed (LP, n = 3) were used for RNA sequencing (RNA-seq) to identify and compare the expression levels of DEGs in the LDM. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs. Results The results revealed that for the DSE, WJ, and LP libraries, more than 66, 65, and 71 million clean reads were generated by transcriptome sequencing, respectively. A total of 11,213 genes were identified in the LDM tissue of these pig breeds, of which 7,127 were co-expressed in the muscle tissue of the three samples. In total, 441 and 339 DEGs were identified between DSE vs. WJ and LP vs. DSE in the study, with 254, 193 up-regulated genes and 187, 193 down-regulated genes in DSE compared to WJ and LP. GO analysis and KEGG signaling pathway analysis showed that DEGs are significantly related to contractile fiber, sarcolemma, and dystrophin-associated glycoprotein complex, myofibril, sarcolemma, and myosin II complex, Glycolysis/Gluconeogenesis, Propanoate metabolism, and Pyruvate metabolism, etc. In combination with functional annotation of DEGs, key genes such as ENO3 and JUN were identified by PPI network analysis. Discussion In conclusion, the present study revealed key genes including DES, FLNC, PSMD1, PSMD6, PSME4, PSMB4, RPL11, RPL13A, ROS23, RPS29, MYH1, MYL9, MYL12B, TPM1, TPM4, ENO3, PGK1, PKM2, GPI, and the unannotated new gene ENSSSCG00000020769 and related signaling pathways that influence the difference in muscle growth and could provide a theoretical basis for improving pig muscle growth traits in the future.
Collapse
Affiliation(s)
- Qiuyan Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Meilin Hao
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, China
| | - Junhong Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Lanlan Yi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wenjie Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yuxiao Xie
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- College of Biology and Agriculture, Zunyi Normal University, Zunyi, China
| | - Sumei Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
2
|
Wang T, Luo Y, Kong X, Yu B, Zheng P, Huang Z, Mao X, Yu J, Luo J, Yan H, He J. Genetic- and Fiber-Diet-Mediated Changes in Antibiotic Resistance Genes in Pig Colon Contents and Feces and Their Driving Factors. Microorganisms 2023; 11:2370. [PMID: 37894028 PMCID: PMC10609257 DOI: 10.3390/microorganisms11102370] [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: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
Comprehensive studies on the effects of genetics and fiber diets on antibiotic resistance genes (ARGs) remain scarce. In this study, we analyzed the profiles of ARGs in colonic contents and fecal samples of Taoyuan, Duroc, and Xiangcun pigs (n = 10) fed at different fiber levels. Through macrogenomic analysis, we identified a total of 850 unique types of ARGs and classified them into 111 drug resistance classes. The abundance of partially drug-resistant ARGs was higher in the colonic contents of local pig breeds under a large-scale farming model. ARGs were found to be widely distributed among a variety of bacteria, predominantly in the phyla Firmicutes, Proteobacteria, and Bacteroidetes. Fiber diets reduce the abundance of ARGs in colonic contents and feces, and mobile genetic elements (MGEs) and short-chain fatty acids (SCFAs) are important drivers in mediating the effect of fiber diets on the abundance of ARGs. In vitro fermentation experiments confirmed that butyric acid significantly reduced the abundance of ARGs. In summary, the results of this study enhanced our understanding of the distribution and composition of ARGs in the colon of different breeds of pigs and revealed that a fiber diet can reduce ARGs in feces through its Butyric acid, providing reference data for environmental safety.
Collapse
Affiliation(s)
- Tao Wang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Yuheng Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Xiangfeng Kong
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Ping Zheng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Xiangbing Mao
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Jie Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Junqiu Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Hui Yan
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| | - Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Animal Disease-Resistant Nutrition, Chengdu 611130, China
| |
Collapse
|
3
|
Yang H, Xu XL, Ma HM, Jiang J. Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed. BMC Genet 2016; 17:80. [PMID: 27296698 PMCID: PMC4906580 DOI: 10.1186/s12863-016-0389-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/02/2016] [Indexed: 11/08/2022] Open
Abstract
Background The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry. Results Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig. Conclusions Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0389-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hu Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.,College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Xing-Li Xu
- College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Hai-Ming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| |
Collapse
|
4
|
Identification of genes showing differential expression profile associated with growth rate in skeletal muscle tissue of Landrace weanling pig. J Genet 2016; 95:341-7. [DOI: 10.1007/s12041-016-0643-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
5
|
Schellander K. Identifying genes associated with quantitative traits in pigs: integrating quantitative and molecular approaches for meat quality. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.s2.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
6
|
Dal Monego S, Colitti M, Pallavicini A, D’Andrea M, Pilla F, Graziosi G, Stefanon B. Evaluation of gene expression profiles of pig skeletal muscle in response to energy content of the diets using human microarrays. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2007.45] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
7
|
Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs. BMC Genomics 2015; 16:377. [PMID: 25962502 PMCID: PMC4437458 DOI: 10.1186/s12864-015-1580-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/24/2015] [Indexed: 12/18/2022] Open
Abstract
Background The growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 developmental periods (30, 40, 55, 63, 70, 90, and 105 days of gestation, and 0, 1, 3, and 5 weeks of age) using digital gene expression on Solexa/Illumina’s Genome Analyzer platform to investigate the differences in prenatal and postnatal skeletal muscle between the two breeds. Results Muscle morphological changes indicate the importance of primary fiber formation from 30 to 40 dpc (days post coitus), and secondary fiber formation from 55 to 70 dpc. We screened 4,331 differentially expressed genes in TC and 2,259 in YK (log2 ratio >1 and probability >0.7). Cluster analysis showed different gene expression patterns between TC and YK pigs. The transcripts were annotated in terms of Gene Ontology related to muscle development. We found that the genes CXCL10, EIF2B5, PSMA6, FBXO32, and LOC100622249 played vital roles in the muscle regulatory networks in the TC breed, whereas the genes SGCD, ENG, THBD, AQP4, and BTG2 played dominant roles in the YK breed. These genes showed breed-specific and development-dependent differential expression patterns. Furthermore, 984 genes were identified in myogenesis. A heat map showed that significantly enriched pathways (FDR <0.05) had stage-specific functional regulatory mechanisms. Finally, the differentially expressed genes from our sequencing results were confirmed by real-time quantitative polymerase chain reaction. Conclusions This study detected many functional genes and showed differences in the molecular mechanisms of skeletal muscle development between TC and YK pigs. TC pigs showed slower muscle growth and more complicated genetic regulation than YK pigs. Many differentially expressed genes showed breed-specific expression patterns. Our data provide a better understanding of skeletal muscle developmental differences and valuable information for improving pork quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1580-7) contains supplementary material, which is available to authorized users.
Collapse
|
8
|
Hwang JH, Kwon SG, Park DH, Kim TW, Kang DG, Ha J, Kim SW, Kim CW. Molecular characterization of porcine PGM1 gene associated with meat quality traits. CANADIAN JOURNAL OF ANIMAL SCIENCE 2015. [DOI: 10.4141/cjas-2014-098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hwang, J. H., Kwon, S. G., Park, D. H., Kim, T. W., Kang, D. G., Ha, J., Kim, S. W. and Kim, C. W. 2015. Molecular characterization of porcine PGM1 gene associated with meat quality traits. Can. J. Anim. Sci. 95: 31–36. The PGM1 gene from four porcine breeds (Berkshire, Duroc, Landrace, and Yorkshire) is highly expressed in liver tissue at the transcriptional level. Single nucleotide polymorphisms (SNPs) of PGM1 were examined to analyze association with increased expression of PGM1 gene in the Berkshire liver. A Leu525 synonymous SNP of Chr6:137174682A>G (c.1575A>G) was identified and showed significant (P<0.05) differences to backfat thickness, drip loss, protein content, fat content, Warner–Bratzler shear force, and post-mortem pH24h. Therefore, it is concluded that PGM1 synonymous SNP is an important factor regulating meat quality.
Collapse
Affiliation(s)
- Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Seul Gi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Sam Woong Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 660-758, South Korea
| |
Collapse
|
9
|
Óvilo C, Benítez R, Fernández A, Núñez Y, Ayuso M, Fernández AI, Rodríguez C, Isabel B, Rey AI, López-Bote C, Silió L. Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. BMC Genomics 2014; 15:413. [PMID: 24885501 PMCID: PMC4070551 DOI: 10.1186/1471-2164-15-413] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/27/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. RESULTS Loin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types. CONCLUSION These results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions.
Collapse
Affiliation(s)
- Cristina Óvilo
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Rita Benítez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Almudena Fernández
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Yolanda Núñez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Miriam Ayuso
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | | | - Carmen Rodríguez
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| | - Beatriz Isabel
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - Ana Isabel Rey
- />Dpto Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | | | - Luis Silió
- />Dpto Mejora Genética Animal, INIA, Ctra Coruña km 7.5, Madrid, 28040 Spain
| |
Collapse
|
10
|
Pena RN, Quintanilla R, Manunza A, Gallardo D, Casellas J, Amills M. Application of the microarray technology to the transcriptional analysis of muscle phenotypes in pigs. Anim Genet 2014; 45:311-21. [DOI: 10.1111/age.12146] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2014] [Indexed: 01/09/2023]
Affiliation(s)
- R. N. Pena
- Department of Animal Production; University of Lleida-Agrotecnio Center; 25198 Lleida Spain
| | | | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - J. Casellas
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| |
Collapse
|
11
|
Onteru SK, Gorbach DM, Young JM, Garrick DJ, Dekkers JCM, Rothschild MF. Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig. PLoS One 2013; 8:e61756. [PMID: 23840294 PMCID: PMC3694077 DOI: 10.1371/journal.pone.0061756] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/11/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency. METHODOLOGY/PRINCIPAL FINDINGS Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping. CONCLUSIONS/SIGNIFICANCE Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.
Collapse
Affiliation(s)
- Suneel K. Onteru
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Danielle M. Gorbach
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Jennifer M. Young
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dorian J. Garrick
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Jack C. M. Dekkers
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Max F. Rothschild
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| |
Collapse
|
12
|
Siengdee P, Trakooljul N, Murani E, Schwerin M, Wimmers K, Ponsuksili S. Transcriptional profiling and miRNA-dependent regulatory network analysis of longissimus dorsi muscle during prenatal and adult stages in two distinct pig breeds. Anim Genet 2013; 44:398-407. [PMID: 23506348 DOI: 10.1111/age.12032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2013] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) and mRNAs establish a complex regulatory network influencing diverse biological pathways including muscle development and growth. Elucidating miRNA-dependent regulatory networks involved in muscle development could provide additional insights into muscle traits largely predefined during prenatal development. The present study aimed to determine differentially expressed transcripts and functional miRNA-mRNA relationships associated with different stages of skeletal muscle development in two pig breeds, German Landrace and Pietrain, distinct in muscle characteristics. A comparative transcriptional profiling of longissimus dorsi muscle tissues from fetuses at 35, 63 and 91 days post-conception as well as adult pigs (180 days postnatum) was performed using the Affymetrix GeneChip porcine genome microarray. Differential expression patterns were identified to be associated with muscularly developmental stages and breed types. The integration of miRNA expression data and ingenuity pathways analysis (ipa) pathway analysis revealed several miRNA-dependent regulatory networks related to muscle growth and development. The present results provide insights into muscle biology for further improvement of porcine meat quality.
Collapse
Affiliation(s)
- P Siengdee
- Leibniz Institute for Farm Animals Biology FBN, Research Group 'Functional Genome Analysis', Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | | | | | | | | | | |
Collapse
|
13
|
Xu H, Xu Y, Liang X, Wang Y, Jin F, Liu D, Ma Y, Yuan H, Song X, Zeng W. Porcine skeletal muscle differentially expressed gene ATP5B: molecular characterization, expression patterns, and association analysis with meat quality traits. Mamm Genome 2013; 24:142-50. [PMID: 23420545 DOI: 10.1007/s00335-013-9446-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Accepted: 12/27/2012] [Indexed: 10/27/2022]
Abstract
The 2-DE/MS-based proteomics approach was used to investigate the differences of porcine skeletal muscle, and ATP5B was identified as one differential expression protein. In the present study, ATP5B gene was further cloned by RT-PCR, the sequence was analyzed using the bioinformatics method, and the mRNA expression was detected by qRT-PCR. Sequence analysis showed that the porcine ATP5B gene contains an ORF encoding 528-amino-acid residues with 49 and 166 nucleotides in the 5' and 3' UTRs, respectively. The mRNA of ATP5B was widely expressed in all 14 tissues tested, but especially highly expressed in parorchis and fat. The expression pattern of ATP5B was similar in Large White and Meishan breeds, showing that the expression was upregulated by 3 days after birth and downregulated during postnatal development of skeletal muscle. Comparing the two breeds, the mRNA abundance of ATP5B in Large White was more highly expressed than in Meishan at all developmental stages (P < 0.05). Moreover, a synonymous mutation, G75A in exon 8, was identified and association analysis with the traits of meat quality showed that it was significantly associated with the RLF, FMP, IFR, IMF, and IMW (P < 0.05). These results suggested that ATP5B probably plays a key role in porcine skeletal muscle development and may provide further insight into the molecular mechanisms responsible for breed-specific differences in meat quality.
Collapse
Affiliation(s)
- Haixia Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
|
15
|
Comparison of the longissimus muscle proteome between obese and lean pigs at 180 days. Mamm Genome 2012; 24:72-9. [DOI: 10.1007/s00335-012-9440-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/12/2012] [Indexed: 12/28/2022]
|
16
|
Nascimento CS, Peixoto JO, Verardo LL, Campos CF, Weller MMC, Faria VR, Botelho ME, Martins MF, Machado MA, Silva FF, Lopes PS, Guimarães SEF. Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds. GENETICS AND MOLECULAR RESEARCH 2012; 11:3315-28. [PMID: 22782623 DOI: 10.4238/2012.june.15.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In general, genetic differences across different breeds of pig lead to variation in mature body size and slaughter age. The Commercial breeds Duroc and Large White and the local Brazilian breed Piau are ostensibly distinct in terms of growth and muscularity, commercial breeds are much leaner while local breeds grow much slower and are fat type pigs. However, the genetic factors that underlie such distinctions remain unclear. We used expressed sequence tags (ESTs) to characterize and compare transcript profiles in the semimembranosus muscle of these pig breeds. Our aim was to identify differences in breed-related gene expression that might influence growth performance and meat quality. We constructed three non-normalized cDNA libraries from semimembranosus muscle, using two samples from each one, of these three breeds; 6902 high-quality ESTs were obtained. Cluster analysis was performed and these sequences were clustered into 3670 unique sequences; 24.7% of the sequences were categorized as contigs and 75.3% of the sequences were singletons. Based on homology searches against the SwissProt protein database, we were able to assign a putative protein identity to only 1050 unique sequences. Among these, 58.5% were full-length protein sequences and 17.2% were pig-specific sequences. Muscle structural and cytoskeletal proteins, such as actin, and myosin, were the most abundant transcripts (16.7%) followed by those related to mitochondrial function (12.9%), and ribosomal proteins (12.4%). Furthermore, ESTs generated in this study provide a rich source for identification of novel genes and for the comparative analysis of gene expression patterns in divergent pig breeds.
Collapse
Affiliation(s)
- C S Nascimento
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Hocquette JF, Bernard-Capel C, Vidal V, Jesson B, Levéziel H, Renand G, Cassar-Malek I. The GENOTEND chip: a new tool to analyse gene expression in muscles of beef cattle for beef quality prediction. BMC Vet Res 2012; 8:135. [PMID: 22894653 PMCID: PMC3438070 DOI: 10.1186/1746-6148-8-135] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 07/28/2012] [Indexed: 12/02/2022] Open
Abstract
Background Previous research programmes have described muscle biochemical traits and gene expression levels associated with beef tenderness. One of our results concerning the DNAJA1 gene (an Hsp40) was patented. This study aims to confirm the relationships previously identified between two gene families (heat shock proteins and energy metabolism) and beef quality. Results We developed an Agilent chip with specific probes for bovine muscular genes. More than 3000 genes involved in muscle biology or meat quality were selected from genetic, proteomic or transcriptomic studies, or from scientific publications. As far as possible, several probes were used for each gene (e.g. 17 probes for DNAJA1). RNA from Longissimus thoracis muscle samples was hybridised on the chips. Muscles samples were from four groups of Charolais cattle: two groups of young bulls and two groups of steers slaughtered in two different years. Principal component analysis, simple correlation of gene expression levels with tenderness scores, and then multiple regression analysis provided the means to detect the genes within two families (heat shock proteins and energy metabolism) which were the most associated with beef tenderness. For the 25 Charolais young bulls slaughtered in year 1, expression levels of DNAJA1 and other genes of the HSP family were related to the initial or overall beef tenderness. Similarly, expression levels of genes involved in fat or energy metabolism were related with the initial or overall beef tenderness but in the year 1 and year 2 groups of young bulls only. Generally, the genes individually correlated with tenderness are not consistent across genders and years indicating the strong influence of rearing conditions on muscle characteristics related to beef quality. However, a group of HSP genes, which explained about 40% of the variability in tenderness in the group of 25 young bulls slaughtered in year 1 (considered as the reference group), was validated in the groups of 30 Charolais young bulls slaughtered in year 2, and in the 21 Charolais steers slaughtered in year 1, but not in the group of 19 steers slaughtered in year 2 which differ from the reference group by two factors (gender and year). When the first three groups of animals were analysed together, this subset of genes explained a 4-fold higher proportion of the variability in tenderness than muscle biochemical traits. Conclusion This study underlined the relevance of the GENOTEND chip to identify markers of beef quality, mainly by confirming previous results and by detecting other genes of the heat shock family as potential markers of beef quality. However, it was not always possible to extrapolate the relevance of these markers to all animal groups which differ by several factors (such as gender or environmental conditions of production) from the initial population of reference in which these markers were identified.
Collapse
Affiliation(s)
- Jean-Francois Hocquette
- INRA, UMR1213, Unité de Recherches sur les Herbivores, Theix, Saint-Genès-Champanelle, F-63122, France.
| | | | | | | | | | | | | |
Collapse
|
18
|
Damon M, Wyszynska-Koko J, Vincent A, Hérault F, Lebret B. Comparison of muscle transcriptome between pigs with divergent meat quality phenotypes identifies genes related to muscle metabolism and structure. PLoS One 2012; 7:e33763. [PMID: 22470472 PMCID: PMC3312351 DOI: 10.1371/journal.pone.0033763] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 02/17/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Meat quality depends on physiological processes taking place in muscle tissue, which could involve a large pattern of genes associated with both muscle structural and metabolic features. Understanding the biological phenomena underlying muscle phenotype at slaughter is necessary to uncover meat quality development. Therefore, a muscle transcriptome analysis was undertaken to compare gene expression profiles between two highly contrasted pig breeds, Large White (LW) and Basque (B), reared in two different housing systems themselves influencing meat quality. LW is the most predominant breed used in pig industry, which exhibits standard meat quality attributes. B is an indigenous breed with low lean meat and high fat contents, high meat quality characteristics, and is genetically distant from other European pig breeds. METHODOLOGY/PRINCIPAL FINDINGS Transcriptome analysis undertaken using a custom 15 K microarray, highlighted 1233 genes differentially expressed between breeds (multiple-test adjusted P-value<0.05), out of which 635 were highly expressed in the B and 598 highly expressed in the LW pigs. No difference in gene expression was found between housing systems. Besides, expression level of 12 differentially expressed genes quantified by real-time RT-PCR validated microarray data. Functional annotation clustering emphasized four main clusters associated to transcriptome breed differences: metabolic processes, skeletal muscle structure and organization, extracellular matrix, lysosome, and proteolysis, thereby highlighting many genes involved in muscle physiology and meat quality development. CONCLUSIONS/SIGNIFICANCE Altogether, these results will contribute to a better understanding of muscle physiology and of the biological and molecular processes underlying meat quality. Besides, this study is a first step towards the identification of molecular markers of pork quality and the subsequent development of control tools.
Collapse
Affiliation(s)
- Marie Damon
- INRA, UMR1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage (PEGASE), Saint Gilles, France.
| | | | | | | | | |
Collapse
|
19
|
Zhao S, Hulsegge B, Harders FL, Bossers R, Keuning E, Hoekman AJW, Hoving-Bolink R, te Pas MFW. Functional analysis of inter-individual transcriptome differential expression in pig longissimus muscle. J Anim Breed Genet 2012; 130:72-8. [PMID: 23317067 DOI: 10.1111/j.1439-0388.2012.00993.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Selection of pigs for increased meat production or improved meat quality changes muscle mass and muscle composition. This will be related to transcriptome expression profile changes in muscle tissue, generating inter-individual differences. This study investigated the differentially expressed genes in the transcriptome profiles of the longissimus muscle of 75 Large White-Duroc cross sows and castrates. The use of a common reference design enabled to investigate the inter-individual transcriptome expression profile differences between the animals as compared with the means of all animals. The aim of the study was to identify the biological processes related to these inter-individual differences. It was expected that these processes underlie the selection effects. In total, 908 transcripts were differentially expressed. Among them, 762 were mainly downregulated and 146 were mainly upregulated. Gene Ontology and Pathways analyses indicated that the differentially expressed genes belong to three groups of processes involved in protein synthesis and amino acid-protein metabolism, energy metabolism and muscle-specific structure and activity processes. Comparing the functional biological analysis results with previously reported data suggested that the protein synthesis, energy metabolism and muscle-specific structure would contribute to meat production and the meat quality.
Collapse
Affiliation(s)
- S Zhao
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Lelystad, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Song J, Raadsma HW, Thomson PC. Evaluation of false discovery rate and power via sample size in microarray studies. J Appl Stat 2012. [DOI: 10.1080/02664763.2011.602054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
21
|
Casellas J, Ibáñez-Escriche N. Bayesian recursive mixed linear model for gene expression analyses with continuous covariates. J Anim Sci 2011; 90:67-75. [PMID: 21908645 DOI: 10.2527/jas.2010-3750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The analysis of microarray gene expression data has experienced a remarkable growth in scientific research over the last few years and is helping to decipher the genetic background of several productive traits. Nevertheless, most analytical approaches have relied on the comparison of 2 (or a few) well-defined groups of biological conditions where the continuous covariates have no sense (e.g., healthy vs. cancerous cells). Continuous effects could be of special interest when analyzing gene expression in animal production-oriented studies (e.g., birth weight), although very few studies address this peculiarity in the animal science framework. Within this context, we have developed a recursive linear mixed model where not only are linear covariates accounted for during gene expression analyses but also hierarchized and the effects of their genetic, environmental, and residual components on differential gene expression inferred independently. This parameterization allows a step forward in the inference of differential gene expression linked to a given quantitative trait such as birth weight. The statistical performance of this recursive model was exemplified under simulation by accounting for different sample sizes (n), heritabilities for the quantitative trait (h(2)), and magnitudes of differential gene expression (λ). It is important to highlight that statistical power increased with n, h(2), and λ, and the recursive model exceeded the standard linear mixed model with linear (nonrecursive) covariates in the majority of scenarios. This new parameterization would provide new insights about gene expression in the animal science framework, opening a new research scenario where within-covariate sources of differential gene expression could be individualized and estimated. The source code of the program accommodating these analytical developments and additional information about practical aspects on running the program are freely available by request to the corresponding author of this article.
Collapse
Affiliation(s)
- J Casellas
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | | |
Collapse
|
22
|
Sollero BP, Guimarães SEF, Rilington VD, Tempelman RJ, Raney NE, Steibel JP, Guimarães JD, Lopes PS, Lopes MS, Ernst CW. Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace cross-bred pigs. Anim Genet 2011; 42:600-12. [PMID: 22035001 DOI: 10.1111/j.1365-2052.2011.02186.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Skeletal muscle development is a complex process involving the coordinated expression of thousands of genes. The aim of this study was to identify differentially expressed genes in longissimus dorsi (LD) muscle of pigs at 40 and 70 days (d) of gestation (developmental stages encompassing primary and secondary fibre formation) in Yorkshire-Landrace (YL) cross-bred pigs and Piau pigs (a naturalized Brazilian breed), which are two breed types that differ in muscularity. Foetuses were obtained from gilts at each gestational age (n = 3 YL; n = 4 Piau), and transcriptional profiling was performed using the Pigoligoarray microarray containing 20 400 oligonucleotides. A total of 486 oligonucleotides were differentially expressed (fold change (FC) ≥ 1.5; false discovery rate (FDR) ≤ 0.05) between 40 and 70 d gestation in either YL or Piau pigs, and a total of 1300 oligonucleotides were differentially expressed (FC ≥ 1.5; FDR ≤ 0.05) between YL and Piau pigs at either age. Gene ontology annotation and pathway analyses determined functional classifications for differentially expressed genes and revealed breed type-specific developmental expression patterns. Thirteen genes were selected for confirmation by qRT-PCR analyses, and expression patterns for most of these genes were confirmed, providing further insight into the roles of these genes in pig muscle development. This study revealed both developmental and breed type-specific patterns of gene expression in foetal pig skeletal muscle, including genes not previously associated with myogenesis. This information will contribute to future pig genetic improvement efforts.
Collapse
Affiliation(s)
- B P Sollero
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
D'Andrea M, Dal Monego S, Pallavicini A, Modonut M, Dreos R, Stefanon B, Pilla F. Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools. Anim Genet 2011; 42:501-9. [PMID: 21906101 DOI: 10.1111/j.1365-2052.2010.02164.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using an array consisting of 10 665 70-mer oligonucleotide probes, the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana (CT), an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared with that of two cosmopolitan breeds, Large White (LW) and a crossbreed (CB; Duroc × Landrace × Large White). The results were validated by real-time PCR. All animals were of the same age and were raised under the same environmental conditions. Muscle tissues were collected at 3, 6, 9 and 11 months of age, and a total of 173 genes showed significant differential expression between CT and the cosmopolitan genetic types at 3 months of age. Time series cluster analysis indicated that the CT breed had a different pattern of gene expression compared with that of the LW and the CB. Four of the eight clusters highlighted the gene differences between CT and the other two breeds, which were further supported by statistical analyses: clusters 4 and 5 contained a total of 71 genes that were underexpressed at 3 months of age, and cluster 3 and cluster 7 included 28 and 42 genes respectively that were overexpressed at 3 months of age. As expected, differentially expressed genes belonged to the category of genes coding for contractile fibres and transcription factors involved in muscle development and differentiation. These findings highlight muscle expression genes during pig growth and are useful to understand the genetic meaning of the different developmental rates.
Collapse
Affiliation(s)
- M D'Andrea
- University of Molise, SAVA, Campobasso, Italy.
| | | | | | | | | | | | | |
Collapse
|
24
|
Developmental expression changes of the genes involved in IGFI signaling pathway in longissimus dorsi muscle of Tongcheng and Yorkshire pigs during postnatal growth. Mol Biol Rep 2011; 38:5133-8. [PMID: 21246287 DOI: 10.1007/s11033-010-0662-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
Abstract
IGFI signaling pathway is sufficient to regulate myofibre hypertrophy postnatally, which is associated with muscle mass in economically livestock. In the present study, we drafted the developmental expression pattern of eight genes implicated in IGFI system across six stages of postnatal myofibre growth in Yorkshire and Tongcheng pigs. The results indicated that GRB2 may contribute to increased DNA content in postnatal myofibre hypertrophy via GRB2-Ras-Raf-MEK-ERK sub-pathway; INSR, PDK1, IRS1 and eIF4E may contribute to high growth rate via stimulating the rate of protein synthesis and inhibiting the rate of protein degradation. In addition, the results suggested 60 days maybe a very important stage in postnatal myofibre growth. Moreover, higher mRNA level of IRS1 and GLUT4 maybe associated with inferior meat quality in Yorkshire compared to Tongcheng pig. Therefore, IGFI signaling pathway regulates myofibre hypertrophy postnatally via complicated signal effectors, which may have negative impact on meat quality simultaneously.
Collapse
|
25
|
Davoli R, Braglia S, Russo V, Varona L, te Pas MFW. Expression profiling of functional genes in prenatal skeletal muscle tissue in Duroc and Pietrain pigs. J Anim Breed Genet 2010; 128:15-27. [PMID: 21214640 DOI: 10.1111/j.1439-0388.2010.00867.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In livestock, skeletal muscle is a tissue of major economic importance for meat production and muscle mass is largely determined during the prenatal period by the number and the size of muscle fibres. The understanding of gene expression changes during prenatal pig muscle development is still limited. In this study, genes identified as differentially expressed in a previous microarray research and chosen for the function of the coded protein as putative candidate involved in myogenesis were considered to analyse their expression profile during foetal growth of Duroc and Pietrain pigs. The eleven genes were considered by real-time PCR for a time-course evaluation of the transcription level at six stages of prenatal longissimus dorsi development. The results suggest that the most relevant variations in mRNA levels of the analysed genes seem to follow temporal waves of gene expression. Significant changes of transcription were observed at 21-35 and 63-91 days, the two main phases of skeletal muscle development. During the early phases of Pietrain embryos' development, 10 of the 11 genes showed an induction. In Duroc embryos, a second phase of gene up-regulation can be identified in the phase 63-77 days. These results provide new data on developmental changes of expression profile of 11 genes involved in different functional pathways related to prenatal myogenic processes in Duroc and Pietrain pigs.
Collapse
Affiliation(s)
- R Davoli
- DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Villa Levi-Coviolo, Reggio Emilia, Italy.
| | | | | | | | | |
Collapse
|
26
|
Jiang C, Shi P, Li S, Dong R, Tian J, Wei J, Luo S. Gene expression profiling of skeletal muscle of nursing piglets. Int J Biol Sci 2010; 6:627-38. [PMID: 20975821 PMCID: PMC2962265 DOI: 10.7150/ijbs.6.627] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 09/30/2010] [Indexed: 12/31/2022] Open
Abstract
To gain insight into the regulation mechanism associated with the rapid gain in skeletal muscle during neonatal period, gene expression profiles of skeletal muscle of nursing pigs was investigated using Affymetrix Porcine GeneChip. A total of 1094 transcripts were detected as differential expression over time course tested (p<0.01, q<0.05). With combinative use of partitioning around medoid and hierarchical clustering, three clusters of transcripts with distinct temporal expression were defined. Gene functional categories and pathways, particularly involved in cell signaling, cell cycle, cell adhesion, ECM-receptor interaction, glycolysis, protein synthesis and degradation, and intracellular transport, were identified. Moreover, we showed 49 of the differentially expressed genes within published QTL regions or with marked deletion effects. Our study demonstrates previously uncharacterized changes in transcription accompanying early postnatal growth of skeletal muscle of pigs. It has highlighted potential cascades and important candidates for further investigation on controlling of postnatal muscle growth.
Collapse
Affiliation(s)
- Caode Jiang
- School of Life Science, Southwest University, Chongqing 400715, China.
| | | | | | | | | | | | | |
Collapse
|
27
|
Comparative studies of skeletal muscle proteome and transcriptome profilings between pig breeds. Mamm Genome 2010; 21:307-19. [DOI: 10.1007/s00335-010-9264-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Accepted: 03/31/2010] [Indexed: 10/19/2022]
|
28
|
Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat Sci 2010; 86:440-50. [PMID: 20573458 DOI: 10.1016/j.meatsci.2010.05.031] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 11/29/2009] [Accepted: 05/14/2010] [Indexed: 02/06/2023]
Abstract
The objective of this study was to compare the differences of gene expression profiles between intramuscular and subcutaneous adipocytes originated from the isolated preadipocytes in vitro. Cytosolic triglyceride determination indicated that subcutaneous adipocytes accumulated more lipid than intramuscular adipocytes did at the late stage of differentiation. Microarray assay revealed that 172 probes representing 133 genes were differentially expressed, among which 46 genes were highly expressed in intramuscular adipocytes and the other 87 genes were highly expressed in subcutaneous adipocytes. Real-time PCR confirmed that genes related to lipid metabolism, such as LPL, FABP4, FABP5 and OSBPL10, were predominantly expressed in subcutaneous adipocytes, whereas BMP4 and BMP7 were highly expressed in intramuscular adipocytes. The results indicated that the accumulation of lipid mass in subcutaneous adipocytes might be due to the highly expressed genes related to lipid metabolism, and the high levels of BMP4 and BMP7 in intramuscular adipocytes suggested that BMPs might be involved in the differentiation of intramuscular adipocytes.
Collapse
|
29
|
Changes in white muscle transcriptome induced by dietary energy levels in two lines of rainbow trout (Oncorhynchus mykiss) selected for muscle fat content. Br J Nutr 2009; 103:629-42. [PMID: 19874644 DOI: 10.1017/s0007114509992340] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Energy intake and genetic background are major determinants of muscle fat content in most animals, including man. We combined genetic selection and dietary energy supply to study the metabolic pathways involved in genetic and nutritional control of fat deposition in the muscle of rainbow trout (Oncorhynchus mykiss). Two experimental lines of rainbow trout, selected for lean (L) or fat (F) muscle, were fed with diets containing either 10 or 23 % lipids from the first feeding, up to 6 months. At the end of the trial, trout exhibited very different values of muscle fat content (from 4.2 to 10.1 % wet weight). Using microarrays made from a rainbow trout multi-tissue cDNA library, we analysed the molecular changes occurring in the muscle of the two lines when fed the low-energy or high-energy diet. The results from microarray analysis revealed that eleven metabolism-related genes were differentially expressed according to the diet while selection resulted in expression change for twenty-six genes. The most striking observation was the increased level of transcripts encoding the VLDL receptor and fatty acid translocase/CD36 following both the high-fat diet and upward selection for muscle fat content, suggesting that these two genes are relevant molecular markers of fat deposition in the white muscle of rainbow trout.
Collapse
|
30
|
Xu YJ, Jin ML, Wang LJ, Zhang AD, Zuo B, Xu DQ, Ren ZQ, Lei MG, Mo XY, Li FE, Zheng R, Deng CY, Xiong YZ. Differential proteome analysis of porcine skeletal muscles between Meishan and Large White1. J Anim Sci 2009; 87:2519-27. [DOI: 10.2527/jas.2008-1708] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
31
|
Specific proteins allow classification of pigs according to sire breed, rearing environment and gender. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
32
|
Almeida AM, van Harten S, Campos A, Coelho AV, Cardoso LA. The effect of weight loss on protein profiles of gastrocnemius muscle in rabbits: a study using 1D electrophoresis and peptide mass fingerprinting. J Anim Physiol Anim Nutr (Berl) 2009; 94:174-85. [PMID: 19175456 DOI: 10.1111/j.1439-0396.2008.00897.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The study of physiological changes occurring during selection contributes to an improved understanding of relationships leading to efficiencies in animal production. To investigate the effects of food restriction in gastrocnemius muscle protein expression, 20% weight reduction was induced in New Zealand White (meat producing) and wild rabbits, using one-dimensional gel electrophoresis and peptide mass fingerprinting. Lower expression levels of myosin heavy chains were found in the Wild Rabbits Restricted Group, while myosin light chain and alpha-crystallin proteins were not detected in restricted groups. Glyceraldeyde-3-phosphate dehydrogenase and glycogen phosphorylase expression levels were similar for all experimental groups. Phosphopyruvate hydratase beta was not detected in the wild rabbit restricted diet group. Pyruvate kinase levels were 50% lower in the New Zealand Restricted group. LIM protein detection was absent in the control New Zealand group. Results also show relevance of actin in preserving muscle structure in depressed food availability, the sensitivity of both myosin light chain and alpha-crystallin protein to restricted feed and the role of PK in the resistance of New Zealand rabbits to food restriction.
Collapse
Affiliation(s)
- A M Almeida
- Instituto de Investigação Científica Tropical & Centro Interdisciplinar de Investigação em Sanidade Animal, Lisboa, Portugal.
| | | | | | | | | |
Collapse
|
33
|
Ponsuksili S, Murani E, Phatsara C, Jonas E, Walz C, Schwerin M, Schellander K, Wimmers K. Expression profiling of muscle reveals transcripts differentially expressed in muscle that affect water-holding capacity of pork. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2008; 56:10311-10317. [PMID: 18922009 DOI: 10.1021/jf800881y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To identify biological processes as well as molecular markers for drip loss, a parameter for water holding capacity of meat, the M. longissimus dorsi transcriptomes of six divergent sib pairs were analyzed using Affymetrix Porcine Genome Array. Functional categories of differentially regulated transcripts were determined by single-gene analysis and gene set analysis. The transcripts being up-regulated at high drip loss belong to groups of genes functionally categorized as genes of membrane proteins, signal transduction, cell communication, response to stimulus, and cytoskeleton. Among genes down-regulated with high drip loss, functional groups of oxidoreductase activity, lipid metabolism, and electron transport were identified. Differential regulation of the abundance of transcripts of these biological networks in live muscle affect mortem biochemical processes of meat maturation. Knowledge of this functional link is indicative for the identification of candidate genes for improvement of meat quality.
Collapse
Affiliation(s)
- Siriluck Ponsuksili
- Research Institute for the Biology of Farm Animals (FBN), Research Group Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Hollung K, Grove H, Færgestad EM, Sidhu MS, Berg P. Comparison of muscle proteome profiles in pure breeds of Norwegian Landrace and Duroc at three different ages. Meat Sci 2008; 81:487-92. [PMID: 20416601 DOI: 10.1016/j.meatsci.2008.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/19/2008] [Accepted: 10/02/2008] [Indexed: 11/30/2022]
Abstract
We have used proteomics as a tool to unravel the changes in protein composition between two pure pig breeds and three age groups. Forty two female pigs of Norwegian Landrace and Duroc breed slaughtered at 6, 9 and 12 months age were included in the study. Each of the breeds was raised in separate farms and was slaughtered at the same day in a commercial abattoir. A sample from the adductor muscle was collected approximately 45min postmortem. Proteome analyses of the water soluble proteins using 2D electrophoresis showed that of the 1125 analyzed protein spots, 94 and 41 proteins are changed in abundance according to breed and age, respectively. A total of 63 changed proteins were identified by mass spectrometry. The identified proteins were classified as structural proteins, metabolic proteins, stress/defense proteins and other proteins. This demonstrates a difference in metabolism and muscle composition between breeds and age groups and shows that proteomics is a useful tool to uncover the molecular basis for physiological differences in muscles between pig breeds and age groups.
Collapse
Affiliation(s)
| | - Harald Grove
- Matforsk AS, Nofima Food, Osloveien 1, N-1430 Ås, Norway
| | | | - Maan Singh Sidhu
- Animalia - The Norwegian Meat and Poultry Research Centre, P.O. Box 396, Økern, N-0513 Oslo, Norway
| | - Per Berg
- Animalia - The Norwegian Meat and Poultry Research Centre, P.O. Box 396, Økern, N-0513 Oslo, Norway
| |
Collapse
|
35
|
Li X, Yang X, Shan B, Shi J, Xia D, Wegner J, Zhao R. Meat quality is associated with muscle metabolic status but not contractile myofiber type composition in premature pigs. Meat Sci 2008; 81:218-23. [PMID: 22063985 DOI: 10.1016/j.meatsci.2008.07.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2008] [Revised: 07/19/2008] [Accepted: 07/22/2008] [Indexed: 12/24/2022]
Abstract
Longissimus muscles were sampled from Erhualian (EHL) and Pietrain (PIE) pigs at 20kg of body weight. No breed differences were detected in either the proportions or the mRNA/protein expression of respective MyHC isoforms, or the mRNA expression of PGC-1α (all P>0.10). However, meat quality traits were already divergent between breeds, and were associated with distinct energy metabolic status, as reflected by dramatically lower AMPK activity yet higher CK and LDH activities (all P<0.01) in longissimus muscle of EHL pigs. Moreover, mRNA expression of glucocorticoid receptor (GR) was found to be higher (P<0.05) in longissimus muscle of EHL pigs. These results indicate that the differences in meat quality traits occur early in premature pigs, and these are attributed to skeletal muscle energy metabolism and not contractile myofiber type composition. Breed-specific GR expression in muscle may be related to the pattern of energy metabolism and meat quality, yet the mechanism awaits further investigation.
Collapse
Affiliation(s)
- X Li
- Key Laboratory of Animal Physiology and Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China
| | | | | | | | | | | | | |
Collapse
|
36
|
Ferraz ALJ, Ojeda A, López-Béjar M, Fernandes LT, Castelló A, Folch JM, Pérez-Enciso M. Transcriptome architecture across tissues in the pig. BMC Genomics 2008; 9:173. [PMID: 18416811 PMCID: PMC2335121 DOI: 10.1186/1471-2164-9-173] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 04/16/2008] [Indexed: 11/24/2022] Open
Abstract
Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.
Collapse
Affiliation(s)
- André L J Ferraz
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | | | | | | | | | | | | |
Collapse
|
37
|
Comparisons of longissimus muscle metabolic enzymes and muscle fiber types in Korean and western pig breeds. Meat Sci 2008; 78:455-60. [DOI: 10.1016/j.meatsci.2007.07.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 07/11/2007] [Accepted: 07/12/2007] [Indexed: 11/19/2022]
|
38
|
Su CH, Hsieh BT, Leung SW, Wu CJ, Chiu SY, Lin CS. Increased expression of nuclear NF-kappaB after coronary artery balloon injury can be inhibited by intracoronary beta-irradiation. Int J Radiat Biol 2008; 83:707-16. [PMID: 17729165 DOI: 10.1080/09553000701596126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE Molecular mechanisms by which balloon angioplasty injury-induced neointimal hyperplasia can be reduced by intravascular brachytherapy are unclear. We investigated the role of nuclear factor-kappaB (NF-kappaB) in neointimal hyperplasia following intracoronary irradiation. MATERIALS AND METHODS Fifty-four coronary arteries from 30 pigs were divided into 6 groups: sham control, balloon angioplasty injury alone, beta-irradiation at doses of 14 or 20 Gy, and 14 or 20 Gy beta-irradiation immediately followed by balloon injury. Coronary arteries were injured by overstretch balloon angioplasty and then the arteries were irradiated using a Rhenium-188 ((188)Re) beta-emitting solution-filled balloon. Pigs were scarified one day or one week after coronary interventions for molecular detection and six weeks after the procedures for histological examination. RESULTS Six weeks after coronary interventions, the histological results show that balloon angioplasty injury had induced intimal hyperplasia in coronary artery but the response was significantly reduced by 28% and 60% when the injury was immediately treated by 14 and 20 Gy (188)Re beta-irradiation, respectively. The expression of arterial NF-kappaB p65, intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) were detected at one day and one week after the procedures. The treatment of balloon injury could significantly induce the NF-kappaB p65 expression in both gene and protein levels, and such induction could be significantly reduced by (188)Re beta-irradiation at dose of 20 Gy. However, the similar result on the regulation of gene expression affected by the beta-irradiation could not be observed in ICAM-1 and VCAM-1. CONCLUSION The inhibitory effect of intracoronary brachytherapy on neointimal formation following overstretch balloon angioplasty could involve inhibition of NF-kappaB p65.
Collapse
Affiliation(s)
- Chun-Hui Su
- Department Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | | | | | | | | | | |
Collapse
|
39
|
Jennen DGJ, Brings AD, Liu G, Jüngst H, Tholen E, Jonas E, Tesfaye D, Schellander K, Phatsara C. Genetic aspects concerning drip loss and water-holding capacity of porcine meat. J Anim Breed Genet 2007; 124 Suppl 1:2-11. [DOI: 10.1111/j.1439-0388.2007.00681.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
40
|
Lin CS, Kuo CL, Wang JP, Cheng JS, Huang ZW, Chen CF. Growth inhibitory and apoptosis inducing effect of Perilla frutescens extract on human hepatoma HepG2 cells. JOURNAL OF ETHNOPHARMACOLOGY 2007; 112:557-67. [PMID: 17574356 DOI: 10.1016/j.jep.2007.05.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 03/29/2007] [Accepted: 05/01/2007] [Indexed: 05/15/2023]
Abstract
Perilla frutescens (L.) Britt. (Lamiaceae) has traditionally been used to treat diseases, including tumors, but the antitumorigenesis mechanism is unclear. We evaluated the effects of Perilla frutescens leaf extract (PLE) on proliferation and apoptosis inducing in human hepatoma HepG2 cells using a cell proliferation assay, flow cytometry, and cDNA microarrays. Gene expression and apoptosis were also assessed in HepG2 cells treated with a major constituent of PLE, rosmarinic acid (RosA). In the PLE-treated HepG2 cells, antiproliferative activity (105 microg/mL) were observed, flow cytometry revealed significant apoptosis, and microarray data indicated that the expression of a lot apoptosis-related genes were regulated in a time-dependent manner. Compared with PLE, RosA (10 microg/mL; a dose equivalent to 105 microg/mL of PLE) was less effective in increasing the expression of apoptosis-related genes and apoptosis inducing in HepG2 cells. Thus, additional PLE constituents may influence apoptosis in HepG2 cells. The results of our study suggest that the PLE should be further investigated as a promising to treat hepatocellular carcinoma.
Collapse
Affiliation(s)
- Chih-Sheng Lin
- Department of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu 30050, Taiwan.
| | | | | | | | | | | |
Collapse
|
41
|
Lin CS, Lai LP, Lin JL, Sun YL, Hsu CW, Chen CL, Mao SJT, Huang SKS. Increased expression of extracellular matrix proteins in rapid atrial pacing-induced atrial fibrillation. Heart Rhythm 2007; 4:938-49. [PMID: 17599682 DOI: 10.1016/j.hrthm.2007.03.034] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 03/21/2007] [Indexed: 10/23/2022]
Abstract
BACKGROUND Atrial fibrillation (AF) is characterized by structural remodeling of the extracellular matrix (ECM) in cardiac atrium. OBJECTIVE The purpose of this study was to gain further insight into atrial ECM remodeling at the molecular level and to test whether altered expression of ECM proteins was associated with the disease. METHODS Sustained AF was induced in nine adult pigs after 3-4 weeks of continuous rapid atrial pacing at a rate of 600 bpm. Histologic studies and immunohistochemical stain were performed to identify the potential pathologic substrate underlying abnormalities in atrial tissues with sustained AF. RESULTS In the pathologic findings, the fraction of myocardial ECM (ECM%) was measured, with a significantly greater ECM% found in the AF group compared with the sham operated group (n = 6; i.e., pigs with normal sinus rhythm [SR]). A set of 9,182 genes was screened with cDNA microarray analysis. In AF animals, expression of 121 genes increased and 24 genes decreased by > or =1.75-fold compared with SR animals. Significant up-regulation of fibronectin-1 (4.9-fold), fibrillin-1 (3.1-fold), and fibromodulin (1.9-fold) in the fibrillating atria was confirmed by quantitative real-time reverse transcriptase-polymerase chain reaction. Western blot analysis revealed significantly increased atrial fibronectin-1, fibrillin-1, and fibromodulin in the AF group compared with the SR group (1.5-, 2.7-, and 2.1-fold, respectively). Immunohistochemical staining of AF tissue displayed increased accumulation of fibronectin-1 and fibrillin-1 in the atrial interstitial space. CONCLUSION Increased expression of ECM proteins in fibrillating atria supports the hypothesis that ECM metabolism contributes to the development of AF.
Collapse
Affiliation(s)
- Chih-Sheng Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Reecy JM, Spurlock DM, Stahl CH. Gene expression profiling: insights into skeletal muscle growth and development. J Anim Sci 2007; 84 Suppl:E150-4. [PMID: 16582087 DOI: 10.2527/2006.8413_supple150x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microarray technology is now available for many livestock species, and animal scientists are beginning to utilize the technology to address issues of importance to animal agriculture. This review discusses how microarray technology has been applied to study global gene expression changes in skeletal muscle. For example, microarrays have been used to elucidate gene function in knockout mice, evaluate breed differences, evaluate the effects of hormone administration, and evaluate the effects of diet. Data generated from these global gene expression studies are providing new insights to stimulate future hypothesis-driven research.
Collapse
Affiliation(s)
- J M Reecy
- Department of Animal Science, Iowa State University, Ames, 50011-3150, USA.
| | | | | |
Collapse
|
43
|
Chen CL, Lin JL, Lai LP, Pan CH, Huang SKS, Lin CS. Altered expression of FHL1, CARP, TSC-22 and P311 provide insights into complex transcriptional regulation in pacing-induced atrial fibrillation. Biochim Biophys Acta Mol Basis Dis 2007; 1772:317-29. [PMID: 17174532 DOI: 10.1016/j.bbadis.2006.10.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 10/23/2006] [Accepted: 10/24/2006] [Indexed: 11/28/2022]
Abstract
Atrial fibrillation (AF) is the most common progressive disease in patients with cardiac arrhythmia. AF is accompanied by complex atrial remodeling and changes in gene expression, but only a limited number of transcriptional regulators have been identified. Using a low-density cDNA array, we identified 31 genes involved in transcriptional regulation, signal transduction or structural components, which were either significantly upregulated or downregulated in porcine atria with fibrillation (induced by rapid atrial pacing at a rate of 400-600 bpm for 4 weeks that was then maintained without pacing for 2 weeks). The genes for four and a half LIM domains protein-1 (FHL1), transforming growth factor-beta (TGF-beta)-stimulated clone 22 (TSC-22), and cardiac ankyrin repeat protein (CARP) were significantly upregulated, and chromosome 5 open reading frame gene 13 (P311) was downregulated in the fibrillating atria. FHL1 and CARP play important regulatory roles in cardiac remodeling by transcriptional regulation and myofilament assembly. Induced mRNA expression of both FHL1 and CARP was also observed when cardiac H9c2 cells were treated with an adrenergic agonist. Increasing TSC-22 and marked P311 deficiency could enhance the activity of TGF-beta signaling and the upregulated TGF-beta1 and -beta2 expressions were identified in the fibrillating atria. These results implicate that observed alterations of underlying molecular events were involved in the rapid-pacing induced AF, possibly via activation of the beta-adrenergic and TGF-beta signaling.
Collapse
Affiliation(s)
- Chien-Lung Chen
- Department of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu 30005, Taiwan
| | | | | | | | | | | |
Collapse
|
44
|
Tuggle CK, Wang Y, Couture O. Advances in swine transcriptomics. Int J Biol Sci 2007; 3:132-52. [PMID: 17384733 PMCID: PMC1802012 DOI: 10.7150/ijbs.3.132] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 01/02/2007] [Indexed: 01/23/2023] Open
Abstract
The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.
Collapse
Affiliation(s)
- Christopher K Tuggle
- Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
| | | | | |
Collapse
|
45
|
Pan CH, Lin JL, Lai LP, Chen CL, Stephen Huang SK, Lin CS. Downregulation of angiotensin converting enzyme II is associated with pacing-induced sustained atrial fibrillation. FEBS Lett 2007; 581:526-34. [PMID: 17254576 DOI: 10.1016/j.febslet.2007.01.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Accepted: 01/04/2007] [Indexed: 11/16/2022]
Abstract
Atrial fibrillation (AF), the most common cardiac arrhythmia, is frequently accompanied by atrial interstitial fibrosis. Angiotensin II (Ang II) dependent signaling pathways have been implicated in interstitial fibrosis during the development of AF. However, Ang II could be further degraded by angiotensin converting enzyme II (ACE2). We examined expression of ACE2 in the fibrillating atria of pigs and its involvement in fibrotic pathogenesis during AF. Nine adult pigs underwent continuous rapid atrial pacing to induce sustained AF and six pigs were sham controls (i.e., sinus rhythm; SR). In the histological examinations, extensive accumulation of extracellular matrix in the interstitial space of the atria, as evidenced by Masson's trichrome stain, were found in fibrillating atria. The relative amount of collagen type I in the atria with AF was significantly increased as compared with that in the SR. Local ACE activity in the fibrillating atria was also markedly higher than that in the SR subjects. ACE2 gene and protein expression in the AF subjects were significantly decreased compared with those in the SR subjects, whereas expression of mitogen-activated/ERK kinase 1/2 (MEK1/2), extracellular signal-regulated protein kinase 2 (ERK2), and activated ERK2 were significantly greater in the AF subjects. We propose that decreasing ACE2 expression during AF may affect the Ang II-dependent signaling pathway. In addition, our results suggest that atrial fibrosis in AF may be induced by antagonistic regulation between ACE and ACE2 expression.
Collapse
Affiliation(s)
- Chun-Hsu Pan
- Department of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu 30005, Taiwan
| | | | | | | | | | | |
Collapse
|
46
|
Recent advances in cattle functional genomics and their application to beef quality. Animal 2007; 1:159-73. [DOI: 10.1017/s1751731107658042] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
47
|
Guan HY, Tang ZQ, Li H. Correlation analysis between single-nucleotide polymorphism of malate dehydrogenase gene 5'-flanking region and growth and body composition traits in chicken. YI CHUAN XUE BAO = ACTA GENETICA SINICA 2006; 33:501-6. [PMID: 16800380 DOI: 10.1016/s0379-4172(06)60078-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Malate dehydrogenase (MD) is a key enzyme that plays an important role in energy metabolism. It catalyzes the oxidative decarboxylation of L-malate to yield CO2 and pyruvate, while simultaneously generating NADPH from NADP+. The NADPH generated can be utilized in de novo synthesis of palmitate, which is the precursor molecule for the formation of other long-chain fatty acids. And high levels of MD will also activate muscle development. The current study was designed to investigate the effects of MD gene on growth and body-composition traits in chicken. The eighth generation population of Northeast Agricultural University broiler lines divergently selected for its abdominal fat and Northeast Agricultural University F2 resource population were used in the research. Polymorphisms were detected by DNA sequencing and PCR-RFLP method was then developed to screen the population. A single mutation at the position of the 235 bp (Accession No. U49693) of MD 5'-flanking region was found. The correlation analysis between the polymorphism of the MD gene and growth and body composition traits was carried out using the appropriate statistic model. Least-square analysis showed that the BB genotype birds had much higher pectoralis major weight and percentage of pectoralis major than AA genotype birds (P<0.05). The abdominal fat weight, percentage of abdominal fat, the liver weight and percentage of liver weight of the AA genotype birds were much higher than those of BB genotype birds (P<0.05). These results indicate that MD gene is the major gene or is linked to the major gene that affects the growth and body composition traits in chicken.
Collapse
Affiliation(s)
- Hong-Ying Guan
- College of Animal Science, Northeast Agricultural University, Harbin, China
| | | | | |
Collapse
|