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Mohan NH, Pathak P, Buragohain L, Deka J, Bharati J, Das AK, Thomas R, Singh R, Sarma DK, Gupta VK, Das BC. Comparative muscle transcriptome of Mali and Hampshire breeds of pigs: a preliminary study. Anim Biotechnol 2023; 34:3946-3961. [PMID: 37587839 DOI: 10.1080/10495398.2023.2244988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Muscle development is an important priority of pig breeding programs. There is a considerable variation in muscularity between the breeds, but the regulation mechanisms of genes underlying myogenesis are still unclear. Transcriptome data from two breeds of pigs with divergent muscularity (Mali and Hampshire) were integrated with histology, immunofluorescence and meat yield to identify differences in myogenesis during the early growth phase. The muscle transcriptomics analysis revealed 17,721 common, 1413 and 1115 unique transcripts to Hampshire and Mali, respectively. This study identified 908 differentially expressed genes (p < 0.05; log2FC > ±1) in the muscle samples, of which 550 were upregulated and 358 were downregulated in Hampshire pigs, indicating differences in physiological process related to muscle function and development. Expression of genes related to myoblast fusion (MYMK), skeletal muscle satellite cell proliferation (ANGPT1, CDON) and growth factors (HGF, IGF1, IGF2) were higher in Hampshire than Mali, even though transcript levels of several other myogenesis-related genes (MYF6, MYOG, MSTN) were similar. The number of fibers per fascicle and the expression of myogenic marker proteins (MYOD1, MYOG and PAX7) were more in Hampshire as compared to Mali breed of pig, supporting results of transcriptome studies. The results suggest that differences in muscularity between breeds could be related to the regulation of myoblast fusion and myogenic activities. The present study will help to identify genes that could be explored for their utility in the selection of animals with different muscularities.
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Affiliation(s)
| | | | | | - Juri Deka
- ICAR-National Research Centre on Pig, Guwahati, Assam, India
| | - Jaya Bharati
- ICAR-National Research Centre on Pig, Guwahati, Assam, India
| | - Anil Kumar Das
- ICAR-National Research Centre on Pig, Guwahati, Assam, India
| | | | - Rajendra Singh
- ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
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2
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Wang C, Lei B, Liu Y. An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits. Animals (Basel) 2023; 13:3581. [PMID: 38003198 PMCID: PMC10668843 DOI: 10.3390/ani13223581] [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: 09/30/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The development and growth of porcine skeletal muscle determine pork quality and yield. While genetic regulation of porcine skeletal muscle development has been extensively studied using various omics data, the role of transposable elements (TEs) in this context has been less explored. To bridge this gap, we constructed a comprehensive atlas of TE expression throughout the developmental stages of porcine skeletal muscle. This was achieved by integrating porcine TE genomic coordinates with whole-transcriptome RNA-Seq data from 27 developmental stages. We discovered that in pig skeletal muscle, active Tes are closely associated with active epigenomic marks, including low levels of DNA methylation, high levels of chromatin accessibility, and active histone modifications. Moreover, these TEs include 6074 self-expressed TEs that are significantly enriched in terms of muscle cell development and myofibril assembly. Using the TE expression data, we conducted a weighted gene co-expression network analysis (WGCNA) and identified a module that is significantly associated with muscle tissue development as well as genome-wide association studies (GWAS) of the signals of pig meat and carcass traits. Within this module, we constructed a TE-mediated gene regulatory network by adopting a unique multi-omics integration approach. This network highlighted several established candidate genes associated with muscle-relevant traits, including HES6, CHRNG, ACTC1, CHRND, MAMSTR, and PER2, as well as novel genes like ENSSSCG00000005518, ENSSSCG00000033601, and PIEZO2. These novel genes hold promise for regulating muscle-related traits in pigs. In summary, our research not only enhances the TE-centered dissection of the genetic basis underlying pork production traits, but also offers a general approach for constructing TE-mediated regulatory networks to study complex traits or diseases.
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Affiliation(s)
- Chao Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.W.); (B.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bowen Lei
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.W.); (B.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.W.); (B.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China
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3
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Ai Y, Zhu Y, Wang L, Zhang X, Zhang J, Long X, Gu Q, Han H. Dynamic Changes in the Global Transcriptome of Postnatal Skeletal Muscle in Different Sheep. Genes (Basel) 2023; 14:1298. [PMID: 37372481 DOI: 10.3390/genes14061298] [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: 05/18/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Sheep growth performance, mainly skeletal muscle growth, provides direct economic benefits to the animal husbandry industry. However, the underlying genetic mechanisms of different breeds remain unclear. We found that the cross-sectional area (CSA) of skeletal muscle in Dorper (D) and binary cross-breeding (HD) was higher than that in Hu sheep (H) from 3 months to 12 months after birth. The transcriptomic analysis of 42 quadriceps femoris samples showed that a total of 5053 differential expression genes (DEGs) were identified. The differences in the global gene expression patterns, the dynamic transcriptome of skeletal muscle development, and the transcriptome of the transformation of fast and slow muscles were explored using weighted correlation network analysis (WGCNA) and allele-specific expression analysis. Moreover, the gene expression patterns of HD were more similar to D rather than H from 3 months to 12 months, which might be the reason for the difference in muscle growth in the three breeds. Additionally, several genes (GNB2L1, RPL15, DVL1, FBXO31, etc.) were identified as candidates related to skeletal muscle growth. These results should serve as an important resource revealing the molecular basis of muscle growth and development in sheep.
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Affiliation(s)
- Yue Ai
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yaning Zhu
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Linli Wang
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaosheng Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin 301700, China
| | - Jinlong Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin 301700, China
| | - Xianlei Long
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingyi Gu
- Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongbing Han
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Zhang X, Li Y, Zhu C, Li F, Liu Z, Li X, Shen X, Wu Z, Fu M, Xu D, Tian Y, Huang Y. DNA Demethylation of Myogenic Genes May Contribute to Embryonic Leg Muscle Development Differences between Wuzong and Shitou Geese. Int J Mol Sci 2023; 24:ijms24087188. [PMID: 37108353 PMCID: PMC10138404 DOI: 10.3390/ijms24087188] [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: 02/21/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Skeletal muscle development from embryonic stages to hatching is critical for poultry muscle growth, during which DNA methylation plays a vital role. However, it is not yet clear how DNA methylation affects early embryonic muscle development between goose breeds of different body size. In this study, whole genome bisulfite sequencing (WGBS) was conducted on leg muscle tissue from Wuzong (WZE) and Shitou (STE) geese on embryonic day 15 (E15), E23, and post-hatch day 1. It was found that at E23, the embryonic leg muscle development of STE was more intense than that of WZE. A negative correlation was found between gene expression and DNA methylation around transcription start sites (TSSs), while a positive correlation was observed in the gene body near TTSs. It was also possible that earlier demethylation of myogenic genes around TSSs contributes to their earlier expression in WZE. Using pyrosequencing to analyze DNA methylation patterns of promoter regions, we also found that earlier demethylation of the MyoD1 promoter in WZE contributed to its earlier expression. This study reveals that DNA demethylation of myogenic genes may contribute to embryonic leg muscle development differences between Wuzong and Shitou geese.
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Affiliation(s)
- Xumeng Zhang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yong Li
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Chenyu Zhu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Fada Li
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhiyuan Liu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xiujin Li
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xu Shen
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhongping Wu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Mengsi Fu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Danning Xu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunbo Tian
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunmao Huang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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Corbett RJ, Ford LM, Raney NE, Grabowski JM, Ernst CW. Pig fetal skeletal muscle development is associated with genome-wide DNA hypomethylation and corresponding alterations in transcript and microRNA expression. Genome 2023; 66:68-79. [PMID: 36876850 DOI: 10.1139/gen-2022-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Fetal myogenesis represents a critical period of porcine skeletal muscle development and requires coordinated expression of thousands of genes. Epigenetic mechanisms, including DNA methylation, drive transcriptional regulation during development; however, these processes are understudied in developing porcine tissues. We performed bisulfite sequencing to assess DNA methylation in pig longissimus dorsi muscle at 41- and 70-days gestation (dg), as well as RNA- and small RNA-sequencing to identify coordinated changes in methylation and expression between myogenic stages. We identified 45 739 differentially methylated regions (DMRs) between stages, and the majority (N = 34 232) were hypomethylated at 70 versus 41 dg. Integration of methylation and transcriptomic data revealed strong associations between differential gene methylation and expression. Differential miRNA methylation was significantly negatively correlated with abundance, and dynamic expression of assayed miRNAs persisted postnatally. Motif analysis revealed significant enrichment of myogenic regulatory factor motifs among hypomethylated regions, suggesting that DNA hypomethylation may function to increase accessibility of muscle-specific transcription factors. We show that developmental DMRs are enriched for GWAS SNPs for muscle- and meat-related traits, demonstrating the potential for epigenetic processes to influence phenotypic diversity. Our results enhance understanding of DNA methylation dynamics of porcine myogenesis and reveal putative cis-regulatory elements governed by epigenetic processes.
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Affiliation(s)
- R J Corbett
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - L M Ford
- Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - N E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - J M Grabowski
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - C W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
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Cai S, Hu B, Wang X, Liu T, Lin Z, Tong X, Xu R, Chen M, Duo T, Zhu Q, Liang Z, Li E, Chen Y, Li J, Liu X, Mo D. Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig. BMC Biol 2023; 21:19. [PMID: 36726129 PMCID: PMC9893630 DOI: 10.1186/s12915-023-01519-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Skeletal muscle development is a multistep process whose understanding is central in a broad range of fields and applications, from the potential medical value to human society, to its economic value associated with improvement of agricultural animals. Skeletal muscle initiates in the somites, with muscle precursor cells generated in the dermomyotome and dermomyotome-derived myotome before muscle differentiation ensues, a developmentally regulated process that is well characterized in model organisms. However, the regulation of skeletal muscle ontogeny during embryonic development remains poorly defined in farm animals, for instance in pig. Here, we profiled gene expression and chromatin accessibility in developing pig somites and myotomes at single-cell resolution. RESULTS We identified myogenic cells and other cell types and constructed a differentiation trajectory of pig skeletal muscle ontogeny. Along this trajectory, the dynamic changes in gene expression and chromatin accessibility coincided with the activities of distinct cell type-specific transcription factors. Some novel genes upregulated along the differentiation trajectory showed higher expression levels in muscular dystrophy mice than that in healthy mice, suggesting their involvement in myogenesis. Integrative analysis of chromatin accessibility, gene expression data, and in vitro experiments identified EGR1 and RHOB as critical regulators of pig embryonic myogenesis. CONCLUSIONS Collectively, our results enhance our understanding of the molecular and cellular dynamics in pig embryonic myogenesis and offer a high-quality resource for the further study of pig skeletal muscle development and human muscle disease.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Bin Hu
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tongni Liu
- Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Zhuhu Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Rong Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Meilin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Qi Zhu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Ziyun Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Enru Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Jianhao Li
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
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7
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Haplotypes within the regulatory region of MYL4 are associated with pig muscle fiber size. Gene 2023; 850:146934. [DOI: 10.1016/j.gene.2022.146934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
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Crespo-Piazuelo D, Acloque H, González-Rodríguez O, Mongellaz M, Mercat MJ, Bink MCAM, Huisman AE, Ramayo-Caldas Y, Sánchez JP, Ballester M. Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues. Gigascience 2022; 12:giad042. [PMID: 37354463 PMCID: PMC10290502 DOI: 10.1093/gigascience/giad042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/13/2023] [Accepted: 05/25/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle. RESULTS More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region. CONCLUSIONS The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.
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Affiliation(s)
- Daniel Crespo-Piazuelo
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
| | - Hervé Acloque
- GABI, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas (78350), France
| | | | - Mayrone Mongellaz
- GABI, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas (78350), France
| | | | - Marco C A M Bink
- Hendrix Genetics Research Technology & Services B.V., Boxmeer (5830 AC), The Netherlands
| | | | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
| | - Juan Pablo Sánchez
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui (08140), Spain
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Wang X, Wang L, Shi L, Zhang P, Li Y, Li M, Tian J, Wang L, Zhao F. GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data. Int J Mol Sci 2022; 23:13338. [PMID: 36362120 PMCID: PMC9656588 DOI: 10.3390/ijms232113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 12/09/2023] Open
Abstract
Total number born (TNB), number of stillborn (NSB), and gestation length (GL) are economically important traits in pig production, and disentangling the molecular mechanisms associated with traits can provide valuable insights into their genetic structure. Genotype imputation can be used as a practical tool to improve the marker density of single-nucleotide polymorphism (SNP) chips based on sequence data, thereby dramatically improving the power of genome-wide association studies (GWAS). In this study, we applied Beagle software to impute the 50 K chip data to the whole-genome sequencing (WGS) data with average imputation accuracy (R2) of 0.876. The target pigs, 2655 Large White pigs introduced from Canadian and French lines, were genotyped by a GeneSeek Porcine 50K chip. The 30 Large White reference pigs were the key ancestral individuals sequenced by whole-genome resequencing. To avoid population stratification, we identified genetic variants associated with reproductive traits by performing within-population GWAS and cross-population meta-analyses with data before and after imputation. Finally, several genes were detected and regarded as potential candidate genes for each of the traits: for the TNB trait: NOTCH2, KLF3, PLXDC2, NDUFV1, TLR10, CDC14A, EPC2, ORC4, ACVR2A, and GSC; for the NSB trait: NUB1, TGFBR3, ZDHHC14, FGF14, BAIAP2L1, EVI5, TAF1B, and BCAR3; for the GL trait: PPP2R2B, AMBP, MALRD1, HOXA11, and BICC1. In conclusion, expanding the size of the reference population and finding an optimal imputation strategy to ensure that more loci are obtained for GWAS under high imputation accuracy will contribute to the identification of causal mutations in pig breeding.
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Affiliation(s)
- Xiaoqing Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ligang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Liangyu Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Laboratory of Genetic Breeding, Reproduction and Precision Livestock Farming, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Pengfei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mianyan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jingjing Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Genetic regulation and variation of expression of miRNA and mRNA transcripts in fetal muscle tissue in the context of sex, dam and variable fetal weight. Biol Sex Differ 2022; 13:24. [PMID: 35550009 PMCID: PMC9103043 DOI: 10.1186/s13293-022-00433-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Impaired skeletal muscle growth in utero can result in reduced birth weight and pathogenesis of intrauterine growth restriction. Fetal and placental growth is influenced by many factors including genetic, epigenetic and environmental factors. In fact, the sex and genotype of the fetus itself, as well as the mother providing it with a suitable environment, influence the growth of the fetus. Hence, our goal was to decipher and elucidate the molecular pathways of developmental processes mediated by miRNAs and mRNAs in fetal muscle tissue in the context of sex, dam, and fetal weight. Therefore, we analyse the variation of miRNA and mRNA expression in relation to these factors. In addition, the coincidence of genetic regulation of these mRNAs and miRNAs, as revealed by expression quantitative trait loci (eQTL) analyses, with sex-, mother- and weight-associated expression was investigated. METHODS A three-generation pig F2 population (n = 118) based on reciprocal crossing of German Landrace (DL) and Pietrain (Pi) was used. Genotype information and transcriptomic data (mRNA and miRNA) from longissimus dorsi muscle (LDM) of pig fetuses sampled at 63 days post-conception (dpc) were used for eQTL analyses. RESULTS The transcript abundances of 13, 853, and 275 probe-sets were influenced by sex, dam and fetal weight at 63 dpc, respectively (FDR < 5%). Most of significant transcripts affected by sex were located on the sex chromosomes including KDM6A and ANOS1 or autosomes including ANKS1B, LOC100155138 and miR-153. The fetal muscle transcripts associated with fetal weight indicated clearer metabolic directions than maternally influenced fetal muscle transcripts. Moreover, coincidence of genetic regulation (eQTL) and variation in transcript abundance due to sex, dam and fetal weight were identified. CONCLUSIONS Integrating information on eQTL, sex-, dam- and weight-associated differential expression and QTL for fetal weight allowed us to identify molecular pathways and shed light on the basic biological processes associated with differential muscle development in males and females, with implications for adaptive fetal programming.
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Dey P, Soyer MA, Dey BK. MicroRNA-24-3p promotes skeletal muscle differentiation and regeneration by regulating HMGA1. Cell Mol Life Sci 2022; 79:170. [PMID: 35238991 PMCID: PMC11072726 DOI: 10.1007/s00018-022-04168-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 11/30/2022]
Abstract
Numerous studies have established the critical roles of microRNAs in regulating post-transcriptional gene expression in diverse biological processes. Here, we report on the role and mechanism of miR-24-3p in skeletal muscle differentiation and regeneration. miR-24-3p promotes myoblast differentiation and skeletal muscle regeneration by directly targeting high mobility group AT-hook 1 (HMGA1) and regulating it and its direct downstream target, the inhibitor of differentiation 3 (ID3). miR-24-3p knockdown in neonatal mice increases PAX7-positive proliferating muscle stem cells (MuSCs) by derepressing Hmga1 and Id3. Similarly, inhibition of miR-24-3p in the tibialis anterior muscle prevents Hmga1 and Id3 downregulation and impairs regeneration. These findings provide evidence that the miR-24-3p/HMGA1/ID3 axis is required for MuSC differentiation and skeletal muscle regeneration in vivo.
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Affiliation(s)
- Paromita Dey
- The RNA Institute, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Miles A Soyer
- The RNA Institute, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Bijan K Dey
- The RNA Institute, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA.
- Department of Biological Sciences, University at Albany, State University of New York (SUNY), 1400 Washington Avenue, Albany, NY, 12222, USA.
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12
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Wang Y, Wang J, Hu H, Wang H, Wang C, Lin H, Zhao X. Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development. BMC Genom Data 2021; 22:32. [PMID: 34488628 PMCID: PMC8419915 DOI: 10.1186/s12863-021-00984-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 08/02/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing. RESULTS According to the pairwise comparisons between the libraries of the muscle samples at the four postnatal stages, a total of 4115 differentially expressed genes (DEGs) were identified in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01. Short-time series expression miner (STEM) analysis of the DEGs identified eight significantly different expression profiles, which were divided into two clusters based on the expression pattern. DEGs in cluster I displayed a pattern of decreasing to a nadir, and then a rise, and the significantly enriched gene ontology (GO) terms detected using them were involved in multiple processes, of which the cell cycle, immunocyte activation and proliferation, as well as actin cytoskeleton organization, were the top three overrepresented processes based on the GO terms functional classification. DEGs in cluster II displayed a pattern of increasing to a peak, then declining, which mainly contributed to protein metabolism. Furthermore, besides the pathways related to immune system, a few diseases, and protein metabolism, the DEGs in clusters I and II were significantly enriched in pathways related to muscle growth and development, such as the Rap1, PI3K-Akt, AMPK, and mTOR signaling pathways. CONCLUSIONS This study revealed GO terms and pathways that could affect the postnatal muscle growth and development in piglets. In addition, this study provides crucial information concerning the molecular mechanisms of muscle growth and development as well as an overview of the piglet transcriptome dynamics throughout the postnatal period in terms of growth and development.
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Affiliation(s)
- Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Huaizhong Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Cheng Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Haichao Lin
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China.
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Ali A, Murani E, Hadlich F, Liu X, Wimmers K, Ponsuksili S. Prenatal Skeletal Muscle Transcriptome Analysis Reveals Novel MicroRNA-mRNA Networks Associated with Intrauterine Growth Restriction in Pigs. Cells 2021; 10:cells10051007. [PMID: 33923344 PMCID: PMC8145024 DOI: 10.3390/cells10051007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Intrauterine growth restriction (IUGR) occurs in 15–20% of pig neonates and poses huge economic losses to the pig industry. IUGR piglets have reduced skeletal muscle growth, which may persist after birth. Prenatal muscle growth is regulated by complex molecular pathways that are not well understood. MicroRNAs (miRNAs) have emerged as the main regulators of vital pathways and biological processes in the body. This study was designed to identify miRNA–mRNA networks regulating prenatal skeletal muscle development in pigs. We performed an integrative miRNA–mRNA transcriptomic analysis in longissimus dorsi muscle from IUGR fetuses and appropriate for gestational age (AGA) fetuses at 63 days post conception. Our data showed that 47 miRNAs and 3257 mRNAs were significantly upregulated, and six miRNAs and 477 mRNAs were significantly downregulated in IUGR compared to AGA fetuses. Moreover, 47 upregulated miRNAs were negatively correlated and can potentially target 326 downregulated genes, whereas six downregulated miRNAs were negatively correlated and can potentially target 1291 upregulated genes. These miRNA–mRNA networks showed enrichment in biological processes and pathways critical for fetal growth, development, and metabolism. The miRNA–mRNA networks identified in this study can potentially serve as indicators of prenatal fetal growth and development as well as postnatal carcass quality.
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Affiliation(s)
- Asghar Ali
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Xuan Liu
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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Li X, Xie S, Qian L, Cai C, Bi H, Cui W. Identification of genes related to skeletal muscle growth and development by integrated analysis of transcriptome and proteome in myostatin-edited Meishan pigs. J Proteomics 2020; 213:103628. [DOI: 10.1016/j.jprot.2019.103628] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/08/2019] [Accepted: 12/22/2019] [Indexed: 12/29/2022]
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15
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Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs. PLoS One 2020; 15:e0227861. [PMID: 31990923 PMCID: PMC6986718 DOI: 10.1371/journal.pone.0227861] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.
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Expression of apoptosis and myogenesis related genes during prenatal life in two divergent breeds of pigs. Theriogenology 2020; 145:67-76. [PMID: 32004820 DOI: 10.1016/j.theriogenology.2020.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 12/05/2019] [Accepted: 01/16/2020] [Indexed: 11/24/2022]
Abstract
We aimed to evaluate apoptosis and myogenesis related genes expression in embryos and fetuses from two divergent genetic groups of pigs: Piau breed and a commercial line. Thirty females (15 Piau and 15 commercial line) were selected at 120 days of age. Estrous cycle was observed and on the third estrus females were considered sexually mature. Gilts were inseminated with semen from males of the respective breed. Three females from each breed were slaughtered at five different gestational ages: 15, 30, 45, 60 and 90 days. Whole embryos (15 and 30 d) and samples of longissimus dorsi muscle from fetuses (45, 60 and 90 d) were collected for RNA extraction. Expression of apoptosis and myogenesis related genes (BAX, BCL2, FGF4, IHH, HHIP, SHH, SOX2, WNT1 and WNT4) were evaluated by quantitative real time PCR. There was significant effect of interaction between breeds and gestational ages for all genes evaluated (P < 0.05). The BCL2 gene expression differed throughout pregnancy in Piau group with lower expression on day 15. The IHH gene expression throughout pregnancy was lower on days 15 and 60 in Piau group and lower on day 90 in commercial line group; and the SHH gene expression throughout pregnancy was higher on day 30 and lower on day 60 in Piau group and lower on day 45 in commercial group. The WNT1 gene expression along pregnancy was lower on day 15 and higher on days 30 and 45 in Piau group, and it was higher on day 30 than days 15 and 60 in commercial group. WNT4 gene expression throughout pregnancy was lower on day 15 in Piau group, and it was lower on day 30 in commercial pigs. Piau group presented higher expression of the FGF4 gene on days 45, 60 and 90, and commercial group showed higher expression on day 15 and 90. SOX2 gene expression was lower on day 15 in Piau pigs and it was constant throughout pregnancy in commercial group. Overall, the expression of IHH, SHH, WNT1, WNT4 and FGF4 genes were higher in commercial than Piau pigs on day 15, besides expression of BCL2 gene in Piau embryos was lower on day 15; these results might indicate that the muscle precursor cells are allowed to proliferate for a longer time in commercial than in Piau embryos by the balance of proliferative and apoptotic genes. Therefore, the expression differential between breeds can stimulate proliferation and differentiation of cells in different ways, explaining the postnatal differences in the muscularity between pigs from Piau breed and a commercial line.
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Zhang Z, Chen Z, Ye S, He Y, Huang S, Yuan X, Chen Z, Zhang H, Li J. Genome-Wide Association Study for Reproductive Traits in a Duroc Pig Population. Animals (Basel) 2019; 9:ani9100732. [PMID: 31561612 PMCID: PMC6826494 DOI: 10.3390/ani9100732] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Reproductive traits are economically important in the pig industry, and it is critical to explore their underlying genetic architecture. Hence, four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. Through a genome-wide association study in a Duroc pig herd, several candidate single-nucleotide polymorphisms (SNPs) and genes were found potentially associated with the traits of interest. These findings help to understand the genetic basis of porcine reproductive traits and could be applied in pig breeding programs. Abstract In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs.
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Affiliation(s)
- Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zitao Chen
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaopan Ye
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yingting He
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shuwen Huang
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zanmou Chen
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hao Zhang
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Huang S, Rabah H, Ferret-Bernard S, Le Normand L, Gaucher F, Guerin S, Nogret I, Le Loir Y, Chen XD, Jan G, Boudry G, Jeantet R. Propionic fermentation by the probiotic Propionibacterium freudenreichii to functionalize whey. J Funct Foods 2019. [DOI: 10.1016/j.jff.2018.11.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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19
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Rabah H, Ferret-Bernard S, Huang S, Le Normand L, Cousin FJ, Gaucher F, Jeantet R, Boudry G, Jan G. The Cheese Matrix Modulates the Immunomodulatory Properties of Propionibacterium freudenreichii CIRM-BIA 129 in Healthy Piglets. Front Microbiol 2018; 9:2584. [PMID: 30420848 PMCID: PMC6215859 DOI: 10.3389/fmicb.2018.02584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022] Open
Abstract
Propionibacterium freudenreichii is a beneficial bacterium, used as a cheese starter, which presents versatile probiotic properties. These properties are strain-dependent. We hypothesized they may also be delivery vehicle-dependent. In this study, we thus explored in healthy piglets how the cheese matrix affects the immunomodulatory properties of P. freudenreichii. During 2 weeks, three groups of weaned piglets consumed, respectively, P. freudenreichii as a liquid culture (PF-culture), P. freudenreichii under the form of a cheese (PF-cheese), or a control sterile cheese matrix (Cheese-matrix). The in vivo metabolic activity of P. freudenreichii was assessed by determining short chain fatty acids (SCFA) concentration and bifidobacteria population in feces. Whatever the delivery vehicle, P. freudenreichii was metabolically active in piglets' colon and enhanced both bifidobacteria and SCFA in feces. P. freudenreichii consumption decreased the secretion of TNFα and of IL-10 by peripheral blood mononuclear cells (PBMC). It did not alter IL-10, IFNγ, IL-17, and TNFα secretion in mesenteric lymph node immune cells (MLNC). PF-cheese enhanced significantly Treg phenotype, while PF-culture decreased significantly Th17 phenotype in PBMC and MLNC. Remarkably, only PF-cheese induced an increase of Th2 phenotype in PBMC and MLNC. Ex vivo stimulation of PBMC and MLNC by Lipopolysaccharides and Concanavalin A emphasized the difference in the immunomodulatory responses between PF-culture and PF-cheese group, as well as between PBMC and MLNC. This study shows the importance to consider the delivery vehicle for probiotic administration. It confirms the anti-inflammatory potential of P. freudenreichii. It opens new perspectives for the use propionibacteria-fermented products as preventive agents for inflammatory bowel diseases and intestinal infectious diseases.
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Affiliation(s)
- Houem Rabah
- STLO, INRA, Agrocampus Ouest, Rennes, France
- Pôle Agronomique Ouest, Rennes, France
| | | | - Song Huang
- STLO, INRA, Agrocampus Ouest, Rennes, France
| | - Laurence Le Normand
- INRA, INSERM, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, France
| | | | - Floriane Gaucher
- STLO, INRA, Agrocampus Ouest, Rennes, France
- Bioprox, Levallois-Perret, France
| | | | - Gaëlle Boudry
- INRA, INSERM, Univ Rennes, Nutrition Metabolisms and Cancer, NuMeCan, Rennes, France
| | - Gwénaël Jan
- STLO, INRA, Agrocampus Ouest, Rennes, France
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20
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Wang S, Wang B, He H, Sun A, Guo C. A new set of reference housekeeping genes for the normalization RT-qPCR data from the intestine of piglets during weaning. PLoS One 2018; 13:e0204583. [PMID: 30256841 PMCID: PMC6157878 DOI: 10.1371/journal.pone.0204583] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 09/11/2018] [Indexed: 01/09/2023] Open
Abstract
The intestinal mucosal development of piglets (Sus scrofa) during the weaning stage is important to their disease susceptibility and later growth. Quantitative real-time PCR (RT-qPCR) is commonly used to screen for differentially expressed genes and, for accurate results, proper reference housekeeping genes are essential. Here we assessed the mRNA expression of 18 well-known candidate reference genes at different parts of the gastrointestinal tract (GIT) of piglets during the weaning process by RT-qPCR assay. GeNorm analysis revealed that B2M/HMBS/HPRT1 were the three most stable reference genes and GAPDH was the least stable gene in the duodenum, jejunum, ileum, colon, and whole GIT. BestKeeper analysis found that B2M/HMBS/PGK11, HMBS/B2M/HPRT1, B2M/HMBS/HSPCB, B2M/HPRT1/HMBS, and B2M/HMBS/HPRT1 were the most stable genes in the duodenum, jejunum, ileum, colon, and whole GIT, respectively, whereas GAPDH, B-actin, and 18S rRNA were the least stable genes at different parts of the GIT. To confirm the crucial role of appropriate housekeeping genes in obtaining reliable results, we analyzed the expression of ALP using each of the 18 reference genes to normalize the RT-qPCR data. We found that the expression levels of ALP normalized using the most stable reference genes (B2M/HMBS/HPRT1) differed greatly from the expression levels obtained when the data were normalized using the least stable genes (GAPDH, B-actin, and 18S). We concluded that B2M/HMBS/HPRT1 were the optimal reference genes for gene expression analysis by RT-qPCR in the intestinal mucosal development stages of piglets at weaning. Our findings provide a set of porcine housekeeping reference genes for studies of mRNA expression in different parts of the pig intestine.
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Affiliation(s)
- Shujin Wang
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Department of Molecular Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - Binxing Wang
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
| | - Huan He
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
| | - Aomin Sun
- Department of Molecular Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - Chunhua Guo
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
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Shu Y, Xia J, Yu Q, Wang G, Zhang J, He J, Wang H, Zhang L, Wu H. Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between adult female and male Chinese concave-eared frogs (Odorrana tormota). Gene 2018; 678:241-251. [PMID: 30103010 DOI: 10.1016/j.gene.2018.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
Abstract
The Chinese concave-eared torrent frog (Odorrana tormota) is the first known non-mammalian vertebrate that can communicate using ultrasound. In this species, females are approximately four times as large as males, in which the female growth rate is obviously higher than that of male. Until now, the molecular mechanisms underlying muscle growth development differences between male and female frogs have not been reported. Here, we integrated mRNA and miRNA expression profiles to reveal growth differences in the hindlimb muscles of 2-year-old frogs. Among 569 differentially expressed genes (DEGs), 69 were associated with muscle growth and regeneration. Fifty-one up-regulated genes in females were potentially involved in promoting muscle growth and regeneration, whereas 18 up-regulated genes in males may lead to muscle growth inhibition and fast-twitch muscle fiber contraction. 244 DEGs were enriched in mTOR and other protein synthesis signaling pathways, and protein degradation pathways, including lysosomal protease, calpain, caspase, and ubiquitin-proteasome system pathways. It may interpret why female muscles grow faster than males. Based on expression differences of genes involved in glycolysis and oxidative metabolism, we speculated that the proportion of slow muscle fiber was higher and that of fast muscle fiber was lower in female compared with male muscle. Additionally, 767 miRNAs were identified, including 217 new miRNAs, and 6248 miRNA-negatively regulated mRNAs were predicted. The miRNA target genes were enriched in pathways related to muscle growth, protein synthesis, and degradation. Thus, in addition to the identified mRNA differential expressions, miRNAs may play other important roles in the differential regulation of hindlimb muscle growth between female and male O. tormota.
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Affiliation(s)
- Yilin Shu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jinquan Xia
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Qiang Yu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Gang Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jihui Zhang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jun He
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Huan Wang
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ling Zhang
- Department of Occupational and Environmental Health, School of Public Health, Wuhan University of Science and Technology, China; Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China.
| | - Hailong Wu
- Key Laboratory for the Conservation and Utilization of Important Biological Resources of Anhui Province, Wuhu 241000, China; College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
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22
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High mobility group A2 (HMGA2) deficiency in pigs leads to dwarfism, abnormal fetal resource allocation, and cryptorchidism. Proc Natl Acad Sci U S A 2018; 115:5420-5425. [PMID: 29735702 PMCID: PMC6003518 DOI: 10.1073/pnas.1721630115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Expression of HMGA2 is strongly associated with body size and growth in mice and humans. In mice, inactivation of one or both alleles of Hmga2 results in body-size reductions of 20% and 60%, respectively. In humans, microdeletions involving the HMGA2 locus result in short stature, suggesting the function of the HMGA2 protein is conserved among mammals. To test this hypothesis, we generated HMGA2-deficient pigs via gene editing and somatic cell nuclear transfer (SCNT). Examination of growth parameters revealed that HMGA2-/+ male and female pigs were on average 20% lighter and smaller than HMGA2+/+ matched controls (P < 0.05). HMGA2-/- boars showed significant size reduction ranging from 35 to 85% of controls depending on age (P < 0.05), and organ weights were also affected (P < 0.05). HMGA2-/+ gilts and boars exhibited normal reproductive development and fertility, while HMGA2-/- boars were sterile due to undescended testes (cryptorchidism). Crossbreeding HMGA2-/+ boars and gilts produced litters lacking the HMGA2-/- genotype. However, analysis of day (D) D40 and D78 pregnancies indicated that HMGA2-/- fetuses were present at the expected Mendelian ratio, but placental abnormalities were seen in the D78 HMGA2-/- concepti. Additionally, HMGA2-/- embryos generated by gene editing and SCNT produced multiple pregnancies and viable offspring, indicating that lack of HMGA2 is not lethal per se. Overall, our results show that the effect of HMGA2 with respect to growth regulation is highly conserved among mammals and opens up the possibility of regulating body and organ size in a variety of mammalian species including food and companion animals.
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Xu X, Mishra B, Qin N, Sun X, Zhang S, Yang J, Xu R. Differential Transcriptome Analysis of Early Postnatal Developing Longissimus Dorsi Muscle from Two Pig Breeds Characterized in Divergent Myofiber Traits and Fatness. Anim Biotechnol 2018; 30:63-74. [PMID: 29471750 DOI: 10.1080/10495398.2018.1437045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Meat quality traits (MQTs) are very important in the porcine industry, which are mainly determined by skeletal muscle fiber composition, extra-muscular and/or intramuscular fat content. To identify the differentially expressed candidate genes affecting the meat quality traits, first we compared the MQTs and skeletal muscle fiber characteristics in the longissimus dorsi muscle (LDM) of the Northeast Min pig (NM) and the Changbaishan wild boar (CW) with their body weight approaching 90 kg. The significant divergences in the skeletal muscle fiber phenotypes and fatness traits between the two porcine breeds established an ideal model system for further identifying potential key functional genes that dominated MQTs. Further, a transcriptome profile analysis was performed using the Illumina sequencing method in early postnatal developing LDM from the two breeds at the ages of 42 days. Comparative analysis between these two cDNA libraries showed that there were 17,653 and 22,049 unambiguous tag-mapped sense transcripts detected from NM and CW, respectively. 4522 differentially expressed genes (DEGs) were revealed between the two tissue samples, of them, 4176 genes were found as having been upregulated and 346 genes were identified as having been downregulated in the NM library. By pathway enrichment analysis, a set of significantly enriched pathways were identified for the DEGs, which are potentially involved in myofiber development, differentiation and growth, lipogenesis and lipolysis in porcine skeletal muscle. The expression levels of 30 out of the DEGs were validated by real-time quantitative reverse transcriptase PCR (qRT-PCR) and the observed result was consistent noticeably with the Illumina transcriptome profiles. The findings from this study can contribute to future investigations of skeletal muscle growth and development mechanism and to establishing molecular approaches to improve meat quality traits in pig breeding.
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Affiliation(s)
- Xiaoxing Xu
- a Department of Human Nutrition, Food, and Animal Sciences , University of Hawaii at Manoa , Honolulu , HI , USA
| | - Birendra Mishra
- a Department of Human Nutrition, Food, and Animal Sciences , University of Hawaii at Manoa , Honolulu , HI , USA
| | - Ning Qin
- b College of Animal Science and Technology , Jilin Agricultural University , Changchun , China
| | - Xue Sun
- b College of Animal Science and Technology , Jilin Agricultural University , Changchun , China
| | - Shumin Zhang
- c Institute of Pig Science , Academy of Agricultural Sciences of Jilin Province , Gongzhuling , China
| | - Jinzeng Yang
- a Department of Human Nutrition, Food, and Animal Sciences , University of Hawaii at Manoa , Honolulu , HI , USA
| | - Rifu Xu
- b College of Animal Science and Technology , Jilin Agricultural University , Changchun , China
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24
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Seaborne RA, Strauss J, Cocks M, Shepherd S, O'Brien TD, van Someren KA, Bell PG, Murgatroyd C, Morton JP, Stewart CE, Sharples AP. Human Skeletal Muscle Possesses an Epigenetic Memory of Hypertrophy. Sci Rep 2018; 8:1898. [PMID: 29382913 PMCID: PMC5789890 DOI: 10.1038/s41598-018-20287-3] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/16/2018] [Indexed: 12/25/2022] Open
Abstract
It is unknown if adult human skeletal muscle has an epigenetic memory of earlier encounters with growth. We report, for the first time in humans, genome-wide DNA methylation (850,000 CpGs) and gene expression analysis after muscle hypertrophy (loading), return of muscle mass to baseline (unloading), followed by later hypertrophy (reloading). We discovered increased frequency of hypomethylation across the genome after reloading (18,816 CpGs) versus earlier loading (9,153 CpG sites). We also identified AXIN1, GRIK2, CAMK4, TRAF1 as hypomethylated genes with enhanced expression after loading that maintained their hypomethylated status even during unloading where muscle mass returned to control levels, indicating a memory of these genes methylation signatures following earlier hypertrophy. Further, UBR5, RPL35a, HEG1, PLA2G16, SETD3 displayed hypomethylation and enhanced gene expression following loading, and demonstrated the largest increases in hypomethylation, gene expression and muscle mass after later reloading, indicating an epigenetic memory in these genes. Finally, genes; GRIK2, TRAF1, BICC1, STAG1 were epigenetically sensitive to acute exercise demonstrating hypomethylation after a single bout of resistance exercise that was maintained 22 weeks later with the largest increase in gene expression and muscle mass after reloading. Overall, we identify an important epigenetic role for a number of largely unstudied genes in muscle hypertrophy/memory.
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Affiliation(s)
- Robert A Seaborne
- Institute for Science and Technology in Medicine (ISTM), School of Medicine, Keele University, Staffordshire, United Kingdom.,Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Juliette Strauss
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Matthew Cocks
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Sam Shepherd
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Thomas D O'Brien
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Ken A van Someren
- Department of Sport, Exercise and Rehabilitation, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Phillip G Bell
- Department of Sport, Exercise and Rehabilitation, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Christopher Murgatroyd
- School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom
| | - James P Morton
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Claire E Stewart
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Adam P Sharples
- Institute for Science and Technology in Medicine (ISTM), School of Medicine, Keele University, Staffordshire, United Kingdom. .,Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.
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25
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Oster M, Trakooljul N, Reyer H, Zeyner A, Muráni E, Ponsuksili S, Wimmers K. Sex-Specific Muscular Maturation Responses Following Prenatal Exposure to Methylation-Related Micronutrients in Pigs. Nutrients 2017; 9:nu9010074. [PMID: 28106759 PMCID: PMC5295118 DOI: 10.3390/nu9010074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 01/22/2023] Open
Abstract
Supplementation of micronutrients involved in DNA methylation, particularly during pregnancy, is recommended because of its impacts on human health, but further evidence is needed regarding the effects of over-supplementation and differences between sexes. Here, a porcine model was used to assess effects of maternal supplementation with one-carbon-cycle compounds during prenatal and postnatal stages on offspring muscle development. Sows received either a standard diet (CON) or a standard diet supplemented with folate, B6, B12, methionine, choline, and zinc (MET) throughout gestation. Myogenesis-, growth-, and nutrient utilization-related transcript expression was assessed using quantitative PCR. Organismal phenotype and gene expression effects differed significantly between males and females. Male MET-offspring showed increased fetal weight during late pregnancy but decreased live weight postnatally, with compensatory transcriptional responses comprising myogenic key drivers (Pax7, MyoD1, myogenin). In contrast, female weights were unaffected by diet, and mRNA abundances corresponded to a phenotype of cellular reorganization via FABP3, FABP4, SPP1 and Insulin-like Growth Factor-signaling. These findings in an animal model suggest that supplementation during pregnancy with methylation-related micronutrients can promote sex-specific myogenic maturation processes related to organismal growth and muscle metabolism. The usage of maternal dietary supplements should be more carefully considered regarding its ability to promote fetal and postnatal health.
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Affiliation(s)
- Michael Oster
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Henry Reyer
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Annette Zeyner
- Martin-Luther-University Halle-Wittenberg, Department of Animal Nutrition, Theodor-Lieser-Str. 11, 06120 Halle (Saale), Germany.
| | - Eduard Muráni
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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26
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Reis EPD, Paixão DM, Brustolini OJB, Silva FFE, Silva W, Araújo FMGD, Salim ACDM, Oliveira G, Guimarães SEF. Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs. Genet Mol Biol 2016; 39:589-599. [PMID: 27801482 PMCID: PMC5127148 DOI: 10.1590/1678-4685-gmb-2015-0295] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/20/2016] [Indexed: 11/22/2022] Open
Abstract
This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods.
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Affiliation(s)
| | | | | | | | - Walmir Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil
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27
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Comparison of muscle characteristics and underpinning mechanisms between Texel and Ujumqin sheep aged from day 70 to 135 of gestation. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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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]
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29
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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]
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30
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Ghosh M, Sodhi SS, Sharma N, Mongre RK, Kim N, Singh AK, Lee SJ, Kim DC, Kim SW, Lee HK, Song KD, Jeong DK. An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs. BMC Genet 2016; 17:35. [PMID: 26847462 PMCID: PMC4741023 DOI: 10.1186/s12863-016-0341-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/25/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association. RESULTS The NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (-466.5 Kcal mol(-1)), van der Walls energy (-87.3 Kcal mol(-1)), and interaction energy (-835.7 Kcal mol(-1)) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2-0.55 nm) and lower root-mean-square fluctuation (approximately 0.08-0.3 nm) as compared to the mutant complexes. CONCLUSIONS The results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for the poor growth performance for this breed. This study is a pioneering in-depth in silico analysis of polymorphic MYH1 and will serve as a valuable resource for further targeted molecular diagnosis and population-based studies conducted for improving the growth performance of JNP.
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Affiliation(s)
- Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Neelesh Sharma
- Sher-e-Kashmir University of Agricultural Sciences and Technology, R.S. Pura, Jammu, India.
| | - Raj Kumar Mongre
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Nameun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Amit Kumar Singh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon, 200-701, Republic of Korea.
| | - Dae Cheol Kim
- Livestock Promotion Institute, Jeju Special Self-governing Province, Jeju-Do, 690-756, Republic of Korea.
| | - Sung Woo Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Rural Administration, Namwon, Republic of Korea.
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Ki-Duk Song
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
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31
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Integrative transcriptomics and proteomics analysis of longissimus dorsi muscles of Canadian double-muscled Large White pigs. Gene 2016; 577:14-23. [DOI: 10.1016/j.gene.2015.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/28/2015] [Accepted: 11/09/2015] [Indexed: 11/23/2022]
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32
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Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos. PLoS One 2015; 10:e0143378. [PMID: 26630129 PMCID: PMC4667915 DOI: 10.1371/journal.pone.0143378] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/04/2015] [Indexed: 12/18/2022] Open
Abstract
Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM) and the pectoral muscle (PM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P) at the same developmental stage (embryonic 15 days). Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China) on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos) genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DEGs (differentially expression genes). The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only improves our understanding of the location-specific and breed-specific genes and pathways but also provides some candidate molecular targets for increasing muscle products and meat quality by genetic control.
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Liu X, Du Y, Trakooljul N, Brand B, Muráni E, Krischek C, Wicke M, Schwerin M, Wimmers K, Ponsuksili S. Muscle Transcriptional Profile Based on Muscle Fiber, Mitochondrial Respiratory Activity, and Metabolic Enzymes. Int J Biol Sci 2015; 11:1348-62. [PMID: 26681915 PMCID: PMC4671993 DOI: 10.7150/ijbs.13132] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022] Open
Abstract
Skeletal muscle is a highly metabolically active tissue that both stores and consumes energy. Important biological pathways that affect energy metabolism and metabolic fiber type in muscle cells may be identified through transcriptomic profiling of the muscle, especially ante mortem. Here, gene expression was investigated in malignant hyperthermia syndrome (MHS)-negative Duroc and Pietrian (PiNN) pigs significantly differing for the muscle fiber types slow-twitch-oxidative fiber (STO) and fast-twitch-oxidative fiber (FTO) as well as mitochondrial activity (succinate-dependent state 3 respiration rate). Longissimus muscle samples were obtained 24 h before slaughter and profiled using cDNA microarrays. Differential gene expression between Duroc and PiNN muscle samples were associated with protein ubiquitination, stem cell pluripotency, amyloid processing, and 3-phosphoinositide biosynthesis and degradation pathways. In addition, weighted gene co-expression network analysis within both breeds identified several co-expression modules that were associated with the proportion of different fiber types, mitochondrial respiratory activity, and ATP metabolism. In particular, Duroc results revealed strong correlations between mitochondrion-associated co-expression modules and STO (r = 0.78), fast-twitch glycolytic fiber (r = -0.98), complex I (r=0.72) and COX activity (r = 0.86). Other pathways in the protein-kinase-activity enriched module were positively correlated with STO (r=0.93), while negatively correlated with FTO (r = -0.72). In contrast to PiNN, co-expression modules enriched in macromolecule catabolic process, actin cytoskeleton, and transcription activator activity were associated with fiber types, mitochondrial respiratory activity, and metabolic enzyme activities. Our results highlight the importance of mitochondria for the oxidative capacity of porcine muscle and for breed-dependent molecular pathways in muscle cell fibers.
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Affiliation(s)
- Xuan Liu
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Yang Du
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Nares Trakooljul
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Bodo Brand
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Eduard Muráni
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Carsten Krischek
- 2. 2 Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, D-30173 Hannover, Germany
| | - Michael Wicke
- 3. 3 Department of Animal Science, Quality of Food of Animal Origin, Georg-August-University Goettingen, D-37075 Goettingen, Germany
| | - Manfred Schwerin
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Klaus Wimmers
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Siriluck Ponsuksili
- 1. Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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34
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Tang Z, Yang Y, Wang Z, Zhao S, Mu Y, Li K. Integrated analysis of miRNA and mRNA paired expression profiling of prenatal skeletal muscle development in three genotype pigs. Sci Rep 2015; 5:15544. [PMID: 26496978 PMCID: PMC4620456 DOI: 10.1038/srep15544] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in muscle development by binding to messenger RNAs (mRNAs). Based on prenatal skeletal muscle at 33, 65 and 90 days post-coitus (dpc) from Landrace, Tongcheng and Wuzhishan pigs, we carried out integrated analysis of miRNA and mRNA expression profiling. We identified 33, 18 and 67 differentially expressed miRNAs and 290, 91 and 502 mRNA targets in Landrace, Tongcheng and Wuzhishan pigs, respectively. Subsequently, 12 mRNAs and 3 miRNAs differentially expressed were validated using quantitative real-time PCR (qPCR), and 5 predicted miRNA targets were confirmed via dual luciferase reporter or western blot assays. We identified a set of miRNAs and mRNA genes differentially expressed in muscle development. Gene ontology (GO) enrichment analysis suggests that the miRNA targets are primarily involved in muscle contraction, muscle development and negative regulation of cell proliferation. Our data indicated that more mRNAs are regulated by miRNAs at earlier stages than at later stages of muscle development. Landrace and Tongcheng pigs also had longer phases of myoblast proliferation than Wuzhishan pigs. This study will be helpful to further explore miRNA-mRNA interactions in myogenesis and aid to uncover the molecular mechanisms of muscle development and phenotype variance in pigs.
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Affiliation(s)
- Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yalan Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zishuai Wang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuanping Zhao
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Institute of Animal Science, Anhui Academy of Agricultural Sciences, Hefei, 230031, P. R. China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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35
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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.
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Zhao W, Mu Y, Ma L, Wang C, Tang Z, Yang S, Zhou R, Hu X, Li MH, Li K. Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development. Sci Rep 2015; 5:8957. [PMID: 25753296 DOI: 10.1038/srep08957] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/12/2015] [Indexed: 02/05/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process.
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Affiliation(s)
- Weimin Zhao
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lei Ma
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chen Wang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shulin Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Rong Zhou
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoju Hu
- 1] CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Siengdee P, Trakooljul N, Murani E, Brand B, Schwerin M, Wimmers K, Ponsuksili S. Pre- and post-natal muscle microRNA expression profiles of two pig breeds differing in muscularity. Gene 2015; 561:190-8. [PMID: 25724393 DOI: 10.1016/j.gene.2015.02.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/12/2015] [Accepted: 02/12/2015] [Indexed: 12/21/2022]
Abstract
miRNAs regulate the expression of target genes in diverse cellular processes and hence play important roles in physiological processes including developmental timing, patterning, embryogenesis, organogenesis, cell lineage, myogenesis and growth control. A comparative expression analysis of miRNAs expressed in the longissimus dorsi muscle at two prenatal stages (63 and 91 days post-conception (dpc)), and one adult stage (180 days post-natum) in both German Landrace (DL) and Pietrain (Pi) pig breeds was performed using a custom-designed array. During the prenatal stages, miR-199 and the miR-17 families were significantly up-regulated at 63 dpc, whereas miR-1 and miR-133a were overexpressed at 91 dpc. The abundance of several miRNAs was increased in the adult stage compared to 91 dpc including miR-1, miR-133, miR-22(a/b) and miR-29a. Some miRNAs were breed-specific, such as miR-199 and the miR-17 families which were all up-regulated in Pi pigs, while miR-133, miR-181 and miR-214 were up-regulated in DL pigs. Several pathways related to muscle development were enriched with predicted targets for the differentially expressed miRNAs. The dynamic expression and breed-associated regulation of porcine muscle miRNAs suggests a functional role for miRNA-mediated gene regulation during muscle development and phenotypic variations of muscle traits.
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Affiliation(s)
- Puntita Siengdee
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Molecular Biology 18196 Dummerstorf, Germany.
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Molecular Biology 18196 Dummerstorf, Germany.
| | - Bodo Brand
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Manfred Schwerin
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Molecular Biology 18196 Dummerstorf, Germany.
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Research Unit Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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Ropka-Molik K, Zukowski K, Eckert R, Gurgul A, Piórkowska K, Oczkowicz M. Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method. Anim Genet 2014; 45:674-84. [PMID: 24961663 DOI: 10.1111/age.12184] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 02/03/2023]
Abstract
Next-generation sequencing RNA-Seq technology is a powerful tool that creates new possibilities for whole-transcriptome analysis. In our study, the RNA-Seq method was applied to analyze global changes in transcriptome from muscle tissue (m. semimembranosus) in two pig breeds (Pietrain and Polish Landrace, PL). The breeds differ in terms of muscularity, growth rate and reproduction traits. Using three different approaches (deseq, cufflinks and edger) and taking into account the most restrictive criteria, 35 genes differentially expressed between Pietrain and PL pigs were identified. In both breeds, the most abundant were transcripts encoding ribosomal and cytoskeletal proteins (TPM3, TCAP, TMOD4, TPM2, TNNC1) and calcium-binding proteins involved in muscle contraction, calcium-mediated signaling or cation transport (CASQ1, MLC2V, SLC25A4, MYL3). In PL pigs, we identified up-regulation of several genes that play crucial roles in reproduction: female gamete generation (BDP1, PTPN21, USP9X), fertilization (EGFR) and embryonic development (CPEB4). In the Pietrain breed, only seven genes were over-expressed (CISH, SPP1, TUBA8, ATP6V1C2, IGKC, predicted LOC100510960 and LOC100626400), and they play important roles in, for example, negative regulation of apoptosis, immune response, cell-cell signaling, cell growth and migration as well as the metabolic process. The functions of the majority of selected genes were consistent with phenotypic variation in investigated breeds; thus, we proposed a new panel of candidate genes that can be associated with economically important pig traits.
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Affiliation(s)
- Katarzyna Ropka-Molik
- Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
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Hildyard JCW, Wells DJ. Identification and validation of quantitative PCR reference genes suitable for normalizing expression in normal and dystrophic cell culture models of myogenesis. PLOS CURRENTS 2014; 6. [PMID: 24634799 PMCID: PMC3948689 DOI: 10.1371/currents.md.faafdde4bea8df4aa7d06cd5553119a6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The coordinated differentiation of myoblasts to mature muscle is essential for muscle development and repair, and study of the myogenic program in health and disease is critical to the understanding and treatment of muscle pathologies. Use of quantitative RT-PCR to analyse gene expression in cell culture models of muscle differentiation can be highly informative, but data must be normalized to one or more suitable reference genes. Myogenesis is highly dynamic, thus identification of genes with stable expression throughout this process is challenging. Establishing a common set of reference genes suitable for measuring expression in both healthy and disease models would be of considerable advantage. We measured expression of 11 candidate normalization genes (Cdc40, Htatsf1, Ap3d1, Csnk2a2, Fbxw2, Fbxo38, Pak1ip1, Zfp91, GAPDH, ActB, 18S) in three cell culture models of myogenesis (C2C12 , H2K2B4, and the dystrophic line H2KSF1). Strong and weak normalization candidates were identified using the software packages Bestkeeper, geNorm and Normfinder, then validated against several known myogenic markers (MyoD, myogenin, MEF2C, dystrophin). Our data show that Csnk2a2 and Ap3d1 are suitable for normalizing gene expression during differentiation in both healthy and dystrophic cell-culture models, and that the commonly-used reference standards 18S, ActB and GAPDH are exceptionally poor candidates.
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Affiliation(s)
- John C W Hildyard
- Department of Comparative and Biomedical Sciences, Royal Veterinary College, London, UK
| | - Dominic J Wells
- Department of Comparative and Biomedical Sciences, Royal Veterinary College, London, UK
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40
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Pagel CN, Wasgewatte Wijesinghe DK, Taghavi Esfandouni N, Mackie EJ. Osteopontin, inflammation and myogenesis: influencing regeneration, fibrosis and size of skeletal muscle. J Cell Commun Signal 2013; 8:95-103. [PMID: 24318932 DOI: 10.1007/s12079-013-0217-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022] Open
Abstract
Osteopontin is a multifunctional matricellular protein that is expressed by many cell types. Through cell-matrix and cell-cell interactions the molecule elicits a number of responses from a broad range of target cells via its interaction with integrins and the hyaluronan receptor CD44. In many tissues osteopontin has been found to be involved in important physiological and pathological processes, including tissue repair, inflammation and fibrosis. Post-natal skeletal muscle is a highly differentiated and specialised tissue that retains a remarkable capacity for regeneration following injury. Regeneration of skeletal muscle requires the co-ordinated activity of inflammatory cells that infiltrate injured muscle and are responsible for initiating muscle fibre degeneration and phagocytosis of necrotic tissue, and muscle precursor cells that regenerate the injured muscle fibres. This review focuses on the current evidence that osteopontin plays multiple roles in skeletal muscle, with particular emphasis on its role in regeneration and fibrosis following injury, and in determining the severity of myopathic diseases such as Duchenne muscular dystrophy.
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Affiliation(s)
- Charles N Pagel
- Faculty of Veterinary Science, University of Melbourne, Parkville, Victoria, 3010, Australia,
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41
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Reyer H, Ponsuksili S, Wimmers K, Murani E. Transcript variants of the porcine glucocorticoid receptor gene (NR3C1). Gen Comp Endocrinol 2013; 189:127-33. [PMID: 23684967 DOI: 10.1016/j.ygcen.2013.04.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 04/28/2013] [Indexed: 11/28/2022]
Abstract
Glucocorticoid receptor (GR) is a transcription factor activated by circulating glucocorticoids and mediates their effects on various biological functions in the body. The final cellular activity of GR is modulated by alternative splicing and cell-type specific expression of its encoding gene NR3C1. To enhance the current knowledge of alternative processing of NR3C1 in mammalian species and to facilitate future studies of its regulation in the pig we explored here structural diversity, and tissue-specific distribution of transcript variants of the porcine NR3C1, and the correlation between usage of alternative promoters and alternative splicing. We experimentally identified ten alternatively used untranslated first exons (1A, 1B, 1C, 1D, 1E, 1F, 1G, 1H, 1H2 and 1J) and four transcript variants encoding different GR subtypes (GR-alpha, GR-beta, GR-P and GR-gamma). Expression profiling of nine most important target tissues of glucocorticoids revealed that the promoter of exon 1C drives constitutive expression of the predominant GR-alpha subtype. We found compelling evidence that the occurrence of exon 1D influences abundance of the GR-P splice variant, while both seems to play an important role in regulating GR activity in neuroendocrine tissues. Exons 1A and 1B in turn appear to be important for the regulation of the expression of the porcine NR3C1 in liver and spleen. Our results demonstrate that tissue-specific actions of GR depend on the usage of alternative promoter regions that favour the processing of certain GR subtypes.
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Affiliation(s)
- Henry Reyer
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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42
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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.
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Affiliation(s)
- P Siengdee
- Leibniz Institute for Farm Animals Biology FBN, Research Group 'Functional Genome Analysis', Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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Gahr SA, Weber GM, Rexroad CE. Identification and expression of Smads associated with TGF-β/activin/nodal signaling pathways in the rainbow trout (Oncorhynchus mykiss). FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:1233-1244. [PMID: 22290475 DOI: 10.1007/s10695-012-9611-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/19/2012] [Indexed: 05/31/2023]
Abstract
The Smad proteins are essential components of the TGF-β/activin/nodal family signaling pathway. We report the identification and expression of transcripts representing three receptor Smads (Smad2a, Smad2b, and Smad3), two common Smads (Smad4a and Smad4b), and one inhibitory Smad (Smad7). Phylogenetic analysis suggests this gene family evolved through the combination of ancient and more recent salmonid genome duplication events. Tissue distribution, embryonic expression, and expression in growth hormone (GH) treated fish were assessed by reverse transcription PCR or qPCR. All six Smad transcripts were ubiquitously expressed in adult tissues. We observed the highest expression of the receptor Smads in unfertilized eggs, generally decreasing during early embryonic development and slightly increasing around 11 days post-fertilization (dpf). Smad7 expression was low for most of embryonic development, with a dramatic increase at the onset of muscle development (6 dpf), and at hatch (24 dpf). Smad4 expression was low during early embryonic development and increased after 14 dpf. The increased expression of Smad4 and Smad7 during late embryonic development may indicate modulation of gene expression by GH axis, which initiates activity during late embryonic development. These data were supported by the modulation of these Smads in the gill filament, stomach, and muscle following a GH treatment. Additionally, these changes are concurrent with the modulation of expression of TGF-β family members. Most significantly, the increased expression of Smad7 in the muscle is simultaneous with increased expression of MSTN1A and not MSTN1B during both embryonic development and following GH treatment. These data indicate a promyogenic role for Smad7 as previously identified in other non-fish species.
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Affiliation(s)
- Scott A Gahr
- Biology Department, St. Vincent College, 300 Fraser Purchase Rd., Latrobe, PA 15650, USA.
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Oster M, Murani E, Metges CC, Ponsuksili S, Wimmers K. A gestational high protein diet affects the abundance of muscle transcripts related to cell cycle regulation throughout development in porcine progeny. PLoS One 2012; 7:e34519. [PMID: 22496824 PMCID: PMC3322122 DOI: 10.1371/journal.pone.0034519] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In various animal models pregnancy diets have been shown to affect offspring phenotype. Indeed, the underlying programming of development is associated with modulations in birth weight, body composition, and continual diet-dependent modifications of offspring metabolism until adulthood, producing the hypothesis that the offspring's transcriptome is permanently altered depending on maternal diet. METHODOLOGY/PRINCIPAL FINDINGS To assess alterations of the offspring's transcriptome due to gestational protein supply, German Landrace sows were fed isoenergetic diets containing protein levels of either 30% (high protein--HP) or 12% (adequate protein--AP) throughout their pregnancy. Offspring muscle tissue (M. longissimus dorsi) was collected at 94 days post conception (dpc), and 1, 28, and 188 days post natum (dpn) for use with Affymetrix GeneChip Porcine Genome Arrays and subsequent statistical and Ingenuity pathway analyses. Numerous transcripts were found to have altered abundance at 94 dpc and 1 dpn; at 28 dpn no transcripts were altered, and at 188 dpn only a few transcripts showed a different abundance between diet groups. However, when assessing transcriptional changes across developmental time points, marked differences were obvious among the dietary groups. Depending on the gestational dietary exposure, short- and long-term effects were observed for mRNA expression of genes related to cell cycle regulation, energy metabolism, growth factor signaling pathways, and nucleic acid metabolism. In particular, the abundance of transcripts related to cell cycle remained divergent among the groups during development. CONCLUSION Expression analysis indicates that maternal protein supply induced programming of the offspring's genome; early postnatal compensation of the slight growth retardation obvious at birth in HP piglets resulted, as did a permanently different developmental alteration and responsiveness to the common environment of the transcriptome. The transcriptome modulations are interpreted as the molecular equivalent of developmental plasticity of the offspring that necessitates adaptation and maintenance of the organismal phenotype.
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Affiliation(s)
- Michael Oster
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Eduard Murani
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Cornelia C. Metges
- Research Unit Nutritional Physiology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Research Group Functional Genomics, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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Wang XQ, Yang WJ, Yang Z, Shu G, Wang SB, Jiang QY, Yuan L, Wu TS. The differential proliferative ability of satellite cells in Lantang and Landrace pigs. PLoS One 2012; 7:e32537. [PMID: 22427853 PMCID: PMC3302802 DOI: 10.1371/journal.pone.0032537] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Accepted: 01/30/2012] [Indexed: 12/15/2022] Open
Abstract
Here, for the first time, we evaluate the hypothesis that the proliferative abilities of satellite cells (SCs) isolated from Lantang (indigenous Chinese pigs) and Landrace pigs, which differ in muscle characteristics, are different. SCs were isolated from the longissimus dorsi muscle of neonatal Lantang and Landrace pigs. Proliferative ability was estimated by the count and proliferative activity of viable cells using a hemocytometer and MTT assay at different time points after seeding, respectively. Cell cycle information was detected by flow cytometry. Results showed that there was a greater (P<0.05) number of SCs in Lantang pigs compared with Landrace pigs after 72 h of culture. The percentage of cell population in S phase and G2/M phases in Lantang pigs were higher (P<0.05), while in G0/G1 phase was lower (P<0.05) in comparison with the Landrace pigs. The mRNA abundances of MyoD, Myf5, myogenin and Pax7 in SCs from Lantang pigs were higher (P<0.05), while those of myostatin, Smad3 and genes in the mammalian target of rapamycin (mTOR) pathway (with the exception of 4EBP1) were lower (P<0.05) than the Landrace pigs. Protein levels of MyoD, myogenin, myostatin, S6K, phosphorylated mTOR and phosphorylated eIF4E were consistent with the corresponding mRNA abundance. Collectively, these findings suggested that SCs in the two breeds present different proliferative abilities, and the proliferative potential of SCs in Lantang pigs is higher than in Landrace pigs.
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Affiliation(s)
- Xiu-qi Wang
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong Province, China.
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Porcine SPP1 gene polymorphism association with phenotypic traits in the Landrace × Jeju (Korea) black pig F2 population. Mol Biol Rep 2012; 39:7705-9. [DOI: 10.1007/s11033-012-1606-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 02/02/2012] [Indexed: 10/28/2022]
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Zhao X, Mo D, Li A, Gong W, Xiao S, Zhang Y, Qin L, Niu Y, Guo Y, Liu X, Cong P, He Z, Wang C, Li J, Chen Y. Comparative analyses by sequencing of transcriptomes during skeletal muscle development between pig breeds differing in muscle growth rate and fatness. PLoS One 2011; 6:e19774. [PMID: 21637832 PMCID: PMC3102668 DOI: 10.1371/journal.pone.0019774] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 04/05/2011] [Indexed: 01/25/2023] Open
Abstract
Understanding the dynamics of muscle transcriptome during development and between breeds differing in muscle growth is necessary to uncover the complex mechanism underlying muscle development. Herein, we present the first transcriptome-wide longissimus dorsi muscle development research concerning Lantang (LT, obese) and Landrace (LR, lean) pig breeds during 10 time-points from 35 days-post-coitus (dpc) to 180 days-post-natum (dpn) using Solexa/Illumina's Genome Analyzer. The data demonstrated that myogenesis was almost completed before 77 dpc, but the muscle phenotypes were still changed from 77 dpc to 28 dpn. Comparative analysis of the two breeds suggested that myogenesis started earlier but progressed more slowly in LT than in LR, the stages ranging from 49 dpc to 77 dpc are critical for formation of different muscle phenotypes. 595 differentially expressed myogenesis genes were identified, and their roles in myogenesis were discussed. Furthermore, GSK3B, IKBKB, ACVR1, ITGA and STMN1 might contribute to later myogenesis and more muscle fibers in LR than LT. Some myogenesis inhibitors (ID1, ID2, CABIN1, MSTN, SMAD4, CTNNA1, NOTCH2, GPC3 and HMOX1) were higher expressed in LT than in LR, which might contribute to more slow muscle differentiation in LT than in LR. We also identified several genes which might contribute to intramuscular adipose differentiation. Most important, we further proposed a novel model in which MyoD and MEF2A controls the balance between intramuscular adipogenesis and myogenesis by regulating CEBP family; Myf5 and MEF2C are essential during the whole myogenesis process while MEF2D affects muscle growth and maturation. The MRFs and MEF2 families are also critical for the phenotypic differences between the two pig breeds. Overall, this study contributes to elucidating the mechanism underlying muscle development, which could provide valuable information for pig meat quality improvement. The raw data have been submitted to Gene Expression Omnibus (GEO) under series GSE25406.
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Affiliation(s)
- Xiao Zhao
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Delin Mo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Anning Li
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wen Gong
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shuqi Xiao
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yue Zhang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Limei Qin
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yuna Niu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yunxue Guo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Chong Wang
- College of Animal Science, South China of Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Jiaqi Li
- College of Animal Science, South China of Agricultural University, Guangzhou, Guangdong, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
- * E-mail:
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48
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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.
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Affiliation(s)
- B P Sollero
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
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49
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Advances in research on the prenatal development of skeletal muscle in animals in relation to the quality of muscle-based food. II – Genetic factors related to animal performance and advances in methodology. Animal 2011; 5:718-30. [DOI: 10.1017/s1751731110002454] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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50
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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.
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Affiliation(s)
- R Davoli
- DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Villa Levi-Coviolo, Reggio Emilia, Italy.
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