1
|
Wang S, Shi M, Zhang Y, Niu J, Li W, Yuan J, Cai C, Yang Y, Gao P, Guo X, Li B, Lu C, Cao G. Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages. Curr Issues Mol Biol 2024; 46:340-354. [PMID: 38248324 PMCID: PMC10814722 DOI: 10.3390/cimb46010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
The development of skeletal muscle in pigs might determine the quality of pork. In recent years, long non-coding RNAs (lncRNAs) have been found to play an important role in skeletal muscle growth and development. In this study, we investigated the whole transcriptome of the longissimus dorsi muscle (LDM) of Jinfen White pigs at three developmental stages (1, 90, and 180 days) and performed a comprehensive analysis of lncRNAs, mRNAs, and micro-RNAs (miRNAs), aiming to find the key regulators and interaction networks in Jinfen White pigs. A total of 2638 differentially expressed mRNAs (DE mRNAs) and 982 differentially expressed lncRNAs (DE lncRNAs) were identified. Compared with JFW_1d, there were 497 up-regulated and 698 down-regulated DE mRNAs and 212 up-regulated and 286 down-regulated DE lncRNAs in JFW_90d, respectively. In JFW_180d, there were 613 up-regulated and 895 down-regulated DE mRNAs and 184 up-regulated and 131 down-regulated DE lncRNAs compared with JFW_1d. There were 615 up-regulated and 477 down-regulated DE mRNAs and 254 up-regulated and 355 down-regulated DE lncRNAs in JFW_180d compared with JFW_90d. Compared with mRNA, lncRNA has fewer exons, fewer ORFs, and a shorter length. We performed GO and KEGG pathway functional enrichment analysis for DE mRNAs and the potential target genes of DE lncRNAs. As a result, several pathways are involved in muscle growth and development, such as the PI3K-Akt, MAPK, hedgehog, and hippo signaling pathways. These are among the pathways through which mRNA and lncRNAs function. As part of this study, bioinformatic screening was used to identify miRNAs and DE lncRNAs that could act as ceRNAs. Finally, we constructed an lncRNA-miRNA-mRNA regulation network containing 26 mRNAs, 7 miRNAs, and 17 lncRNAs; qRT-PCR was used to verify the key genes in these networks. Among these, XLOC_022984/miR-127/ENAH and XLOC_016847/miR-486/NRF1 may function as key ceRNA networks. In this study, we obtained transcriptomic profiles from the LDM of Jinfen White pigs at three developmental stages and screened out lncRNA-miRNA-mRNA regulatory networks that may provide crucial information for the further exploration of the molecular mechanisms during skeletal muscle development.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, No. 1 Mingxian South Road, Taigu 030801, China; (S.W.); (M.S.); (Y.Z.); (J.N.); (W.L.); (J.Y.); (C.C.); (Y.Y.); (P.G.); (X.G.); (B.L.)
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, No. 1 Mingxian South Road, Taigu 030801, China; (S.W.); (M.S.); (Y.Z.); (J.N.); (W.L.); (J.Y.); (C.C.); (Y.Y.); (P.G.); (X.G.); (B.L.)
| |
Collapse
|
2
|
Yu B, Liu J, Cai Z, Mu T, Gu Y, Xin G, Zhang J. miRNA-mRNA associations with inosine monophosphate specific deposition in the muscle of Jingyuan chicken. Br Poult Sci 2022; 63:821-832. [PMID: 35895079 DOI: 10.1080/00071668.2022.2106777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Inosine monophosphate (IMP), is an essential component for meat flavour and microRNAs (miRNAs) play a vital role in its post-transcriptional regulation. However, the mechanism of how miRNA expression affects muscle-specific IMP deposition is unclear.2. The following study performed transcriptome sequencing and bioinformatics analysis of breast and leg muscle, which have significantly different IMP content in Jingyuan chicken. The differential miRNA-mRNAs were screened out and correlation analysis with IMP content was performed.3. A total of 39 differentially expressed miRNAs (DE miRNAs) and 666 differentially expressed mRNAs (DE mRNAs) were identified between breast muscles and leg muscles. Using miRNA-mRNA integrated analysis, 29 miRNA-target gene pairs were obtained, composed of 13 DE miRNAs and 28 DE mRNAs. Next, purine metabolism, glycolysis/gluconeogenesis, pyruvate metabolism and the biosynthesis of amino acid pathways as necessary for muscle IMP-specific deposition were identified. The differentially expressed gene PKM2, which was significantly enriched in all four pathways, is involved in IMP anabolism in the form of energy metabolism and enzyme activity regulation. The correlation analysis suggested that the gga-miR-107-3p-KLHDC2 negative interaction may be a key regulator in IMP deposition.4. This study explores the functional mechanism of IMP-specific deposition in Jingyuan chicken muscles at the miRNA and mRNA levels and highlights multiple candidate miRNAs and mRNAs for molecular-assisted breeding.
Collapse
Affiliation(s)
- Baojun Yu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Jiamin Liu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Zhengyun Cai
- College of Agriculture, Ningxia University, Yinchuan China
| | - Tong Mu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Yaling Gu
- College of Agriculture, Ningxia University, Yinchuan China
| | - Guosheng Xin
- School of Life Sciences, Ningxia University/Ningxia Feed Engineering Technology Research Center, Yinchuan China
| | - Juan Zhang
- College of Agriculture, Ningxia University, Yinchuan China
| |
Collapse
|
3
|
Daza KR, Velez-Irizarry D, Casiró S, Steibel JP, Raney NE, Bates RO, Ernst CW. Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle. Front Genet 2021; 12:644091. [PMID: 33859669 PMCID: PMC8042294 DOI: 10.3389/fgene.2021.644091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/24/2021] [Indexed: 01/19/2023] Open
Abstract
Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from longissimus dorsi muscle samples with genotypic and phenotypic data from the same animals. We identified 23 miRNA expression Quantitative Trait Loci (miR-eQTL) at the genome-wide level and examined their potential effects on these important production phenotypes through miRNA target prediction, correlation, and colocalization analyses. One miR-eQTL miRNA, miR-874, has target genes that colocalize with phenotypic QTL for 12 production traits across the genome including backfat thickness, dressing percentage, muscle pH at 24 h post-mortem, and cook yield. The results of our study reveal genomic regions underlying variation in miRNA expression and identify miRNAs and genes for future validation of their regulatory effects on traits of economic importance to the global pig industry.
Collapse
Affiliation(s)
- Kaitlyn R Daza
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Deborah Velez-Irizarry
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Sebastian Casiró
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ronald O Bates
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| |
Collapse
|
4
|
Miretti S, Lecchi C, Ceciliani F, Baratta M. MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock. Front Vet Sci 2020; 7:578193. [PMID: 33392281 PMCID: PMC7775535 DOI: 10.3389/fvets.2020.578193] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.
Collapse
Affiliation(s)
- Silvia Miretti
- Department of Veterinary Sciences, University of Torino, Grugliasco, Italy
| | - Cristina Lecchi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Fabrizio Ceciliani
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Mario Baratta
- Department of Veterinary Sciences, University of Torino, Grugliasco, Italy
| |
Collapse
|
5
|
Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages. Animals (Basel) 2020; 10:ani10071198. [PMID: 32679676 PMCID: PMC7401622 DOI: 10.3390/ani10071198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 06/18/2020] [Accepted: 07/11/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary The pigs is the most popular agricultural animal in the world. Muscle growth—which has the highest economic value in pigs—can be regulated by multiple genes and involves complex regulatory mechanisms. It is necessary to understand the dynamics of muscle transcriptome during development to understand the muscle development mechanism. However, the genes and miRNAs that play regulatory roles underlying differences in the meat quality of pigs remain unclear. In the current study, qRT-PCR, miRNA-Seq, and RNA-Seq were applied to analyze and verify muscle tissues of pigs from three different developmental stages and screened genes, miRNAs and pathways related to pig muscle development. This study focused on analyzing the mechanisms of muscle development and uncover the development differences in muscle from embryo to adult. Abstract The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.
Collapse
|
6
|
Škrlep M, Tomažin U, Lukač NB, Poklukar K, Čandek-Potokar M. Proteomic Profiles of the Longissimus Muscles of Entire Male and Castrated Pigs as Related to Meat Quality. Animals (Basel) 2019; 9:E74. [PMID: 30818748 PMCID: PMC6465998 DOI: 10.3390/ani9030074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 01/21/2023] Open
Abstract
There are indications of reduced meat quality in entire male pigs (EMs) in comparison to surgically castrated pigs (SCs); however, the differences are not strongly confirmed, and the etiology is not clarified. In the present study, samples of the longissimus dorsi, pars lumborum muscle (LL) from EMs (n = 12) and SCs (n = 12) of the same age and weight were evaluated at the physico-chemical and proteomic level. EMs exhibited lower intramuscular fat content, higher collagen content with higher solubility, a higher level of protein carbonyl groups (indicating higher protein oxidation), lower water holding capacity, and tougher meat than SCs. Proteomic analysis revealed differences in heat shock proteins expression, while a greater abundance of several other identified proteins (malate dehydrogenase, Na/K-transporting adenosintriphosphatase (ATP-ase) subunit alpha-1, and blood plasma proteins) indicates that EMs have a more oxidative metabolic profile than that of SCs. More abundant protein fragments (mainly actin and myosin heavy chain) suggest a higher degree of proteolysis in EMs, which was not followed by lower meat toughness.
Collapse
Affiliation(s)
- Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Urška Tomažin
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Nina Batorek Lukač
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Marjeta Čandek-Potokar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
- University of Maribor, Faculty of Agriculture and Life Sciences, Pivola 10, 2311 Hoče, Slovenia.
| |
Collapse
|
7
|
Ropka-Molik K, Pawlina-Tyszko K, Żukowski K, Piórkowska K, Żak G, Gurgul A, Derebecka N, Wesoły J. Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data. Int J Mol Sci 2018; 19:ijms19041208. [PMID: 29659518 PMCID: PMC5979540 DOI: 10.3390/ijms19041208] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Abstract
Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Pietrain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-β signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.
Collapse
Affiliation(s)
- Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Grzegorz Żak
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Artur Gurgul
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.
| |
Collapse
|
8
|
Yang W, Tang K, Wang Y, Zan L. MiR-27a-5p Increases Steer Fat Deposition Partly by Targeting Calcium-sensing Receptor (CASR). Sci Rep 2018; 8:3012. [PMID: 29445089 PMCID: PMC5813002 DOI: 10.1038/s41598-018-20168-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/15/2018] [Indexed: 12/18/2022] Open
Abstract
Castration increases fat deposition, improving beef quality in cattle. Here, the steer group exhibited a significantly higher intramuscular fat (IMF) content than the bull group. To determine the potential roles of microRNAs (miRNAs) in castration-induced fat deposition, differential expression patterns of miRNA in liver tissue were investigated in bulls and steers. A total of 7,827,294 clean reads were obtained from the bull liver library, and 8,312,483 were obtained from the steer liver library; 452 conserved bovine miRNAs and 20 novel miRNAs were identified. The results showed that the expression profiles of miRNA in liver tissue were changed by castration, and 12 miRNAs that were differentially expressed between bulls and steers were identified. Their target genes were majorly involved in the metabolic, PI3K-Akt, and MAPK signaling pathways. Furthermore, six differentially expressed miRNAs were validated by quantitative real-time PCR, and luciferase reporter assays verified that calcium-sensing receptor (CASR) was the direct target of miR-27a-5p. Meantime, we found that the expression level of CASR was significantly higher in steers than in bulls, and revealed that CASR gene silencing in bovine hepatocytes significantly inhibited triacylglycerol (TAG) accumulation and reduced secretion of very low density lipoprotein (VLDL). These results obtained in the liver indicate that miR-27a-5p may increase fat deposition partly by targeting CASR in steers.
Collapse
Affiliation(s)
- Wucai Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Keqiong Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yaning Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
9
|
Daza KR, Steibel JP, Velez-Irizarry D, Raney NE, Bates RO, Ernst CW. Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F 2 Duroc × Pietrain pig resource population. GENOMICS DATA 2017; 13:50-53. [PMID: 28736700 PMCID: PMC5508516 DOI: 10.1016/j.gdata.2017.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 11/12/2022]
Abstract
To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~ 5.5 months of age) from a Duroc × Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1 × 50 bp format. After processing, 232,826,977 total reads were aligned to the Sus scrofa reference genome (v10.2.79), with 74.8% of total reads mapping successfully. The miRDeep2 software package was utilized to quantify annotated Sus scrofa mature miRNAs from miRBase (Release 21) and to predict candidate novel miRNA precursors. Among the retained 295 normalized mature miRNA expression profiles sscmiR1, sscmiR133a3p, sscmiR378, sscmiR206, and sscmiR10b were the most abundant, all of which have previously been shown to be expressed in pig skeletal muscle. Additionally, 27 unique candidate novel miRNA precursors were identified exhibiting homologous sequence to annotated human miRNAs. The composition of classes of small RNA present in this dataset was also characterized; while the majority of unique expressed sequence tags were not annotated in any of the queried databases, the most abundantly expressed class of small RNA in this dataset was miRNAs. This data provides a resource to evaluate miRNA regulation of gene expression and effects on complex trait phenotypes in adult pig skeletal muscle. The raw sequencing data were deposited in the Sequence Read Archive, BioProject PRJNA363073.
Collapse
Affiliation(s)
- Kaitlyn R Daza
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | | | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Ronald O Bates
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
10
|
Xing B, Bai X, Guo H, Chen J, Hua L, Zhang J, Ma Q, Ren Q, Wang H, Wang J. Long non-coding RNA analysis of muscular responses to testosterone deficiency in Huainan male pigs. Anim Sci J 2017; 88:1451-1456. [DOI: 10.1111/asj.12777] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 11/01/2016] [Accepted: 12/12/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Baosong Xing
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Xianxiao Bai
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Hongxia Guo
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Junfeng Chen
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Liushuai Hua
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Jiaqing Zhang
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Qiang Ma
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Qiaoling Ren
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| | - Huashuai Wang
- Henan Xing Rui agriculture and animal husbandry technology Co.; LTD; Xinyang China
| | - Jing Wang
- Institute of Animal Husbandry and Veterinary Science; Henan Academy of Agricultural Sciences; Zhengzhou China
| |
Collapse
|
11
|
Wang J, Chen J, Zhang J, Gao B, Bai X, Lan Y, Lin P, Guo H, Gao Y, Xing B. Castration-induced changes in the expression profiles and promoter methylation of the GHR gene in Huainan male pigs. Anim Sci J 2016; 88:1113-1119. [PMID: 27925358 DOI: 10.1111/asj.12739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/31/2016] [Accepted: 09/23/2016] [Indexed: 12/13/2022]
Abstract
Castration plays a regulatory role in growth and carcass traits, particularly in fat deposition, but its molecular mechanisms are still not clear. The present study showed that castration significantly reduced the serum growth hormone and the responses of the growth hormone receptor (GHR), insulin-like growth factor 1 (IGF-I), IGF-IR and peroxisome proliferator-activated receptor gamma (PPARγ) to castration were similar in different adipose tissues. However, the GHR expression trends were opposite between the liver and the adipose tissues; bisulfite sequencing PCR (BSP) showed that its methylation in these two tissues was different. In particular, the GHR methylation rate in the liver of castrated and intact pigs were 93.33% and 0, respectively, which was consistent with its higher expression level in the intact group. It was predicted that there were potential binding sites for 11 transcription factors in the ninth CpG site (which was methylated and demethylated in subcutaneous adipose tissue of the intact and castrated groups, respectively), including androgen receptor (AR), CCAAT/enhancer binding protein-α (C/EBPα) and C/EBPβ, all of which are important factors in lipid metabolism. These results indicate that DNA methylation may participate in castration-induced fat deposition.
Collapse
Affiliation(s)
- Jing Wang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Junfeng Chen
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Jiaqing Zhang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Binwen Gao
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Xianxiao Bai
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Yali Lan
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Ping Lin
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Hongxia Guo
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| | - Yuan Gao
- Henan Xing Rui agricultural and animal husbandry technology Co., LTD, Henan, China
| | - Baosong Xing
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Henan, China
| |
Collapse
|
12
|
Liu L, Qian K, Wang C. Discovery of porcine miRNA-196a/b may influence porcine adipogenesis in longissimus dorsi muscle by miRNA sequencing. Anim Genet 2016; 48:175-181. [DOI: 10.1111/age.12520] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Linqing Liu
- Institute of Animal Sciences and Veterinary Medicine; Anhui Academy of Agricultural Sciences; Hefei 230031 Anhui Province China
| | - Kun Qian
- Institute of Animal Sciences and Veterinary Medicine; Anhui Academy of Agricultural Sciences; Hefei 230031 Anhui Province China
| | - Chonglong Wang
- Institute of Animal Sciences and Veterinary Medicine; Anhui Academy of Agricultural Sciences; Hefei 230031 Anhui Province China
| |
Collapse
|
13
|
Bovo S, Mazzoni G, Calò DG, Galimberti G, Fanelli F, Mezzullo M, Schiavo G, Scotti E, Manisi A, Samoré AB, Bertolini F, Trevisi P, Bosi P, Dall'Olio S, Pagotto U, Fontanesi L. Deconstructing the pig sex metabolome: Targeted metabolomics in heavy pigs revealed sexual dimorphisms in plasma biomarkers and metabolic pathways. J Anim Sci 2016; 93:5681-93. [PMID: 26641177 DOI: 10.2527/jas.2015-9528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolomics has opened new possibilities to investigate metabolic differences among animals. In this study, we applied a targeted metabolomic approach to deconstruct the pig sex metabolome as defined by castrated males and entire gilts. Plasma from 545 performance-tested Italian Large White pigs (172 castrated males and 373 females) sampled at about 160 kg live weight were analyzed for 186 metabolites using the Biocrates AbsoluteIDQ p180 Kit. After filtering, 132 metabolites (20 AA, 11 biogenic amines, 1 hexose, 13 acylcarnitines, 11 sphingomyelins, 67 phosphatidylcholines, and 9 lysophosphatidylcholines) were retained for further analyses. The multivariate approach of the sparse partial least squares discriminant analysis was applied, together with a specifically designed statistical pipeline, that included a permutation test and a 10 cross-fold validation procedure that produced stability and effect size statistics for each metabolite. Using this approach, we identified 85 biomarkers (with metabolites from all analyzed chemical families) that contributed to the differences between the 2 groups of pigs ( < 0.05 at the stability statistic test). All acylcarnitines and almost all biogenic amines were higher in castrated males than in gilts. Metabolites involved in tryptophan catabolism had the largest differences (i.e., delta = 20% for serotonin) between castrated males (higher) and gilts (lower). The level of several AA (Ala, Arg, Gly, His, Lys, Ser, Thr, and Trp) was higher in gilts (delta was from approximately 1.0 to approximately 4.8%) whereas products of AA catabolism (taurine, 2-aminoadipic acid, and methionine sulfoxide) were higher in castrated males (delta was approximately 5.0-6.0%), suggesting a metabolic shift in castrated males toward energy storage and lipid production. Similar general patterns were observed for most sphingomyelins, phosphatidylcholines, and lysophosphatidylcholines. Metabolomic pathway analysis and pathway enrichment identified several differences between the 2 sexes. This metabolomic overview opened new clues on the biochemical mechanisms underlying sexual dimorphism that, on one hand, might explain differences in terms of economic traits between castrated male pigs and entire gilts and, on the other hand, could strengthen the pig as a model to define metabolic mechanisms related to fat deposition.
Collapse
|
14
|
Ibrahim A, Ali MM, Abou-Khalil NS, Ali MF. Evaluation of chemical castration with calcium chloride versus surgical castration in donkeys: testosterone as an endpoint marker. BMC Vet Res 2016; 12:46. [PMID: 26956100 PMCID: PMC4784444 DOI: 10.1186/s12917-016-0670-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For the last few years, researchers have been interested in developing a method for chemical sterilization which may be a better alternative to surgical castration. An ideal chemical sterilant would be one that effectively arrests spermatogenesis and androgenesis as well as libido with absence of toxic or other side effects. Calcium chloride in various solutions and concentrations has been tested in many animal species, but few studies have been evaluated it in equines as a chemical sterilant. So, the objective of this study was to evaluate the clinical efficacy of chemical castration with 20% calcium chloride dissolved in absolute ethanol in comparison with surgical castration in donkeys based on the changes in the serum testosterone level and the histopathological changes in treated testes. METHODS Twelve clinically healthy adult male donkeys were used in this study. Donkeys were divided randomly and equally into two groups: a surgical (S) group (n = 6) and a chemical (C) group (n = 6). Animals in the (S) group were subjected to surgical castration while those in the (C) group received a single bilateral intratesticular injection of 20% calcium chloride dissolved in absolute ethanol (20 ml/testis). Animals were kept under clinical observation for 60 days. Changes in animals' behavior and gross changes in external genitalia were monitored daily. Serum concentrations of testosterone were measured prior to treatment and at 15, 30, 45 and 60 days post-treatment. Testicles in the (C) group were examined histopathologically at the end of the experiment. RESULTS Chemical castration with intratesticular calcium chloride vs. surgical castration failed to reduce serum concentrations of testosterone throughout the whole duration of the study; however it induced orchitis that was evident by focal necrotic areas in seminiferous tubules, cellular infiltration of neutrophils, proliferative intertubular fibrosis with a compensatory proliferation of Leydig cells. Donkeys tolerated the intratesticular injection of calcium chloride. There were no detectable changes in the general health status of the animals with the exception of swelling in external genitalia, scrotal ulcerations and fistulas. Food and water consumption and the gait of animals remained unaffected. CONCLUSION Intratesticular calcium chloride can't be considered an effective method for chemical castration in donkeys.
Collapse
Affiliation(s)
- Ahmed Ibrahim
- Department of Surgery, Anesthesiology and Radiology, Faculty of veterinary medicine, Assuit University, Assuit, 70155, Egypt.
| | - Magda M Ali
- Department of Surgery, Anesthesiology and Radiology, Faculty of veterinary medicine, Assuit University, Assuit, 70155, Egypt
| | - Nasser S Abou-Khalil
- Department of Medical physiology, Faculty of medicine, Assuit University, Assuit, Egypt
| | - Marwa F Ali
- Department of Pathology and clinical pathology, Faculty of veterinary medicine, Assuit University, Assuit, Egypt
| |
Collapse
|