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Zheng C, Zhong Y, Zhang P, Guo Q, Li F, Duan Y. Dynamic transcriptome profiles of skeletal muscle growth and development in Shaziling and Yorkshire pigs using RNA-sequencing. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:7301-7314. [PMID: 38647104 DOI: 10.1002/jsfa.13551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/07/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND We previously demonstrated that Shaziling and Yorkshire pigs differ in growth rate and meat quality. However, the molecular mechanisms responsible for such phenotypic differences remain unclear. In the present study, we performed a transcriptomic analysis of 36 longissimus dorsi (LM) and 36 soleus (SM) muscle samples from Shaziling and Yorkshire pigs at six postnatal stages (30, 60, 90, 150, 210 and 300 days) to explore the differences in postnatal skeletal muscle of Shaziling and Yorkshire pigs. RESULTS Muscle morphological changes and the number of differentially expressed genes indicated the two stages of 60-90 days and 150-210 days were critical for the muscle growth and development in Shaziling pigs. Genes such as FLNC, COL1A1, NRAP, SMYD1, TNNI3, CRYAB and PDLIM3 played vital roles in the muscle growth, and genes such as CCDC71L, LPIN1, CPT1A, UCP3, NR4A3 and PDK4 played dominant roles in the lipid metabolism. Additionally, in contrast to the LM, the percentage of slow-twitch muscle fibers in the SM of both breeds consistently decreased from 30 to 150 days of age, but there was a significant rebound at 210 days of age. However, the percentage of slow-twitch muscle fibers in the SM of Shaziling pigs was higher than that in Yorkshire pigs, which may be associated with the calcium signaling pathway and the PPARβ/δ signaling pathway. CONCLUSION The present study detected two critical periods and many functional genes for the muscle growth and development of Shaziling pigs, and showed differences in muscle fiber characteristics between Shaziling and Yorkshire pigs. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Changbing Zheng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yinzhao Zhong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peiwen Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qiuping Guo
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fengna Li
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yehui Duan
- CAS Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Yu M, Feng Y, Yan J, Zhang X, Tian Z, Wang T, Wang J, Shen W. Transcriptomic regulatory analysis of skeletal muscle development in landrace pigs. Gene 2024; 915:148407. [PMID: 38531491 DOI: 10.1016/j.gene.2024.148407] [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] [Received: 10/17/2023] [Revised: 12/28/2023] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
The development of pig skeletal muscle is a complex dynamic regulation process, which mainly includes the formation of primary and secondary muscle fibers, the remodeling of muscle fibers, and the maturation of skeletal muscle; However, the regulatory mechanism of the entire developmental process remains unclear. This study analyzed the whole-transcriptome data of skeletal muscles at 27 developmental nodes (E33-D180) in Landrace pigs, and their key regulatory factors in the development process were identified using the bioinformatics method. Firstly, we constructed a transcriptome expression map of skeletal muscle development from embryo to adulthood in Landrace pig. Subsequently, due to drastic change in gene expression, the perinatal periods including E105, D0 and D9, were focused, and the genes related to the process of muscle fiber remodeling and volume expansion were revealed. Then, though conjoint analysis with miRNA and lncRNA transcripts, a ceRNA network were identified, which consist of 11 key regulatory genes (such as CHAC1, RTN4IP1 and SESN1), 7 miRNAs and 43 lncRNAs, and they potentially play an important role in the process of muscle fiber differentiation, muscle fiber remodeling and volume expansion, intramuscular fat deposition, and other skeletal muscle developmental events. In summary, we reveal candidate genes and underlying molecular regulatory networks associated with perinatal skeletal muscle fiber type remodeling and expansion. These data provide new insights into the molecular regulation of mammalian skeletal muscle development and diversity.
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Affiliation(s)
- Mubin Yu
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanqin Feng
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jiamao Yan
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyuan Zhang
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhe Tian
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Tao Wang
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Junjie Wang
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
| | - Wei Shen
- Key Laboratory of Animal Reproduction and Biotechnology in Universities of Shandong, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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Xiong H, Zhang Y, Zhao Z, Sha Q. Whole-genome SNP allele frequency differences between Tibetan and Large white pigs reveal genes associated with skeletal muscle growth. BMC Genomics 2024; 25:588. [PMID: 38862895 PMCID: PMC11167949 DOI: 10.1186/s12864-024-10508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND The skeletal muscle growth rate and body size of Tibetan pigs (TIB) are lower than Large white pigs (LW). However, the underlying genetic basis attributing to these differences remains uncertain. To address this knowledge gap, the present study employed whole-genome sequencing of TIB (slow growth) and LW (fast growth) individuals, and integrated with existing NCBI sequencing datasets of TIB and LW individuals, enabling the identification of a comprehensive set of genetic variations for each breed. The specific and predominant SNPs in the TIB and LW populations were detected by using a cutoff value of 0.50 for SNP allele frequency and absolute allele frequency differences (△AF) between the TIB and LW populations. RESULTS A total of 21,767,938 SNPs were retrieved from 44 TIB and 29 LW genomes. The analysis detected 2,893,106 (13.29%) and 813,310 (3.74%) specific and predominant SNPs in the TIB and LW populations, and annotated to 24,560 genes. Further GO analysis revealed 291 genes involved in biological processes related to striated and/or skeletal muscle differentiation, proliferation, hypertrophy, regulation of striated muscle cell differentiation and proliferation, and myoblast differentiation and fusion. These 291 genes included crucial regulators of muscle cell determination, proliferation, differentiation, and hypertrophy, such as members of the Myogenic regulatory factors (MRF) (MYOD, MYF5, MYOG, MYF6) and Myocyte enhancer factor 2 (MEF2) (MEF2A, MEF2C, MEF2D) families, as well as muscle growth inhibitors (MSTN, ACVR1, and SMAD1); KEGG pathway analysis revealed 106 and 20 genes were found in muscle growth related positive and negative regulatory signaling pathways. Notably, genes critical for protein synthesis, such as MTOR, IGF1, IGF1R, IRS1, INSR, and RPS6KA6, were implicated in these pathways. CONCLUSION This study employed an effective methodology to rigorously identify the potential genes associated with skeletal muscle development. A substantial number of SNPs and genes that potentially play roles in the divergence observed in skeletal muscle growth between the TIB and LW breeds were identified. These findings offer valuable insights into the genetic underpinnings of skeletal muscle development and present opportunities for enhancing meat production through pig breeding.
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Affiliation(s)
- Heli Xiong
- Animal Nutrition and Swine Institute, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming, 650224, China.
| | - Yan Zhang
- Animal Nutrition and Swine Institute, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming, 650224, China
| | - Zhiyong Zhao
- Animal Nutrition and Swine Institute, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming, 650224, China
| | - Qian Sha
- Animal Nutrition and Swine Institute, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming, 650224, China
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Liu Y, Wu X, Xu Q, Lan X, Li W. Temporal Transcriptome Dynamics of Longissimus dorsi Reveals the Mechanism of the Differences in Muscle Development and IMF Deposition between Fuqing Goats and Nubian Goats. Animals (Basel) 2024; 14:1770. [PMID: 38929389 PMCID: PMC11200590 DOI: 10.3390/ani14121770] [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: 04/25/2024] [Revised: 06/02/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we measured the growth performance and intramuscular fat (IMF) content of the Longissimus dorsi (LD) of Fuqing goats (FQs) and Nubian goats (NBYs), which exhibit extreme phenotypic differences in terms of their production and meat quality traits. RNA-Seq analysis was performed, and transcriptome data were obtained from the LD tissue of 3-month fetuses (E3), 0-month lambs (0M), 3-month lambs (3M), and 12-month lambs (12M) to reveal the differences in the molecular mechanisms regulating the muscle development and IMF deposition between FQs and NBYs. The results showed that a higher body weight and average daily gain were observed in the NBYs at three developmental stages after birth, whereas a higher IMF content was registered in the FQs at 12M. Additionally, transcriptome profiles during the embryonic period and after birth were completely different for both FQs and NBYs. Moreover, DEGs (KIF23, CCDC69, CCNA2, MKI67, KIF11, RACGAP1, NUSAP1, SKP2, ZBTB18, NES, LOC102180034, CAPN6, TUBA1A, LOC102178700, and PEG10) significantly enriched in the cell cycle (ko04110) at E3 (FQs vs. NBYs), and DEGs (MRPS7, RPS8, RPL6, RPL4, RPS11, RPS10, RPL5, RPS6, RPL8, RPS13, RPS24, RPS15, RPL23) significantly enriched in ribosomes (ko03010) at 0M (FQs vs. NBYs) related to myogenic differentiation and fusion were identified. Meanwhile, the differences in glucose and lipid metabolism began at the E3 timepoint and continued to strengthen as growth proceeded in FQs vs. NBYs. DEGs (CD36, ADIROQR2, ACACA, ACACB, CPT1A, IGF1R, IRS2, LDH-A, PKM, HK2, PFKP, PCK1, GPI, FASN, FADS1, ELOVL6, HADHB, ACOK1, ACAA2, and ACSL4) at 3M (FQs vs. NBYs) and 12M (FQs vs. NBYs) significantly enriched in the AMPK signaling pathway (ko04152), insulin resistance (ko04931), the insulin signaling pathway (ko04910), fatty acid metabolism (ko01212), and glycolysis/gluconeogenesis (ko00010) related to IMF deposition were identified. Further, the results from this study provide the basis for future studies on the mechanisms regulating muscle development and IMF deposition in different breeds of goats, and the candidate genes identified could be used in the selection process.
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Affiliation(s)
- Yuan Liu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
| | - Xianfeng Wu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
| | - Qian Xu
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Wenyang Li
- Fujian Provincial Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.L.); (X.W.); (Q.X.)
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Wang X, Gan M, Wang Y, Wang S, Lei Y, Wang K, Zhang X, Chen L, Zhao Y, Niu L, Zhang S, Zhu L, Shen L. Comprehensive review on lipid metabolism and RNA methylation: Biological mechanisms, perspectives and challenges. Int J Biol Macromol 2024; 270:132057. [PMID: 38710243 DOI: 10.1016/j.ijbiomac.2024.132057] [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] [Received: 03/03/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
Adipose tissue plays a crucial role in maintaining energy balance, regulating hormones, and promoting metabolic health. To address disorders related to obesity and develop effective therapies, it is essential to have a deep understanding of adipose tissue biology. In recent years, RNA methylation has emerged as a significant epigenetic modification involved in various cellular functions and metabolic pathways. Particularly in the realm of adipogenesis and lipid metabolism, extensive research is ongoing to uncover the mechanisms and functional importance of RNA methylation. Increasing evidence suggests that RNA methylation plays a regulatory role in adipocyte development, metabolism, and lipid utilization across different organs. This comprehensive review aims to provide an overview of common RNA methylation modifications, their occurrences, and regulatory mechanisms, focusing specifically on their intricate connections to fat metabolism. Additionally, we discuss the research methodologies used in studying RNA methylation and highlight relevant databases that can aid researchers in this rapidly advancing field.
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Affiliation(s)
- Xingyu Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Saihao Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhang Lei
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linyuan Shen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
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Yang P, Shang M, Bao J, Liu T, Xiong J, Huang J, Sun J, Zhang L. Whole-Genome Resequencing Revealed Selective Signatures for Growth Traits in Hu and Gangba Sheep. Genes (Basel) 2024; 15:551. [PMID: 38790179 PMCID: PMC11120742 DOI: 10.3390/genes15050551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/26/2024] Open
Abstract
A genomic study was conducted to uncover the selection signatures in sheep that show extremely significant differences in growth traits under the same breed, age in months, nutrition level, and management practices. Hu sheep from Gansu Province and Gangba sheep from the Tibet Autonomous Region in China were selected. We collected whole-genome data from 40 sheep individuals (24 Hu sheep and 16 Gangba sheep), through whole-genome sequencing. Selection signals were analyzed using parameters such as FST, π ratio, and Tajima's D. We have identified several candidate genes that have undergone strong selection, particularly those associated with growth traits. Specifically, five growth-related genes were identified in both the Hu sheep group (HDAC1, MYH7B, LCK, ACVR1, GNAI2) and the Gangba sheep group (RBBP8, ACSL3, FBXW11, PLAT, CRB1). Additionally, in a genomic region strongly selected in both the Hu and Gangba sheep groups (Chr 22: 51,425,001-51,500,000), the growth-associated gene CYP2E1 was identified, further highlighting the genetic factors influencing growth characteristics in these breeds. This study analyzes the genetic basis for significant differences in sheep phenotypes, identifies candidate genes related to sheep growth traits, lays the foundation for molecular genetic breeding in sheep, and accelerates the genetic improvement in livestock.
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Affiliation(s)
| | | | | | | | | | | | | | - Li Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (P.Y.); (M.S.); (J.B.); (T.L.); (J.X.); (J.H.); (J.S.)
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Xiao L, Qiao J, Huang Y, Tan B, Hong L, Li Z, Cai G, Wu Z, Zheng E, Wang S, Gu T. RASGRP1 targeted by H3K27me3 regulates myoblast proliferation and differentiation in mice and pigs. Acta Biochim Biophys Sin (Shanghai) 2024; 56:452-461. [PMID: 38419500 PMCID: PMC10984873 DOI: 10.3724/abbs.2024011] [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] [Received: 09/09/2023] [Accepted: 11/14/2023] [Indexed: 03/02/2024] Open
Abstract
Skeletal muscle is not only the largest organ in the body that is responsible for locomotion and exercise but also crucial for maintaining the body's energy metabolism and endocrine secretion. The trimethylation of histone H3 lysine 27 (H3K27me3) is one of the most important histone modifications that participates in muscle development regulation by repressing the transcription of genes. Previous studies indicate that the RASGRP1 gene is regulated by H3K27me3 in embryonic muscle development in pigs, but its function and regulatory role in myogenesis are still unclear. In this study, we verify the crucial role of H3K27me3 in RASGRP1 regulation. The gain/loss function of RASGRP1 in myogenesis regulation is performed using mouse myoblast C2C12 cells and primarily isolated porcine skeletal muscle satellite cells (PSCs). The results of qPCR, western blot analysis, EdU staining, CCK-8 assay and immunofluorescence staining show that overexpression of RASGRP1 promotes cell proliferation and differentiation in both skeletal muscle cell models, while knockdown of RASGRP1 leads to the opposite results. These findings indicate that RASGRP1 plays an important regulatory role in myogenesis in both mice and pigs.
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Affiliation(s)
- Liyao Xiao
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Jiaxin Qiao
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Yiyang Huang
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Baohua Tan
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangzhou510000China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and TechnologyGuangzhou510000China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingGuangzhou510000China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- Guangdong Wens Breeding Swine Technology Co.Ltd.Yunfu527400China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresourcesGuangzhou510000China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and TechnologyGuangzhou510000China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingGuangzhou510000China
- Guangdong Wens Breeding Swine Technology Co.Ltd.Yunfu527400China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
| | - Shanshan Wang
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
- College of Life ScienceHubei UniversityWuhan430000China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou510000China
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Chen JF, Wang J, Chai J, Jin W, Ren QL, Ma Q, Lu QX, Sun JJ, Mo DL, Zhang JQ, Xing BS. Transcriptome profiling of longissimus dorsi during different prenatal stages to identify genes involved in intramuscular fat deposition in lean and obese pig breeds. Mol Biol Rep 2024; 51:386. [PMID: 38441676 PMCID: PMC10914898 DOI: 10.1007/s11033-023-09088-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/29/2023] [Indexed: 03/07/2024]
Abstract
BACKGROUND There was significant difference in muscle development between fat-type and lean-type pig breeds. METHODS AND RESULTS In current study, transcriptome analysis and bioinformatics analysis were used to compare the difference in longissimus dorsi (LD) muscle at three time-points (38 days post coitus (dpc), 58 dpc, and 78 dpc ) between Huainan (HN) and Large white (LW) pig breeds. A total of 24500 transcripts were obtained in 18 samples, and 2319, 2799, and 3713 differently expressed genes (DEGs) were identified between these two breeds at 38 dpc, 58 dpc, and 78 dpc, respectively. And the number and foldchange of DEGs were increased, the alternative splice also increased. The cluster analysis of DEGs indicated the embryonic development progress of LD muscle between these two breeds was different. There were 539 shared DEGs between HN and LW at three stages, and the top-shared DEGs were associated with muscle development and lipid deposition, such as KLF4, NR4A1, HSP70, ZBTB16 and so on. CONCLUSIONS The results showed DEGs between Huainan (HN) and Large white (LW) pig breeds, and contributed to the understanding the muscle development difference between HN and LW, and provided basic materials for improvement of meat quality.
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Affiliation(s)
- Jun Feng Chen
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Jing Wang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Jin Chai
- Agricultural Ministry Key Laboratory of Swine Breeding and Genetics & Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Jin
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Qiao Ling Ren
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Qiang Ma
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Qing Xia Lu
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Jia Jie Sun
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - De Lin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jia Qing Zhang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China
| | - Bao Song Xing
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Huayuan Road No.116, Zhengzhou, 450002, Henan, China.
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9
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Sarri L, Balcells J, Seradj AR, de la Fuente G. Protein turnover in pigs: A review of interacting factors. J Anim Physiol Anim Nutr (Berl) 2024; 108:451-469. [PMID: 37975299 DOI: 10.1111/jpn.13906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 08/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Protein turnover defines the balance between two continuous and complex processes of protein metabolism, synthesis and degradation, which determine their deposition in tissues. Although the liver and intestine have been studied extensively for their important roles in protein digestion, absorption and metabolism, the study of protein metabolism has focused mainly on skeletal muscle tissue to understand the basis for its growth. Due to the high adaptability of skeletal muscle, its protein turnover is greatly affected by different internal and external factors, contributing to carcass lean-yield and animal growth. Amino acid (AA) labelling and tracking using isotope tracer methodology, together with the study of myofiber type profiling, signal transduction pathways and gene expression, has allowed the analysis of these mechanisms from different perspectives. Positive stimuli such as increased nutrient availability in the diet (e.g., AA), physical activity, the presence of certain hormones (e.g., testosterone) or a more oxidative myofiber profile in certain muscles or pig genotypes promote increased upregulation of translation and transcription-related genes, activation of mTORC1 signalling mechanisms and increased abundance of satellite cells, allowing for more efficient protein synthesis. However, fasting, animal aging, inactivity and stress, inflammation or sepsis produce the opposite effect. Deepening the understanding of modifying factors and their possible interaction may contribute to the design of optimal strategies to better control tissue growth and nutrient use (i.e., protein and AA), and thus advance the precision feeding strategy.
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Affiliation(s)
- Laura Sarri
- Departament de Ciència Animal, Universitat de Lleida- Agrotecnio-CERCA Center, Lleida, Spain
| | - Joaquim Balcells
- Departament de Ciència Animal, Universitat de Lleida- Agrotecnio-CERCA Center, Lleida, Spain
| | - Ahmad Reza Seradj
- Departament de Ciència Animal, Universitat de Lleida- Agrotecnio-CERCA Center, Lleida, Spain
| | - Gabriel de la Fuente
- Departament de Ciència Animal, Universitat de Lleida- Agrotecnio-CERCA Center, Lleida, Spain
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10
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Yan Z, Song K, Wang P, Gun S, Long X. Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province. Int J Mol Sci 2023; 24:17154. [PMID: 38138983 PMCID: PMC10743271 DOI: 10.3390/ijms242417154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Indigenous pig populations, including Bamei pigs (BM), Hezuo pigs (HZ), Huixian Qingni Black pigs (HX), and Minxian Black pigs (MX) in Gansu Province, live in a particular climate and a relatively closed geographical environment. These local pig breeds are characterized by excellent characteristics (e.g., cold tolerance, robust disease resistance, and superior meat quality). In the past few years, pig populations in Gansu Province have decreased significantly because of their poor lean meat percentage, high fat content, and slow growth rate. Maintaining the diversity of these four breeds can act as a source of new alleles to be incorporated into commercial breeds which are more susceptible to disease and less adaptable to changing conditions because of inbreeding. Genomic data analysis is adequate for determining the genetic diversity and livestock breeding population structure, even in local pig populations. However, the genetic diversity and population structure of the four native pig populations in Gansu Province are still unknown. Thus, we used "Zhongxin-I" porcine chip for the SNP detection of 102 individuals living on four pig conservation farms. A total of 57,466 SNPs were identified among the four pig breeds. The linkage disequilibrium (LD) plot showed that MX had the highest level of LD, followed by BM, HZ, and HX. The observed heterozygosity (Ho) in all four populations was higher than the expected heterozygosity (He). A principal component analysis (PCA) demonstrated that the four local pig populations were isolated. The identity displayed by the state matrix and G matrix heat map results indicated that small numbers of individuals among the four pig breeds had a high genetic distance and weak genetic relationships. The results of the population genetic structure of BM, HZ, HX, and MX pigs showed a slight genetic diversity loss. Our findings enabled us to better understand the genome characteristics of these four indigenous pig populations, which will provide novel insights for the future germplasm conservation and utilization of these indigenous pig populations.
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Affiliation(s)
- Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Kelin Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Z.Y.); (K.S.); (P.W.)
| | - Xi Long
- Chongqing Academy of Animal Sciences, Chongqing 402460, China
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11
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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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12
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He M, Zhang W, Wang S, Ge L, Cao X, Wang S, Yuan Z, Lv X, Getachew T, Mwacharo JM, Haile A, Sun W. Effects of YAP1 on proliferation and differentiation of Hu sheep skeletal muscle satellite cells in vitro. Anim Biotechnol 2023; 34:2691-2700. [PMID: 36001393 DOI: 10.1080/10495398.2022.2112688] [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: 11/01/2022]
Abstract
This study aimed to understand the expression level of YAP1 in the skeletal muscle of Hu sheep and to reveal the regulatory mechanism of YAP1 on Hu sheep skeletal muscle satellite cells (SMSCs). Previous research by our group has found that YAP1 may affect the growth and development of Hu sheep skeletal muscle. In the present study, we found the expression of YAP1 in the skeletal muscle is higher than in other tissues of Hu sheep. Then, we detected the effect of YAP1 on proliferation and differentiation in Hu sheep SMSCs. According to the results of qPCR, CCK-8, EDU, and Western blot, compared to the group of negative control, overexpression of YAP1 promoted the proliferation and inhibited the differentiation of SMSCs according to the results of qPCR, CCK-8, EDU, Western blot, while the interference of YAP1 was on the contrary. Overall, our study suggests that YAP1 is an important functional molecule in the growth and development of skeletal muscle by regulating the proliferation and differentiation of SMSCs. These findings are of great use for understanding the roles of YAP1 in the skeletal muscle of Hu sheep.
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Affiliation(s)
- Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Shan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Nanjing, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Nanjing, China
| | - Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Nanjing, China
| | - Tesfaye Getachew
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Aynalem Haile
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Nanjing, China
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13
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Yin S, Li Z, Yang F, Guo H, Zhao Q, Zhang Y, Yin Y, Wu X, He J. A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond. Int J Mol Sci 2023; 24:14550. [PMID: 37833998 PMCID: PMC10572203 DOI: 10.3390/ijms241914550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.
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Affiliation(s)
- Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Haimin Guo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Qinghua Zhao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
| | - Yulong Yin
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
- Animal Nutrition Genome and Germplasm Innovation Research Center, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaolin Wu
- Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
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14
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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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15
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El-Shobokshy SA, Abo-Samaha MI, El-Maksoud EMA, Khatab SA, Khafaga AF, Wirtu G. Influence of Nano-Methionine supplementation in drinking water on growth performance, lipid metabolism, and related gene expression in broiler chicken. J Adv Vet Anim Res 2022; 9:743-753. [PMID: 36714509 PMCID: PMC9868780 DOI: 10.5455/javar.2022.i644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/24/2022] [Accepted: 10/29/2022] [Indexed: 01/13/2023] Open
Abstract
Objectives The study aimed to determine how Nano-Methionine (Nano-Meth) affected growth, lipid metabolism, and relative gene expression for acetyl-CoA carboxylase (ACC), fatty acid synthase (FAS), growth hormone receptor (GHR), insulin-like growth factor receptor-1 (IGFR-1), myostatin (MSTN), and cholecystokinin (CCK) genes in broiler chickens. Materials and Methods A total of 100 1-day-old broilers were randomly assigned into 2 groups: 1) the control group received drinking water without any supplements, and 2) the Nano-Meth group received 10 ml/l of 5% Nano-Meth starting from 1 day old until 35 days old (the end of the experiment). Results Nano-Meth improved final body weight, weight gains, feed intake, and feed conversion ratio. Compared to the control group, Nano-Meth significantly lowered the serum levels of triglyceride, cholesterol, very low-density lipoprotein, and low-density lipoprotein in chickens. Nano-Meth significantly increased the serum levels of total protein, albumin, high-density lipoprotein, and glucose more than the control group. Nano-Meth lowered the mRNA gene expression of ACC, FAS, MSTN, and CCK but increased that of GHR and IGFR-1. Conclusions We concluded that supplementation with Nano-Meth enhances growth performance and decreases lipid accumulation in broiler chickens.
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Affiliation(s)
- Set A. El-Shobokshy
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Magda I. Abo-Samaha
- Poultry Breeding and Production, Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Eman M. Abd El-Maksoud
- Biochemistry Department, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Shymaa A. Khatab
- Genetics and Genetic Engineering, Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Asmaa F. Khafaga
- Pathology Department, Faculty of Veterinary Medicine, Alexandria University, Alexandria, Egypt
| | - Gemechu Wirtu
- Department of Biomedical Sciences, College of Veterinary Medicine, Tuskegee University, Tuskegee, AL, USA
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16
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Wang J, Chen JF, Ma Q, Mo DL, Sun JJ, Ren QL, Zhang JQ, Lu QX, Xing BS. Identification and characterization of circRNAs related to meat quality during embryonic development of the longissimus dorsi muscle in two pig breeds. Front Genet 2022; 13:1019687. [PMID: 36457752 PMCID: PMC9705349 DOI: 10.3389/fgene.2022.1019687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/27/2022] [Indexed: 11/26/2023] Open
Abstract
Meat quality, an important economic trait, is regulated by many factors, especially by genetic factors, including coding genes, miRNAs, and lncRNAs. Recent studies have elucidated that circRNAs also play a key role in muscle development and lipid deposition. However, the functions and regulatory mechanisms of circRNAs in meat quality remain mostly unknown. The circRNA expression profiles between Huainan pigs (Chinese indigenous pigs, fat-type, Huainan HN) and Large White pigs (Western commercial pigs, lean-type, LW) in the longissimus dorsi (LD) muscle at 38, 58, and 78 days post conception (dpc) were compared by sequencing. In total, 39,887 circRNAs were identified in 18 samples, and 60, 78, and 86 differentially expressed circRNAs (DECs) were found at the three stages mentioned above between these two breeds. The parent genes of DECs were enriched in myogenesis, proliferation, adipogenesis and muscle fiber-type transition. The circRNA-miRNA interaction networks included 38 DECs and 47 miRNAs, and these miRNAs were involved in muscle development and lipid metabolism. Two shared DECs (circ_0030593 and circ_0032760) of these three stages were selected, their head-to-tail junction sites were validated by Sanger sequencing, and RT‒qPCR results suggested that these two DECs might be involved in intramuscular fat deposition. These findings provide a basis for understanding the role of circRNAs in meat quality.
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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, Zhengzhou, China
| | - Jun-Feng Chen
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qiang Ma
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - De-Lin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jia-Jie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Guangdong Laboratory for Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qiao-Ling Ren
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jia-Qing Zhang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qing-Xia Lu
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bao-Song Xing
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
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17
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Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs. Biomolecules 2022; 12:biom12091294. [PMID: 36139132 PMCID: PMC9496231 DOI: 10.3390/biom12091294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs.
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18
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Yu B, Liu J, Zhang J, Mu T, Feng X, Ma R, Gu Y. Regulatory role of RNA N6-methyladenosine modifications during skeletal muscle development. Front Cell Dev Biol 2022; 10:929183. [PMID: 35990615 PMCID: PMC9389409 DOI: 10.3389/fcell.2022.929183] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/28/2022] [Indexed: 01/07/2023] Open
Abstract
Functional cells in embryonic myogenesis and postnatal muscle development undergo multiple stages of proliferation and differentiation, which are strict procedural regulation processes. N6-methyladenosine (m6A) is the most abundant RNA modification that regulates gene expression in specific cell types in eukaryotes and regulates various biological activities, such as RNA processing and metabolism. Recent studies have shown that m6A modification-mediated transcriptional and post-transcriptional regulation plays an essential role in myogenesis. This review outlines embryonic and postnatal myogenic differentiation and summarizes the important roles played by functional cells in each developmental period. Furthermore, the key roles of m6A modifications and their regulators in myogenesis were highlighted, and the synergistic regulation of m6A modifications with myogenic transcription factors was emphasized to characterize the cascade of transcriptional and post-transcriptional regulation during myogenesis. This review also discusses the crosstalk between m6A modifications and non-coding RNAs, proposing a novel mechanism for post-transcriptional regulation during skeletal muscle development. In summary, the transcriptional and post-transcriptional regulatory mechanisms mediated by m6A and their regulators may help develop new strategies to maintain muscle homeostasis, which are expected to become targets for animal muscle-specific trait breeding and treatment of muscle metabolic diseases.
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Notch signaling leads to a slower progression of embryonic myogenic differentiation in Landrace than in Langtang pigs. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1122-1132. [PMID: 35866607 PMCID: PMC9827795 DOI: 10.3724/abbs.2022095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Delving into porcine embryonic myogenesis is the key to elucidate the complex regulation of breed-specific differences in growth performance and meat production. Increasing evidence proves that pigs with less meat production show earlier embryonic myogenesis, but little is known about the underlying mechanisms. In this study, we examine the longissimus dorsi muscle (LDM) by immunohistochemistry and confirm that the differentiation of myogenic progenitors is increased ( P<0.05) in Lantang (LT, fatty) pigs compared with that in Landrace (LR, lean) pigs, which results in more ( P<0.001) differentiated myoblasts (Pax7 -/MyoD +) and less ( P<0.001) myogenic progenitors (Pax7 +/MyoD -) in LT pigs at 35 days post-conception (35dpc). Additionally, embryonic myogenic progenitors isolated from LT pigs show greater ( P<0.001) differentiation capacity with earlier expression of MyoD compared with those from LR pigs. Moreover, Notch signaling is more active ( P<0.05) in LR pig myogenic progenitors than in LT pig myogenic progenitors. Inhibition of Notch signaling in LR myogenic progenitors suppresses Pax7 expression and increases MyoD expression, thus promoting myogenic differentiation. Consistently, the process of myogenic progenitors differentiating into myoblasts in ex vivo embryo limbs is accelerated when Notch signaling is inhibited. These results indicate that Notch signaling facilitates the maintenance of myogenic progenitors and antagonizes myogenic differentiation by promoting Pax7 expression and preventing MyoD expression in LR pigs.
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20
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Gong X, Zheng M, Zhang J, Ye Y, Duan M, Chamba Y, Wang Z, Shang P. Transcriptomics-Based Study of Differentially Expressed Genes Related to Fat Deposition in Tibetan and Yorkshire Pigs. Front Vet Sci 2022; 9:919904. [PMID: 35754534 PMCID: PMC9218471 DOI: 10.3389/fvets.2022.919904] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Fat deposition traits are one of the key factors in pig production and breeding. The fat deposition capacity of pigs mainly affects the quality of pork and pig productivity. The aim of this study was to analyze the differential expression of mRNA levels in dorsal adipose tissue of Tibetan and York pigs at different growth stages using transcriptomic data to estimate key genes that regulate fat deposition in pigs. The results showed that a total of 32,747 positively expressed genes were present in the dorsal adipose tissue of the two breeds. Differentially expressed gene (DEG) screening of multiple combinations between the two breeds yielded 324 DEGS. Gene ontology (GO) biofunctional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGS were mainly involved in lipid metabolic pathways, steroid biosynthetic pathways and lipid biosynthetic processes, sterol biosynthetic processes, brown adipocyte differentiation, and other pathways related to lipid deposition and metabolism. The results showed that ACACA, SLC2A4 and THRSP genes positively regulated the lipid deposition ability and CHPT1 gene negatively regulated the lipid deposition ability in pigs. The results of this experiment suggest a theoretical basis for further studies on the regulatory mechanisms of fat deposition in pigs.
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Affiliation(s)
- Xinglong Gong
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Min Zheng
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Jian Zhang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Yourong Ye
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Mengqi Duan
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Yangzom Chamba
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Zhongbin Wang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
| | - Peng Shang
- Tibet Agriculture and Animal Husbandry College, Tibet, China.,The Provincial and Ministerial Co-founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Tibet, China
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21
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Identification and characterization of circular RNAs in Longissimus dorsi muscle tissue from two goat breeds using RNA-Seq. Mol Genet Genomics 2022; 297:817-831. [DOI: 10.1007/s00438-022-01887-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
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22
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Zhuang X, Lin Z, Xie F, Luo J, Chen T, Xi Q, Zhang Y, Sun J. Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages. BMC Genomics 2022; 23:294. [PMID: 35410129 PMCID: PMC9004053 DOI: 10.1186/s12864-022-08515-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 03/29/2022] [Indexed: 11/28/2022] Open
Abstract
Background Long-term artificial selection for growth rate and lean meat rate has eventually led to meat quality deterioration. Muscle fiber type is a key factor that markedly affects meat quality. circRNAs have been reported to participate in diverse biological activities, including myofiber growth and development; thus, we herein compared porcine circRNA transcriptome between oxidative and glycolytic muscle tissues. Results Longissimus thoracis muscle tissues were obtained from Lantang and Landrace pigs at birth (LT1D and LW1D, respectively) and 90 postnatal days (LT90D and LW90D, respectively). Hematoxylin and eosin staining and quantitative real-time PCR revealed that all structural traits of the muscle showed large variations between different breeds and growth stages. In total, 329 known miRNAs and 42,081 transcript candidates were identified; 6,962 differentially expressed transcripts were found to play a key role in myogenesis by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In addition, 3,352 circRNAs were identified using five predicting algorithms, and 104 circRNA candidates were differentially expressed. Integrated analysis of differentially expressed miRNAs, mRNAs, and circRNAs led to the identification of 777, 855, and 22 convincing ceRNA interactions in LT1D vs. LT90D, LW1D vs. LW90D, and LT90D vs. LW90D, respectively. Finally, we identified a circRNA candidate circKANSL1L, which showed high homology between mice and pigs, and it was found to inhibit the proliferation of C2C12 cells but promote their differentiation. Conclusions We identified genome-wide circRNAs in 0- and 90-day-old Lantang and Landrace pigs by RNA-seq and found that circRNAs were abundant, differentially expressed, and associated with myogenesis. Our results should serve as a reference for future studies on pork quality. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08515-7.
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Affiliation(s)
- Xiaona Zhuang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Zekun Lin
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Fang Xie
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Junyi Luo
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qianyun Xi
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yongliang Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jiajie Sun
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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23
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MicroRNA-181a Regulates the Proliferation and Differentiation of Hu Sheep Skeletal Muscle Satellite Cells and Targets the YAP1 Gene. Genes (Basel) 2022; 13:genes13030520. [PMID: 35328074 PMCID: PMC8949050 DOI: 10.3390/genes13030520] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
MicroRNA (miRNA) is of great importance to muscle growth and development, including the regulation of the proliferation and differentiation of skeletal muscle satellite cells (SMSCs). In our research group’s previous study, we found that miR-181a is differentially expressed in the longissimus dorsi muscle of Hu sheep at different stages. We speculated that miR-181a may participate in the growth and development process of Hu sheep. To understand the mechanism of miR-181a regulating the growth and development of Hu sheep skeletal muscle, we extracted skeletal muscle satellite cells from the longissimus dorsi muscle of 3-month-old Hu sheep fetuses and performed a series of experiments. Our results showed that miR-181a suppressed SMSCs’ proliferation using QRT-PCR, Western blot, CCK-8, EDU, and Flow cytometry cycle tests. In addition, QRT-PCR, Western blot, and immunofluorescence indicated that miR-181a facilitated the differentiation of SMSCs. Then, we used dual-luciferase reporter gene detection, QRT-PCR, and Western blot to find that the Yes1-related transcription regulator (YAP1) is the target gene of miR-181a. Our study supplies a research basis for understanding the regulation mechanism of miR-181a on the growth of Hu sheep skeletal muscle.
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24
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Cai S, Duo T, Wang X, Tong X, Luo C, Chen Y, Li J, Mo D. A Comparative Analysis of Metabolic Profiles of Embryonic Skeletal Muscle from Lantang and Landrace Pigs. Animals (Basel) 2022; 12:ani12040420. [PMID: 35203128 PMCID: PMC8868109 DOI: 10.3390/ani12040420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The pig is one of the most important domesticated meat animals. Some studies have revealed that pigs with low meat production show more intense myogenesis at the early stage of embryonic muscle development than pigs with high meat production. Here, by gas chromatography–mass spectrometry GC–MS based metabolomics, we concluded that the nucleotide metabolism and energy metabolism of the longissimuslumborum (LL) were increased in Lantang pigs compared with Landrace pigs, indicating rapid synthesis of nucleic acids and ATP to meet the material and energy requirements of rapid cell proliferation and differentiation in Lantang pigs. Abstract Elucidation of the complex regulation of porcine muscle development is key to increasing pork output and improving pork quality. However, the molecular mechanisms involved in early porcine embryonic muscle development in different pig breeds remain largely unknown. Here, GC–MS based metabolomics and metabolomic profiling was used to examine the longissimus lumborum (LL) of the Lantang (LT) and the Landrace (LR) pig at embryonic day 35 (E35). Metabolites showed clear separation between LT and LR, with 40 metabolites having higher abundances in LT and 14 metabolites having lower abundances in LT compared with LR. In addition, these metabolic changes were mainly associated with nucleotide metabolism and energy metabolism, such as purine metabolism, pyrimidine metabolism, the pentose phosphate pathway, and the TCA cycle. More interestingly, the contents of DNA, RNA, and ATP per unit mass of LL tissues were higher in LT, indicating rapid synthesis of nucleic acids and ATP, to meet both the material and energy requirements of rapid cell proliferation and differentiation. Furthermore, enzyme activity associated with the TCA cycle and pentose phosphate pathway, including α-ketoglutaric dehydrogenase (KGDH), malate dehydrogenase (MDH), pyruvate dehydrogenase (PDH), succinate dehydrogenase (SDH), and glucose-6-phosphate dehydrogenase (G6PDH), were higher in LT. Based on these results, we conclude that there are significant differences in nucleotide metabolism and energy metabolism of LL between LT and LR, and we speculate that the enhanced nucleic acid metabolism and energy metabolism in LT can meet the material and energy requirements of rapid cell proliferation and differentiation, making myogenesis more intense in LT compared to LR which might be the metabolic mechanism underlying the distinct skeletal muscle development in the two breeds.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Jianhao Li
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
- Correspondence: (J.L.); (D.M.); Tel.: +86-020-38765361 (J.L.); +86-020-39332991 (D.M.)
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
- Correspondence: (J.L.); (D.M.); Tel.: +86-020-38765361 (J.L.); +86-020-39332991 (D.M.)
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25
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Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, Clark EL. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 (BETHESDA, MD.) 2022; 12:6460335. [PMID: 34897420 PMCID: PMC9210303 DOI: 10.1093/g3journal/jkab424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Shernae A Woolley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Yennifer Cortés Araya
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Claire Stenhouse
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Cheryl J Ashworth
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Francesc X Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Musa A Hassan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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26
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Malgwi IH, Halas V, Grünvald P, Schiavon S, Jócsák I. Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics. Animals (Basel) 2022; 12:ani12020150. [PMID: 35049772 PMCID: PMC8772548 DOI: 10.3390/ani12020150] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The intramuscular fat (IMF) or marbling is an essential pork sensory quality that influences the preference of the consumers and premiums for pork. IMF is the streak of visible fat intermixed with the lean within a muscle fibre and determines sensorial qualities of pork such as flavour, tenderness and juiciness. Fat metabolism and IMF development are controlled by dietary nutrients, genes, and their metabolic pathways in the pig. Nutrigenetics explains how the genetic make-up of an individual pig influences the pig’s response to dietary nutrient intake. Differently, nutrigenomics is the analysis of how the entire genome of an individual pig is affected by dietary nutrient intake. The knowledge of nutrigenetics and nutrigenomics, when harmonized, is a powerful tool in estimating nutrient requirements for swine and programming dietary nutrient supply according to an individual pig’s genetic make-up. The current paper aimed to highlight the roles of nutrigenetics and nutrigenomics in elucidating the underlying mechanisms of fat metabolism and IMF deposition in pigs. This knowledge is essential in redefining nutritional intervention for swine production and the improvement of some economically important traits such as growth performance, backfat thickness, IMF accretion, disease resistance etc., in animals. Abstract Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.
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Affiliation(s)
- Isaac Hyeladi Malgwi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
- Correspondence: ; Tel.: +39-33-17566768
| | - Veronika Halas
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Petra Grünvald
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
| | - Ildikó Jócsák
- Institute of Agronomy, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary;
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Kang X, Amevor FK, Zhang L, Shah AM, Zhu Q, Tian Y, Shu G, Wang Y, Zhao X. Study on the Major Genes Related with Fat Deposition in Liver and Abdominal Fat of Different Breeds of Chicken. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2020-1373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- X Kang
- Sichuan Agricultural University, China
| | - FK Amevor
- Sichuan Agricultural University, China
| | - L Zhang
- Sichuan Agricultural University, China
| | - AM Shah
- Sichuan Agricultural University, China
| | - Q Zhu
- Sichuan Agricultural University, China
| | - Y Tian
- Sichuan Agricultural University, China
| | - G Shu
- Sichuan Agricultural University, China
| | - Y Wang
- Sichuan Agricultural University, China
| | - X Zhao
- Sichuan Agricultural University, China
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28
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Benítez R, Núñez Y, Ayuso M, Isabel B, Fernández-Barroso MA, De Mercado E, Gómez-Izquierdo E, García-Casco JM, López-Bote C, Óvilo C. Changes in Biceps femoris Transcriptome along Growth in Iberian Pigs Fed Different Energy Sources and Comparative Analysis with Duroc Breed. Animals (Basel) 2021; 11:ani11123505. [PMID: 34944282 PMCID: PMC8697974 DOI: 10.3390/ani11123505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The genetic mechanisms that regulate biological processes, such as skeletal muscle development and growth, or intramuscular fat deposition, have attracted great interest, given their impact on production traits and meat quality. In this sense, a comparison of the transcriptome of skeletal muscle between phenotypically different pig breeds, or along growth, could be useful to improve the understanding of the molecular processes underlying the differences in muscle metabolism and phenotypic traits, potentially driving the identification of causal genes, regulators and metabolic pathways involved in their variability. Abstract This experiment was conducted to investigate the effects of developmental stage, breed, and diet energy source on the genome-wide expression, meat quality traits, and tissue composition of biceps femoris muscle in growing pure Iberian and Duroc pigs. The study comprised 59 Iberian (IB) and 19 Duroc (DU) animals, who started the treatment at an average live weight (LW) of 19.9 kg. The animals were kept under identical management conditions and fed two diets with different energy sources (6% high oleic sunflower oil or carbohydrates). Twenty-nine IB animals were slaughtered after seven days of treatment at an average LW of 24.1 kg, and 30 IB animals plus all the DU animals were slaughtered after 47 days at an average LW of 50.7 kg. The main factors affecting the muscle transcriptome were age, with 1832 differentially expressed genes (DEGs), and breed (1055 DEGs), while the effect of diet on the transcriptome was very small. The results indicated transcriptome changes along time in Iberian animals, being especially related to growth and tissue development, extracellular matrix (ECM) composition, and cytoskeleton organization, with DEGs affecting relevant functions and biological pathways, such as myogenesis. The breed also affected functions related to muscle development and cytoskeleton organization, as well as functions related to solute transport and lipid and carbohydrate metabolism. Taking into account the results of the two main comparisons (age and breed effects), we can postulate that the Iberian breed is more precocious than the Duroc breed, regarding myogenesis and muscle development, in the studied growing stage.
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Affiliation(s)
- Rita Benítez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain; (R.B.); (Y.N.); (M.A.F.-B.); (J.M.G.-C.)
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain; (R.B.); (Y.N.); (M.A.F.-B.); (J.M.G.-C.)
| | - Miriam Ayuso
- Department of Veterinary Sciences, Faculty of Biomedical, Pharmaceutical and Veterinary Sciences, University of Antwerp, B-2610 Wilrijk, Belgium;
| | - Beatriz Isabel
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (B.I.); (C.L.-B.)
| | - Miguel A. Fernández-Barroso
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain; (R.B.); (Y.N.); (M.A.F.-B.); (J.M.G.-C.)
| | - Eduardo De Mercado
- Centro de Pruebas de Porcino ITACYL, Hontalbilla, 40353 Segovia, Spain; (E.D.M.); (E.G.-I.)
| | - Emilio Gómez-Izquierdo
- Centro de Pruebas de Porcino ITACYL, Hontalbilla, 40353 Segovia, Spain; (E.D.M.); (E.G.-I.)
| | - Juan M. García-Casco
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain; (R.B.); (Y.N.); (M.A.F.-B.); (J.M.G.-C.)
| | - Clemente López-Bote
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (B.I.); (C.L.-B.)
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), 28040 Madrid, Spain; (R.B.); (Y.N.); (M.A.F.-B.); (J.M.G.-C.)
- Correspondence: ; Tel.: +34-91-3471492
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Yang Y, Yan J, Fan X, Chen J, Wang Z, Liu X, Yi G, Liu Y, Niu Y, Zhang L, Wang L, Li S, Li K, Tang Z. The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs. PLoS Genet 2021; 17:e1009910. [PMID: 34780471 PMCID: PMC8629385 DOI: 10.1371/journal.pgen.1009910] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/29/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Natural and artificial directional selections have resulted in significantly genetic and phenotypic differences across breeds in domestic animals. However, the molecular regulation of skeletal muscle diversity remains largely unknown. Here, we conducted transcriptome profiling of skeletal muscle across 27 time points, and performed whole-genome re-sequencing in Landrace (lean-type) and Tongcheng (obese-type) pigs. The transcription activity decreased with development, and the high-resolution transcriptome precisely captured the characterizations of skeletal muscle with distinct biological events in four developmental phases: Embryonic, Fetal, Neonatal, and Adult. A divergence in the developmental timing and asynchronous development between the two breeds was observed; Landrace showed a developmental lag and stronger abilities of myoblast proliferation and cell migration, whereas Tongcheng had higher ATP synthase activity in postnatal periods. The miR-24-3p driven network targeting insulin signaling pathway regulated glucose metabolism. Notably, integrated analysis suggested SATB2 and XLOC_036765 contributed to skeletal muscle diversity via regulating the myoblast migration and proliferation, respectively. Overall, our results provide insights into the molecular regulation of skeletal muscle development and diversity in mammals.
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Affiliation(s)
- Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiaxing Chen
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Zishuai Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Xiaoqin Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- Guangxi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | | | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - ShuaiCheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
- * E-mail: (SCL); (KL); (ZLT)
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen, China
- * E-mail: (SCL); (KL); (ZLT)
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- Guangxi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Shenzhen, China
- * E-mail: (SCL); (KL); (ZLT)
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Hou X, Wang L, Zhao F, Liu X, Gao H, Shi L, Yan H, Wang L, Zhang L. Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds. Animals (Basel) 2021; 11:ani11113169. [PMID: 34827901 PMCID: PMC8614396 DOI: 10.3390/ani11113169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Variation exists in muscle-related traits, such as muscle growth and meat quality, between obese and lean pigs. In this study, the transcriptome profiles of skeletal muscle between Beijing Blackand Yorkshire pigs were characterized to explore the molecular mechanism underlying skeletal muscle-relatedtraits. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that differentially expressed mRNAs, lncRNAs, and circRNAs involved in skeletal muscle development and fatty acid metabolism played a key role in the determination of muscle-related traits between different pig breeds. These results provide candidate genes responsible for muscle phenotypic variation and are valuable for pig breeding. Abstract RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.
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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: 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: 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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Ren L, Liu A, Wang Q, Wang H, Dong D, Liu L. Transcriptome analysis of embryonic muscle development in Chengkou Mountain Chicken. BMC Genomics 2021; 22:431. [PMID: 34107874 PMCID: PMC8191012 DOI: 10.1186/s12864-021-07740-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. RESULTS Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P < 0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,262 in E12vsE16, 5,058 in E12vsE19, 6139 in E12vsE21, 1,282 in E16vsE19, 2,920 in E16vsE21, and 646 in E19vsE21differentially expressed mRNAs were identified. It is worth noting that 7,572 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The significant enrichment trends included 3,150 DEGs. GO enrichment analysis provided three significantly enriched categories of significantly enriched differential genes, including 65 cellular components, 88 molecular functions, and 453 biological processes. Through KEGG analysis, we explored the biological metabolic pathways involved in differentially expressed genes. A total of 177 KEGG pathways were enriched, including 19 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P < 0.05), MAPK signalingpathway, TGF-beta signaling pathway, PI3K-Akt signaling pathway and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. CONCLUSIONS Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.
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Affiliation(s)
- Lingtong Ren
- College of Animal Science and Technology, Southwest University, Beibei, 400715, Chongqing, P. R. China
| | - Anfang Liu
- College of Animal Science and Technology, Southwest University, Beibei, 400715, Chongqing, P. R. China
| | - Qigui Wang
- ChongQing Academy of Animal Sciences, Rongchang, 402460, Chongqing, P. R. China
| | - Honggan Wang
- College of Animal Science and Technology, Southwest University, Beibei, 400715, Chongqing, P. R. China
| | - Deqiang Dong
- College of Animal Science and Technology, Southwest University, Beibei, 400715, Chongqing, P. R. China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Beibei, 400715, Chongqing, P. R. China.
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Huang C, Zhong L, Zou X, Huang Y, Cai L, Ma J. Evidence Against the Causal Relationship Between a Putative Cis-Regulatory Variant of MYH3 and Intramuscular Fat Content in Pigs. Front Vet Sci 2021; 8:672852. [PMID: 34150892 PMCID: PMC8206472 DOI: 10.3389/fvets.2021.672852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/29/2021] [Indexed: 01/12/2023] Open
Abstract
Improving meat quality has become the main goal of modern pig breeding. Intramuscular fat content (IMF) is an important trait influencing meat quality of livestock, but the molecular mechanism behind this trait is still unclear. Recently, Cho et al. reported the discovery of the first causal mutation affecting IMF and red flesh color (a*) in pigs, namely XM_013981330.2:g.−1805_−1810del, a 6-bp deletion variant in the porcine MYH3 promoter region. The objective of this study was to reassess the causality of this mutation for its potential commercial application. By Sanger sequencing, we firstly identified several new variants (including a 4-bp deletion) at or near the 6-bp deletion site, which formed four haplotypes in multiple breeds. Unexpectedly, the 6-bp deletion allele, previously determined as the MYH3 Q allele because of its significantly positive effect on IMF and a*, was found not only in Chinese indigenous breeds, but also in four western commercial breeds with relatively lower IMF levels, including Duroc, Large White, Landrace and Pietrain. More surprisingly, we found that the MYH3 Q allele and the haplotypes harboring it had no significant effects on IMF, marbling and color score in three large-scale divergent pig populations: the heterogeneous F6 and F7 pigs and commercial crossbred Duroc × (Landrace × Yorkshire) pigs. Transient transfection analysis in porcine satellite cells showed that the 6-bp deletion variants had a negligible effect on transcription of reporter gene, but could attenuate the MRF (myogenesis regulatory factors)-induced increase in luciferase activity of the MYH3 promoter vector. The MYH3 protein level in muscle did not differ significantly among the haplotype groups. Therefore, our results cannot support the causal relationship between the 6-bp deletion in MYH3 and IMF trait, suggesting that the causal mutation for the IMF QTL on SSC12 needs to be further identified.
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Affiliation(s)
- Cong Huang
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Liepeng Zhong
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoxiao Zou
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yizhong Huang
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Liping Cai
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junwu Ma
- State Key Laboratory for Swine Genetics, Breeding, and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Shu Y, He J, Zhang H, Liu G, Li S, Deng S, Wu H. Dynamic transcriptome and histomorphology analysis of developmental traits of hindlimb thigh muscle from Odorrana tormota and its adaptability to different life history stages. BMC Genomics 2021; 22:369. [PMID: 34016051 PMCID: PMC8138932 DOI: 10.1186/s12864-021-07677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/05/2021] [Indexed: 11/10/2022] Open
Abstract
Background Systematic studies on the development and adaptation of hindlimb muscles in anura amphibians are rare. Here, we integrated analysis of transcriptome and histomorphological data for the hindlimb thigh muscle of Odorrana tormota (concave-eared torrent frog) at different developmental stages, to uncover the developmental traits of hindlimb thigh muscle from O. tormota and its adaptability to different life history stages. Results The development of hindlimb thigh muscle from O. tormota has the following characteristics. Before metamorphosis, myogenous cells proliferate and differentiate into myotubes, and form 11 muscle groups at G41; Primary myofibers and secondary myofibers appeared during metamorphosis; 11 muscle groups differentiated continuously to form myofibers, accompanied by myofibers hypertrophy after metamorphosis; During the growth process of O. tormota from G42 to G46, there were differences between the sexes in the muscle groups that differentiate into muscle fibers, indicating that there was sexual dimorphism in the hindlimb thigh muscles of O. tormota at the metamorphosis stages. Some genes and pathways related to growth, development, and movement ability of O. tormota at different developmental stages were obtained. In addition, some pathways associated with adaptation to metamorphosis and hibernation also were enriched. Furthermore, integrated analysis of the number of myofibers and transcriptome data suggested that myofibers of specific muscle groups in the hindlimbs may be degraded through lysosome and ubiquitin pathways to transform into energy metabolism and other energy-related substances to meet the physiological needs of hibernation. Conclusions These results provide further understanding the hindlimb thigh muscle development pattern of frogs and their adaption to life history stages. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07677-0.
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Affiliation(s)
- Yilin Shu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China
| | - Jun He
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China
| | - Huijuan Zhang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China
| | - Guangxuan Liu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China
| | - Shikun Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China
| | - Shuaitao Deng
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China.,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China
| | - Hailong Wu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, China. .,Provincial Key Laboratory of Biotic Environment and Ecological Safety in Anhui, Wuhu, China.
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Li J, Pei Y, Zhou R, Tang Z, Yang Y. Regulation of RNA N 6-methyladenosine modification and its emerging roles in skeletal muscle development. Int J Biol Sci 2021; 17:1682-1692. [PMID: 33994853 PMCID: PMC8120468 DOI: 10.7150/ijbs.56251] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/27/2021] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is one of the most widespread and highly conserved chemical modifications in cellular RNAs of eukaryotic genomes. Owing to the development of high-throughput m6A sequencing, the functions and mechanisms of m6A modification in development and diseases have been revealed. Recent studies have shown that RNA m6A methylation plays a critical role in skeletal muscle development, which regulates myoblast proliferation and differentiation, and muscle regeneration. Exploration of the functions of m6A modification and its regulators provides a deeper understanding of the regulatory mechanisms underlying skeletal muscle development. In the present review, we aim to summarize recent breakthroughs concerning the global landscape of m6A modification in mammals and examine the biological functions and mechanisms of enzymes regulating m6A RNA methylation. We describe the interplay between m6A and other epigenetic modifications and highlight the regulatory roles of m6A in development, especially that of skeletal muscle. m6A and its regulators are expected to be targets for the treatment of human muscle-related diseases and novel epigenetic markers for animal breeding in meat production.
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Affiliation(s)
- Jiju Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Rong Zhou
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yalan Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals. Animals (Basel) 2021; 11:ani11030835. [PMID: 33809500 PMCID: PMC7999090 DOI: 10.3390/ani11030835] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Skeletal muscle mass is an important economic trait, and muscle development and growth is a crucial factor to supply enough meat for human consumption. Thus, understanding (candidate) genes regulating skeletal muscle development is crucial for understanding molecular genetic regulation of muscle growth and can be benefit the meat industry toward the goal of increasing meat yields. During the past years, significant progress has been made for understanding these mechanisms, and thus, we decided to write a comprehensive review covering regulators and (candidate) genes crucial for muscle development and growth in farm animals. Detection of these genes and factors increases our understanding of muscle growth and development and is a great help for breeders to satisfy demands for meat production on a global scale. Abstract Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.
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Ganteil A, Rodriguez-Ramilo ST, Ligonesche B, Larzul C. Characterization of Autozygosity in Pigs in Three-Way Crossbreeding. Front Genet 2021; 11:584556. [PMID: 33584790 PMCID: PMC7876413 DOI: 10.3389/fgene.2020.584556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.
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Affiliation(s)
- Audrey Ganteil
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.,SAS NUCLEUS, Le Rheu, France
| | | | | | - Catherine Larzul
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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Wang Y, Thakali K, Morse P, Shelby S, Chen J, Apple J, Huang Y. Comparison of Growth Performance and Meat Quality Traits of Commercial Cross-Bred Pigs versus the Large Black Pig Breed. Animals (Basel) 2021; 11:ani11010200. [PMID: 33467586 PMCID: PMC7830199 DOI: 10.3390/ani11010200] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/05/2021] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
The meat quality of different pig breeds is associated with their different muscle tissue physiological processes, which involves a large variety of genes related with muscle fat and energy metabolism. Understanding the differences of biological processes of muscle after slaughter is helpful to reveal the meat quality development of different breeds. Therefore, eight native Large Black pigs (BP), with high fat content in meat, and seven cross-bred commercial pigs (CP), which had a high feed efficiency with high lean meat, were used to investigate the differences in their meat quality and RNA transcriptomes. The average daily gain (ADG) and hot carcass weight (HCW) of CP were higher than BP, but the back-fat thickness of BP was higher than CP (p < 0.05). The CP had higher a* (redness) but lower h (hue angle) than BP (p < 0.05). The metmyoglobin (MMb) percentage of CP was higher (p < 0.05) than BP. The fat content and oxygen consumption of longissimus dorsi (LD) muscles in BP were higher (p < 0.05) than CP. BP had higher monounsaturated fatty acids (MUFA) content, but CP had higher polyunsaturated fatty acids (PUFA) content (p < 0.05). The RNA-seq data highlighted 201 genes differentially expressed between the two groups (corrected false discovery rate (FDR) p < 0.05), with 75 up-regulated and 126 down-regulated genes in BP compared with CP using the fold change (FC). The real-time PCR was used to validate the results of RNA-seq for eight genes, and the genes related to lipid and energy metabolism were highly expressed in BP (p < 0.05). Based on the results, BP had superior intramuscular fat content to CP, while the growth performance of CP was better, and the transcriptomic differences between these two groups of pigs may cause the meat quality and growth performance variance.
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Affiliation(s)
- Yongjie Wang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (P.M.); (S.S.)
| | - Keshari Thakali
- Arkansas Children’s Nutrition Center, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72207, USA;
| | - Palika Morse
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (P.M.); (S.S.)
| | - Sarah Shelby
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (P.M.); (S.S.)
| | - Jinglong Chen
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Jason Apple
- Department of Animal Science and Veterinary Technology, Texas A&M University, Kingsville, TX 78363, USA;
| | - Yan Huang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (P.M.); (S.S.)
- Correspondence:
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Transcriptome landscapes of differentially expressed genes related to fat deposits in Nandan-Yao chicken. Funct Integr Genomics 2021; 21:113-124. [PMID: 33404913 DOI: 10.1007/s10142-020-00764-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023]
Abstract
Nandan-Yao chicken is a Chinese native chicken with lower fat deposition and better meat quality. Fat deposition is a quite complex and important economic trait. However, its molecular mechanism is still unknown in chickens. In the current study, Nandan-Yao chicken was divided into two groups based on the rate of abdominal fat at 120 days old, namely the high-fat group and low-fat group. The total RNAs were isolated and sequenced by RNA sequencing (RNA-seq). After quality control, we gained 1222, 902, 784, 624, and 736 differentially expressed genes (DEGs) in abdominal fat, back skin, liver, pectoral muscle, and leg muscle, respectively. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that significantly enriched GO term and KEGG signaling pathway mainly involved cytosolic ribosome, growth development, PPAR signaling pathway, Wnt signaling pathway, and linoleic acid metabolism in abdominal fat, back skin, and liver. While in pectoral muscle and leg muscle, it is mainly enriched in phosphatidylinositol signaling system, adrenergic signaling in cardiomyocytes, cytosolic ribosome, and cytosolic part. Sixteen genes were differentially expressed in all five tissues. Among them, PLA2G4A and RPS4Y1 might be the key regulators for fat deposition in Nandan-Yao chicken. The protein-protein interaction (PPI) network analysis of DEGs showed that PCK1 was the most notable genes. The findings in the current study will help to understand the regulation mechanism of abdominal fat and intramuscular fat in Nandan-Yao chicken and provide a theoretical basis for Chinese local chicken breeding.
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Xincai S, Hui L, Zhonghai Z, Xiaoyan B, Lin C, Huating Y, Xingcai L. Microsatellite Polymorphism and Prokaryotic Expression of Mef2d in Xingyi Duck. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2021. [DOI: 10.1590/1806-9061-2020-1422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- S Xincai
- Guizhou University College of Animal Science, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, China
| | - L Hui
- Guizhou University College of Animal Science, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, China
| | | | - B Xiaoyan
- Guizhou University College of Animal Science, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, China
| | - C Lin
- Guizhou University College of Animal Science, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, China
| | - Y Huating
- Guizhou University College of Animal Science, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, China
| | - L Xingcai
- Guizhou University College of Animal Science, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, China
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Martins R, Machado PC, Pinto LFB, Silva MR, Schenkel FS, Brito LF, Pedrosa VB. Genome-wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture-based systems. J Anim Breed Genet 2020; 138:360-378. [PMID: 33232564 DOI: 10.1111/jbg.12525] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/30/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
Genome-wide association study (GWAS) is a powerful tool to identify candidate genes and genomic regions underlying key biological mechanisms associated with economically important traits. In this context, the aim of this study was to identify genomic regions and metabolic pathways associated with backfat thickness (BFT) and rump fat thickness (RFT) in Nellore cattle, raised in pasture-based systems. Ultrasound-based measurements of BFT and RFT (adjusted to 18 months of age) were collected in 11,750 animals, with 39,903 animals in the pedigree file. Additionally, 1,440 animals were genotyped using the GGP-indicus 35K SNP chip, containing 33,623 SNPs after the quality control. The single-step GWAS analyses were performed using the BLUPF90 family programs. Candidate genes were identified through the Ensembl database incorporated in the BioMart tool, while PANTHER and REVIGO were used to identify the key metabolic pathways and gene networks. A total of 18 genomic regions located on 10 different chromosomes and harbouring 23 candidate genes were identified for BFT. For RFT, 22 genomic regions were found on 14 chromosomes, with a total of 29 candidate genes identified. The results of the pathway analyses showed important genes for BFT, including TBL1XR1, AHCYL2, SLC4A7, AADAT, VPS53, IDH2 and ETS1, which are involved in lipid metabolism, synthesis of cellular amino acids, transport of solutes, transport between Golgi Complex membranes, cell differentiation and cellular development. The main genes identified for RFT were GSK3β, LRP1B, EXT1, GRB2, SORCS1 and SLMAP, which are involved in metabolic pathways such as glycogen synthesis, lipid transport and homeostasis, polysaccharide and carbohydrate metabolism. Polymorphisms located in these candidate genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for carcass fatness. In addition to uncovering biological mechanisms associated with carcass quality, the key gene pathways identified can also be incorporated in biology-driven genomic prediction methods.
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Affiliation(s)
- Rafaela Martins
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Pamela C Machado
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, Brazil
| | | | - Marcio R Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes, Brazil
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Victor B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, Brazil
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Wang J, Chen MY, Chen JF, Ren QL, Zhang JQ, Cao H, Xing BS, Pan CY. LncRNA IMFlnc1 promotes porcine intramuscular adipocyte adipogenesis by sponging miR-199a-5p to up-regulate CAV-1. BMC Mol Cell Biol 2020; 21:77. [PMID: 33148167 PMCID: PMC7640402 DOI: 10.1186/s12860-020-00324-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 02/08/2023] Open
Abstract
Background Local Chinese local pig breeds have thinner muscle fiber and higher intramuscular-fat (IMF) content. But its regulation mechanism has not been discussed in-depth. Studies indicated that long non coding RNAs (lncRNAs) play important role in muscle and fat development. Results The lncRNAs expressional differences in the longissimus dorsi (LD) muscle were identified between Huainan pigs (local Chinese pigs, fat-type, HN) and Large White pigs (lean-type, LW) at 38, 58, and 78 days post conception (dpc). In total, 2131 novel lncRNAs were identified in 18 samples, and 291, 305, and 683 differentially expressed lncRNAs (DELs) were found between these two breeds at three stages, respectively. The mRNAs that co-expressed with these DELs were used for GO and KEGG analysis, and the results showed that muscle development and energy metabolism were more active at 58 dpc in HN, but at 78 dpc in LW pigs. Muscle cell differentiation and myofibril assembly might associated with earlier myogenesis and primary-muscle-fiber assembly in HN, and cell proliferation, insulin, and the MAPK pathway might be contribute to longer proliferation and elevated energy metabolism in LW pigs at 78 dpc. The PI3K/Akt and cAMP pathways were associated with higher IMF deposition in HN. Intramuscular fat deposition-associated long noncoding RNA 1 (IMFlnc1) was selected for functional verification, and results indicated that it regulated the expressional level of caveolin-1 (CAV-1) by acting as competing endogenous RNA (ceRNA) to sponge miR-199a-5p. Conclusions Our data contributed to understanding the role of lncRNAs in porcine-muscle development and IMF deposition, and provided valuable information for improving pig-meat quality. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-020-00324-8.
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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, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Ming-Yue Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, College of Animal Science and Technology, Northwest A&F University, Ministry of Agriculture, Number 22, Xi Nong Road, Yangling, 712100, Shaanxi, China
| | - Jun-Feng Chen
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Qiao-Ling Ren
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Jia-Qing Zhang
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China
| | - Hai Cao
- Henan Xing Rui Agriculture and Animal Husbandry Technology Co., LTD, Number 59, Jie Fang Road, Xinxian, Xinyang, 465550, China
| | - Bao-Song Xing
- Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Number 116, Hua Yuan Road, Jinshui District, Zhengzhou, 450002, China.
| | - Chuan-Ying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, College of Animal Science and Technology, Northwest A&F University, Ministry of Agriculture, Number 22, Xi Nong Road, Yangling, 712100, Shaanxi, China.
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Hu Y, Xia H, Li M, Xu C, Ye X, Su R, Zhang M, Nash O, Sonstegard TS, Yang L, Liu GE, Zhou Y. Comparative analyses of copy number variations between Bos taurus and Bos indicus. BMC Genomics 2020; 21:682. [PMID: 33004001 PMCID: PMC7528262 DOI: 10.1186/s12864-020-07097-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. RESULTS Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. CONCLUSIONS This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.
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Affiliation(s)
- Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxun Li
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Chang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaowei Ye
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruixue Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria
| | | | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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He J, He Y, Yu B, Wang X, Chen D. Transcriptome Characterization of Repressed Embryonic Myogenesis Due to Maternal Calorie Restriction. Front Cell Dev Biol 2020; 8:527. [PMID: 32671071 PMCID: PMC7332729 DOI: 10.3389/fcell.2020.00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
Fetal malnutrition decreases skeletal myofiber number and muscle mass in neonatal mammals, which increases the risk of developing obesity and diabetes in adult life. However, the associated molecular mechanisms remain unclear. Here, we investigated how the nutrient (calorie) availability affects embryonic myogenesis using a porcine model. Sows were given a normal or calorie restricted diet, following which skeletal muscle was harvested from the fetuses at 35, 55, and 90 days of gestation (dg) and used for histochemical analysis and high-throughput sequencing. We observed abrupt repression of primary myofiber formation following maternal calorie restriction (MCR). Transcriptome profiling of prenatal muscles revealed that critical genes and muscle-specific miRNAs associated with increased proliferation and myoblast differentiation were downregulated during MCR-induced repression of myogenesis. Moreover, we identified several novel miRNA-mRNA interactions through an integrative analysis of their expression profiles, devising a putative molecular network involved in the regulation of myogenesis. Interestingly, NC_010454.3_1179 was identified as a novel myogenic miRNA that can base-pair with sequences in the 3'-UTR of myogenic differentiation protein 1 (MyoD1). And we found that this UTR inhibited the expression of a linked reporter gene encoding a key myogenic regulatory factor, resulting in suppression of myogenesis. Our results greatly increase our understanding of the mechanisms underlying the nutrient-modulated myogenesis, and may also serve as a valuable resource for further investigation of fundamental developmental processes or assist in rational target selection ameliorating repressed myogenesis under fetal malnutrition.
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Affiliation(s)
- Jun He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
| | - Ying He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
| | - Bing Yu
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
| | | | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease-Resistance Nutrition, Ministry of Education, Chengdu, China
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Fan Y, Liang Y, Deng K, Zhang Z, Zhang G, Zhang Y, Wang F. Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing. BMC Genomics 2020; 21:327. [PMID: 32349667 PMCID: PMC7191724 DOI: 10.1186/s12864-020-6751-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/21/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic regulatory form that plays an important role in regulating the gene expression and the tissues development.. However, DNA methylation regulators involved in sheep muscle development remain unclear. To explore the functional importance of genome-scale DNA methylation during sheep muscle growth, this study systematically investigated the genome-wide DNA methylation profiles at key stages of Hu sheep developmental (fetus and adult) using deep whole-genome bisulfite sequencing (WGBS). RESULTS Our study found that the expression levels of DNA methyltransferase (DNMT)-related genes were lower in fetal muscle than in the muscle of adults. The methylation levels in the CG context were higher than those in the CHG and CHH contexts, and methylation levels were highest in introns, followed by exons and downstream regions. Subsequently, we identified 48,491, 17, and 135 differentially methylated regions (DMRs) in the CG, CHG, and CHH sequence contexts and 11,522 differentially methylated genes (DMGs). The results of bisulfite sequencing PCR (BSP) correlated well with the WGBS-Seq data. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis revealed that some DMGs were involved in regulating skeletal muscle development and fatty acid metabolism. By combining the WGBS-Seq and previous RNA-Seq data, a total of 159 overlap genes were obtained between differentially expressed genes (DEGs) and DMGs (FPKM > 10 and fold change > 4). Finally, we found that 9 DMGs were likely to be involved in muscle growth and metabolism of Hu sheep. CONCLUSIONS We systemically studied the global DNA methylation patterns of fetal and adult muscle development in Hu sheep, which provided new insights into a better understanding of the epigenetic regulation of sheep muscle development.
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Affiliation(s)
- Yixuan Fan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yaxu Liang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaiping Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guomin Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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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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Mousa NO, Abdellatif A, Fahmy N, Zada S, El-Fawal H, Osman A. Circulating MicroRNAs in Duchenne Muscular Dystrophy. Clin Neurol Neurosurg 2019; 189:105634. [PMID: 31838454 DOI: 10.1016/j.clineuro.2019.105634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The diagnosis of Duchenne Muscular Dystrophy (DMD) currently depends on non-specific measures such as Creatine kinase (CK) levels. MicroRNAs (miRNAs) are a class of small, endogenous RNAs of 21-25 nucleotides, that are important regulators for numerous physiological and pathological processes. The aim of the current study is to assess the potential of miRNAs as non-invasive biomarker for the diagnosis of DMD and for identifying carriers. PATIENTS AND METHODS Thirty healthy subjects and 29 families with one member diagnosed with DMD were enrolled in the study. Peripheral blood samples were collected from all subjects where microRNAs were extracted from plasma followed by the quantification of miR-499, miR-103a-3p, miR-103a-5p, miR-206, miR-208a, miR-223 and miR-191-5p. MLPA and NGS were carried out as a gold standard technique to identify the mutations in the participants. RESULTS Our data revealed that miR-499 was significantly upregulated in all DMD patients, and true carriers (mothers), while 78 % of potential carriers (sisters) exhibited high levels of this miRNA. Similarly, miR-103a-3p showed an increase in the patients' families although to a lesser extent. On the other hand, miR-206 and miR-191-5p were significantly downregulated in the majority of the DMD patients and the tested female family members. MicroRNA miR-103a-5p and miR-208a followed a comparable trend in patients and mothers. CONCLUSIONS Ourresults suggest that the plasma levels of miRNAs have the capability to diagnose DMD patients and more importantly, miRNAs can be used to identify female carriers.
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Affiliation(s)
- Nahla O Mousa
- Biology Department, and Biotechnology Program, School of Sciences & Engineering, The American University in Cairo, School of Sciences and Engineering, 11835, Cairo, Egypt; Biotechnology Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
| | - Ahmed Abdellatif
- Biology Department, and Biotechnology Program, School of Sciences & Engineering, The American University in Cairo, School of Sciences and Engineering, 11835, Cairo, Egypt.
| | - Nagia Fahmy
- Neuromuscular Unit, Neuropsychiatry Department, Faculty of Medicine Ain Shams University, 11566, Cairo, Egypt
| | - Suher Zada
- Biology Department, and Biotechnology Program, School of Sciences & Engineering, The American University in Cairo, School of Sciences and Engineering, 11835, Cairo, Egypt
| | - Hassan El-Fawal
- Biology Department, and Biotechnology Program, School of Sciences & Engineering, The American University in Cairo, School of Sciences and Engineering, 11835, Cairo, Egypt
| | - Ahmed Osman
- Biotechnology Department, Basic and Applied Sciences Institute, Egypt-Japan University of Science and Technology, Borg Al Arab, 21934, Egypt; Biochemistry Department, Faculty of Science, Ain Shams University, 11566, Cairo, Egypt.
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Sciascia QL, Daş G, Maak S, Kalbe C, Metzler-Zebeli BU, Metges CC. Transcript profile of skeletal muscle lipid metabolism genes affected by diet in a piglet model of low birth weight. PLoS One 2019; 14:e0224484. [PMID: 31661531 PMCID: PMC6818798 DOI: 10.1371/journal.pone.0224484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/15/2019] [Indexed: 01/04/2023] Open
Abstract
Dysregulated skeletal muscle metabolism (DSMM) is associated with increased inter- and intramuscular fat deposition in low birth weight (L) individuals. The mechanisms behind DSMM in L individuals are not completely understood but decreased muscle mass and shifts in lipid and carbohydrate utilisation may contribute. Previously, we observed lower fat oxidation in a porcine model of low birth weight. To elucidate the biological activities underpinning this difference microfluidic arrays were used to assess mRNA associated with lipid metabolism in longissimus dorsi (LD) and semitendinosus (ST) skeletal muscle samples from thirty-six female L and normal birth weight (N) pigs. Plasma samples were collected from a sub-population to measure metabolite concentrations. Following overnight fasting, skeletal muscle and plasma samples were collected and the association with birth weight, diet and age was assessed. Reduced dietary fat was associated with decreased LD intermuscular fat deposition and beta-oxidation associated mRNA, in both birth weight groups. Lipid uptake and intramuscular fat deposition associated mRNA was reduced in only L pigs. Abundance of ST mRNA associated with lipolysis, lipid synthesis and transport increased in both birth weight groups. Lipid uptake associated mRNA reduced in only L pigs. These changes were associated with decreased plasma L glucose and N triacylglycerol. Post-dietary fat reduction, LD mRNA associated with lipid synthesis and inter- and intramuscular fat deposition increased in L, whilst beta-oxidation associated mRNA remains elevated for longer in N. In the ST, mRNA associated with lipolysis and intramuscular fat deposition increased in both birth weight groups, however this increase was more significant in L pigs and associated with reduced beta-oxidation. Analysis of muscle lipid metabolism associated mRNA revealed that profile shifts are a consequence of birth weight. Whilst, many of the adaptions to diet and age appear to be similar in birth weight groups, the magnitude of response and individual changes underpin the previously observed lower fat oxidation in L pigs.
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Affiliation(s)
- Quentin L. Sciascia
- Institute of Nutritional Physiology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Gürbüz Daş
- Institute of Nutritional Physiology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Steffen Maak
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Claudia Kalbe
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Barbara U. Metzler-Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - Cornelia C. Metges
- Institute of Nutritional Physiology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
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Ma J, Ren C, Yang H, Zhao J, Wang F, Wan Y. The Expression Pattern of p32 in Sheep Muscle and Its Role in Differentiation, Cell Proliferation, and Apoptosis of Myoblasts. Int J Mol Sci 2019; 20:ijms20205161. [PMID: 31635221 PMCID: PMC6829534 DOI: 10.3390/ijms20205161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/30/2019] [Indexed: 12/21/2022] Open
Abstract
The complement 1q binding protein C (C1QBP), also known as p32, is highly expressed in rapidly growing tissues and plays a crucial role in cell proliferation and apoptosis. However, there are no data interpreting its mechanisms in muscle development. To investigate the role of p32 in sheep muscle development, an 856 bp cDNA fragment of p32 containing an 837 bp coding sequence that encodes 278 amino acids was analyzed. We then revealed that the expression of p32 in the longissimus and quadricep muscles of fetal sheep was more significantly up-regulated than expression at other developmental stages. Furthermore, we found that the expression of p32 was increased during myoblasts differentiation in vitro. Additionally, the knockdown of p32 in sheep myoblasts effectively inhibited myoblast differentiation, proliferation, and promoted cell apoptosis in vitro. The interference of p32 also changed the energy metabolism from Oxidative Phosphorylation (OXPHOS) to glycolysis and activated AMP-activated protein kinase (AMPK) phosphorylation in sheep myoblasts in vitro. Taken together, our data suggest that p32 plays a vital role in the development of sheep muscle and provides a potential direction for future research on muscle development and some muscle diseases.
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Affiliation(s)
- Jianyu Ma
- Institute of Sheep and Goat Science; Nanjing Agricultural University, Nanjing 210095, China.
| | - Caifang Ren
- Institute of Sheep and Goat Science; Nanjing Agricultural University, Nanjing 210095, China.
| | - Hua Yang
- Institute of Sheep and Goat Science; Nanjing Agricultural University, Nanjing 210095, China.
| | - Jie Zhao
- Institute of Sheep and Goat Science; Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Wang
- Institute of Sheep and Goat Science; Nanjing Agricultural University, Nanjing 210095, China.
| | - Yongjie Wan
- Institute of Sheep and Goat Science; Nanjing Agricultural University, Nanjing 210095, China.
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