Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness

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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Mechanism and Functions of Identified miRNAs in Poultry Skeletal Muscle Development – A Review

Annals of Animal Science ◽

10.2478/aoas-2019-0049 ◽

2019 ◽

Vol 19 (4) ◽

pp. 887-904

Author(s):

Asiamah Amponsah Collins ◽

Kun Zou ◽

Zhang Li ◽

Su Ying

Keyword(s):

Skeletal Muscle ◽

Candidate Genes ◽

Skeletal Muscles ◽

Muscle Development ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Single Nucleotide ◽

Complex Processes ◽

Muscle Formation ◽

Gene Regulatory

AbstractDevelopment of the skeletal muscle goes through several complex processes regulated by numerous genetic factors. Although much efforts have been made to understand the mechanisms involved in increased muscle yield, little work is done about the miRNAs and candidate genes that are involved in the skeletal muscle development in poultry. Comprehensive research of candidate genes and single nucleotide related to poultry muscle growth is yet to be experimentally unraveled. However, over a few periods, studies in miRNA have disclosed that they actively participate in muscle formation, differentiation, and determination in poultry. Specifically, miR-1, miR-133, and miR-206 influence tissue development, and they are highly expressed in the skeletal muscles. Candidate genes such as CEBPB, MUSTN1, MSTN, IGF1, FOXO3, mTOR, and NFKB1, have also been identified to express in the poultry skeletal muscles development. However, further researches, analysis, and comprehensive studies should be made on the various miRNAs and gene regulatory factors that influence the skeletal muscle development in poultry. The objective of this review is to summarize recent knowledge in miRNAs and their mode of action as well as transcription and candidate genes identified to regulate poultry skeletal muscle development.

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Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle

PeerJ ◽

10.7717/peerj.9957 ◽

2020 ◽

Vol 8 ◽

pp. e9957

Author(s):

Chao Yuan ◽

Ke Zhang ◽

Yaojing Yue ◽

Tingting Guo ◽

Jianbin Liu ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Expression Profiles ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Fetal Sheep ◽

Lncrna Gene ◽

Skeletal Muscle Growth ◽

Wide Range ◽

Non Coding Rnas

The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation.

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Integrated analysis of miRNA-mediated ceRNA networks in ovine skeletal muscle development

10.21203/rs.3.rs-18319/v1 ◽

2020 ◽

Author(s):

Tianpei Shi ◽

Xinyue WANG ◽

Zhida ZHAO ◽

Wenping HU ◽

Li ZHANG

Keyword(s):

Skeletal Muscle ◽

Transcription Factors ◽

Muscle Development ◽

Muscle Growth ◽

Growth Potential ◽

Regulatory Role ◽

Integrated Analysis ◽

Interaction Patterns ◽

Rna Seq ◽

Skeletal Muscle Development

Abstract Background: The embryo stage is a key period for sheep skeletal muscle growth and development. Proliferation, differentiation, and hypertrophy of fibers affect muscle growth potential directly. Analyzing transcriptome data is of great significance for revealing important time nodes of fetus muscle development and screening related regulation factors. Muscle development is a complex biological process, including a intricate network of multiple factor interactions. Among them, non-coding RNA, especially miRNA-mediated regulation, plays a fine regulatory role. The purpose of this study was to investigate the important genes and transcripts involved in the genetic mechanism of embryos skeletal muscle development in late pregnancy. Results: Herein we did a small RNA sequencing(RNA-Seq) of embryo at 85 days (D85N), 105 days (D105N) and 135 days(D135N), then performed bioinformatic analysis in order to identify the miRNA-mediated co-expression networks. Our findings identified 505 DE-miRNAs. Integrating the current miRNA data and the previously obtained lncRNA data, multiple networks were constructed, including miRNA-mRNA, miRNA-target gene(TG)-pathway, lncRNA-miRNA-mRNA, and miRNA-TG-transcription factor (TF) network. The results showed that the miRNA-mRNA network and lncRNA-miRNA-mRNA network identified three important lncRNAs (MSTRG.3533, MSTRG.4324, and MSTRG.1470) and three miRNAs(miR-493-3p, miR-3959-3p and miR-410-5p). The four genes ( TEAD1 , ZBTB34 , GSK3B, and POGLUT1 ) and three transcription factors (C / EBPbeta, TFIID, and PR B) play a key regulatory role in the miRNA-TG-TF network. Notably, a similar trend of gene expression was reported by RT-qPCR for RNA-seq data. Conclusions: This study identified three miRNAs, three lncRNAs, four genes, and three transcription factors, and revealed their crucial role in fetal fibrogenesis and lipid metabolism. It also shows that D105N is a pivotal turning point from myotube differentiation to fiber hypertrophy. These findings provide valuable references for network interaction patterns, which helps to evaluate the biological significance of skeletal muscle in the late development stage.

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Transcriptome analysis reveals the long intergenic noncoding RNAs contributed to skeletal muscle differences between Yorkshire and Tibetan pig

Scientific Reports ◽

10.1038/s41598-021-82126-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ziying Huang ◽

Qianqian Li ◽

Mengxun Li ◽

Changchun Li

Keyword(s):

Skeletal Muscle ◽

Noncoding Rna ◽

Muscle Development ◽

Target Genes ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Tibetan Pig ◽

The Difference ◽

Long Intergenic Noncoding Rna

AbstractThe difference between the skeletal muscle growth rates of Western and domestic breeds is remarkable, but the potential regulatory mechanism involved is still unclear. Numerous studies have pointed out that long intergenic noncoding RNA (lincRNA) plays a key role in skeletal muscle development. This study used published Yorkshire (LW) and Tibetan pig (TP) transcriptome data to explore the possible role of lincRNA in the difference in skeletal muscle development between the two breeds. 138 differentially expressed lincRNAs (DELs) were obtained between the two breeds, and their potential target genes (PTGs) were predicted. The results of GO and KEGG analysis revealed that PTGs are involved in multiple biological processes and pathways related to muscle development. The quantitative trait loci (QTLs) of DELs were predicted, and the results showed that most QTLs are related to muscle development. Finally, we constructed a co-expression network between muscle development related PTGs (MDRPTGs) and their corresponding DELs on the basis of their expression levels. The expression of DELs was significantly correlated with the corresponding MDRPTGs. Also, multiple MDRPTGs are involved in the key regulatory pathway of muscle fiber hypertrophy, which is the IGF-1-AKT-mTOR pathway. In summary, multiple lincRNAs that may cause differences in skeletal muscle development between the two breeds were identified, and their possible regulatory roles were explored. The findings of this study may provide a valuable reference for further research on the role of lincRNA in skeletal muscle development.

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Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development

Scientific Reports ◽

10.1038/s41598-021-94014-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wenjuan Zhao ◽

Zijing Li ◽

Quan Liu ◽

Su Xie ◽

Mengxun Li ◽

...

Keyword(s):

Skeletal Muscle ◽

Signaling Pathway ◽

Muscle Development ◽

Target Genes ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Protein Coding ◽

Development Stages ◽

Non Coding Rnas ◽

Embryonic Muscle

AbstractSkeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.

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Analysis of Long Intergenic Non-Coding RNAs Transcriptomic Profiling in Skeletal Muscle Growth During Porcine Embryonic Development

10.21203/rs.3.rs-323967/v1 ◽

2021 ◽

Author(s):

Wenjuan Zhao ◽

Zijing Li ◽

Quan Liu ◽

Su Xie ◽

Mengxun Li ◽

...

Keyword(s):

Skeletal Muscle ◽

Signaling Pathway ◽

Muscle Development ◽

Target Genes ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Protein Coding ◽

Development Stages ◽

Non Coding Rnas ◽

Embryonic Muscle

Abstract Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that thousands of long intergenic non-coding RNAs (lincRNAs) have been identified in various species and implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, there were 228 putative lincRNAs identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Differential expression analysis showed that a total of 91 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for DE lincRNAs, 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, a co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs identified may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for exploring further the molecular mechanisms of lincRNAs during skeletal muscle development.

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Transcriptome Analysis Reveals the Long Intergenic Noncoding RNAs Contributed to Skeletal Muscle Differences between Yorkshire and Tibetan Pig

10.21203/rs.2.23862/v3 ◽

2020 ◽

Author(s):

Ziying Huang ◽

Qianqian Li ◽

Mengxun Li ◽

Changchun Li

Keyword(s):

Skeletal Muscle ◽

Noncoding Rna ◽

Muscle Development ◽

Target Genes ◽

Differential Expression Analysis ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Tibetan Pig ◽

The Difference

Abstract Background: The difference between the skeletal muscle growth rates of Western and domestic breeds is remarkable, but the potential regulatory mechanism involved is still unclear. Numerous studies have pointed out that long intergenic noncoding RNA (lincRNA) plays a key role in skeletal muscle development. This study used published Yorkshire (LW) and Tibetan pig (TP) transcriptome data to explore the possible role of lincRNA in the difference in skeletal muscle development between the two breeds. Results: Through differential expression analysis, 138 differentially expressed lincRNAs (DELs) were obtained between the two breeds, and their potential target genes (PTGs) were predicted. The results of Gene Ontology and pathway analysis revealed that PTGs are involved in multiple biological processes and pathways related to muscle development. The quantitative trait loci (QTLs) of DELs were predicted, and the results showed that most QTLs are related to muscle development. Finally, we constructed a co-expression network between muscle development related PTGs (MDRPTGs) and their corresponding DELs on the basis of their expression levels. The expression of DELs was significantly correlated with the corresponding MDRPTGs. Also, multiple MDRPTGs are involved in the key regulatory pathway of muscle fiber hypertrophy, which is the IGF-1-AKT-mTOR pathway. Conclusions: In summary, multiple lincRNAs that may cause differences in skeletal muscle development between the two breeds were identified, and their possible regulatory roles were explored. The findings of this study may provide a valuable reference for further research on the role of lincRNA in skeletal muscle development.

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Transcriptome Analysis Reveals the Long Intergenic Noncoding RNAs Contributed to Skeletal Muscle Differences between Yorkshire and Tibetan Pig

10.21203/rs.2.23862/v1 ◽

2020 ◽

Author(s):

Ziying Huang ◽

Qianqian Li ◽

Mengxun Li ◽

Changchun Li

Keyword(s):

Skeletal Muscle ◽

Noncoding Rna ◽

Muscle Development ◽

Target Genes ◽

Differential Expression Analysis ◽

Muscle Growth ◽

Skeletal Muscle Development ◽

Tibetan Pig ◽

The Difference

Abstract Background The difference between the skeletal muscle growth rates of Western and domestic breeds is remarkable, but the potential regulatory mechanism involved is still unclear. Numerous studies have pointed out that long intergenic noncoding RNA (lincRNA) plays a key role in skeletal muscle development. This study used published Yorkshire (LW) and Tibetan pig (TP) transcriptome data to explore the possible role of lincRNA in the difference in skeletal muscle development between the two breeds. Results Through differential expression analysis, 138 differentially expressed lincRNAs (DELs) were obtained between the two breeds, and their potential target genes (PTGs) were predicted. The results of Gene Ontology and pathway analysis revealed that PTGs are involved in multiple biological processes and pathways related to muscle development. The quantitative trait loci (QTLs) of DELs were predicted, and the results showed that most QTLs are related to muscle development. Finally, we constructed a co-expression network between muscle development related PTGs (MDRPTGs) and their corresponding DELs on the basis of their expression levels. The expression of DELs was significantly correlated with the corresponding MDRPTGs. Also, multiple MDRPTGs are involved in the key regulatory pathway of muscle fiber hypertrophy, which is the IGF-1-AKT-mTOR pathway. Conclusions In summary, multiple lincRNAs that may cause differences in skeletal muscle development between the two breeds were identified, and their possible regulatory roles were explored. The findings of this study may provide a valuable reference for further research on the role of lincRNA in skeletal muscle development.

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Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds

Animals ◽

10.3390/ani11113169 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3169

Author(s):

Xinhua Hou ◽

Ligang Wang ◽

Fuping Zhao ◽

Xin Liu ◽

Hongmei Gao ◽

...

Keyword(s):

Skeletal Muscle ◽

Fatty Acid ◽

Fatty Acid Metabolism ◽

Muscle Development ◽

Target Genes ◽

Acid Metabolism ◽

Differentially Expressed ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Pig Breeds

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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