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

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Autores principales:	Xinhua Hou, Ligang Wang, Fuping Zhao, Xin Liu, Hongmei Gao, Lijun Shi, Hua Yan, Lixian Wang, Longchao Zhang
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	pigs RNA-seq skeletal muscle mRNAs lncRNAs circRNAs Veterinary medicine SF600-1100 Zoology QL1-991
Acceso en línea:	https://doaj.org/article/79f628da56cf4af4825b8beef8321eda
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spelling	oai:doaj.org-article:79f628da56cf4af4825b8beef8321eda2021-11-25T16:17:55ZGenome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds10.3390/ani111131692076-2615https://doaj.org/article/79f628da56cf4af4825b8beef8321eda2021-11-01T00:00:00Zhttps://www.mdpi.com/2076-2615/11/11/3169https://doaj.org/toc/2076-2615RNA-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, <i>longissimus dorsi</i> 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 <i>cis</i> and <i>trans</i>-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.Xinhua HouLigang WangFuping ZhaoXin LiuHongmei GaoLijun ShiHua YanLixian WangLongchao ZhangMDPI AGarticlepigsRNA-seqskeletal musclemRNAslncRNAscircRNAsVeterinary medicineSF600-1100ZoologyQL1-991ENAnimals, Vol 11, Iss 3169, p 3169 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	pigs RNA-seq skeletal muscle mRNAs lncRNAs circRNAs Veterinary medicine SF600-1100 Zoology QL1-991
spellingShingle	pigs RNA-seq skeletal muscle mRNAs lncRNAs circRNAs Veterinary medicine SF600-1100 Zoology QL1-991 Xinhua Hou Ligang Wang Fuping Zhao Xin Liu Hongmei Gao Lijun Shi Hua Yan Lixian Wang Longchao Zhang Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
description	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, <i>longissimus dorsi</i> 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 <i>cis</i> and <i>trans</i>-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.
format	article
author	Xinhua Hou Ligang Wang Fuping Zhao Xin Liu Hongmei Gao Lijun Shi Hua Yan Lixian Wang Longchao Zhang
author_facet	Xinhua Hou Ligang Wang Fuping Zhao Xin Liu Hongmei Gao Lijun Shi Hua Yan Lixian Wang Longchao Zhang
author_sort	Xinhua Hou
title	Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
title_short	Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
title_full	Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
title_fullStr	Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
title_full_unstemmed	Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
title_sort	genome-wide expression profiling of mrnas, lncrnas and circrnas in skeletal muscle of two different pig breeds
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/79f628da56cf4af4825b8beef8321eda
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Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds

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