Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle
Author:
Dehghanian Reyhan Vahid1, Ghafouri Farzad1ORCID, Sadeghi Mostafa1, Miraei-Ashtiani Seyed Reza1, Kastelic John P.2ORCID, Barkema Herman W.2ORCID, Shirali Masoud34
Affiliation:
1. Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran 2. Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada 3. Agri-Food and Biosciences Institute, Hillsborough BT26 6DR, UK 4. School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5AJ, UK
Abstract
Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.
Subject
General Veterinary,Animal Science and Zoology
Reference86 articles.
1. Intramuscular fat content in meat-producing animals: Development, genetic and nutritional control, and identification of putative markers;Hocquette;Animal,2010 2. Huang, J., Feng, X., Zhu, R., Guo, D., Wei, Y., Cao, X., Ma, Y., and Shi, D. (2020). Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo. BMC Genom., 21. 3. Mir, B.A., Reyer, H., Komolka, K., Ponsuksili, S., Kühn, C., and Maak, S. (2020). Differentially expressed miRNA-gene targets related to intramuscular fat in musculus longissimus dorsi of Charolais× Holstein F2-crossbred bulls. Genes, 11. 4. A Study of the Regulatory Mechanism of the CB1/PPARγ2/PLIN1/HSL Pathway for Fat Metabolism in Cattle;Liu;Front. Genet.,2021 5. Differences in muscle and fat accretion in Japanese Black and European cattle;Gotoh;Meat Sci.,2009
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|