Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network for Intramuscular Fat in Pigs

Yanhui Zhao; Shaokang Chen; Jiani Yuan; Yumei Shi; Yan Wang; Yufei Xi; Xiaolong Qi; Yong Guo; Xihui Sheng; Jianfeng Liu; Lei Zhou; Chuduan Wang; Kai Xing

doi:10.3390/genes14010168

Comprehensive Analysis of the lncRNA-miRNA-mRNA Regulatory Network for Intramuscular Fat in Pigs

Genes (Basel). 2023 Jan 7;14(1):168. doi: 10.3390/genes14010168.

Authors

Yanhui Zhao¹, Shaokang Chen², Jiani Yuan¹, Yumei Shi¹, Yan Wang¹, Yufei Xi¹, Xiaolong Qi¹, Yong Guo¹, Xihui Sheng¹, Jianfeng Liu³, Lei Zhou³, Chuduan Wang³, Kai Xing¹

Affiliations

¹ Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China.
² Beijing Animal Husbandry Station, Beijing 100101, China.
³ College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.

Abstract

Intramuscular fat (IMF) is an essential trait closely related to meat quality. The IMF trait is a complex quantitative trait that is regulated by multiple genes. In order to better understand the process of IMF and explore the key factors affecting IMF deposition, we identified differentially expressed mRNA, miRNA, and lncRNA in the longissimus dorsi muscle (LD) between Songliao Black (SL) pigs and Landrace pigs. We obtained 606 differentially expressed genes (DEGs), 55 differentially expressed miRNAs (DEMs), and 30 differentially expressed lncRNAs (DELs) between the SL pig and Landrace pig. Enrichment results from GO and KEGG indicate that DEGs are involved in fatty acid metabolism and some pathways related to glycogen synthesis. We constructed an lncRNA-miRNA-mRNA interaction network with 18 DELs, 11 DEMs, and 42 DEGs. Finally, the research suggests that ARID5B, CPT1B, ACSL1, LPIN1, HSP90AA1, IRS1, IRS2, PIK3CA, PIK3CB, and PLIN2 may be the key genes affecting IMF deposition. The LncRNAs MSTRG.19948.1, MSTRG.13120.1, MSTRG.20210.1, and MSTRG.10023.1, and the miRNAs ssc-miRNA-429 and ssc-miRNA-7-1, may play a regulatory role in IMF deposition through their respective target genes. Our research provides a reference for further understanding the regulatory mechanism of IMF.

Keywords: fatty acid; intramuscular fat; regulatory network.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Gene Expression Profiling / methods
Lipid Metabolism / genetics
MicroRNAs* / genetics
RNA, Long Noncoding* / genetics
RNA, Messenger / genetics
Swine / genetics

Substances

RNA, Long Noncoding
RNA, Messenger
MicroRNAs

Grants and funding

This research was funded by the 2022 Beijing Municipal Education Commission Classification Development Project, earmarked fund for CARS (No. 35), and the National Key R&D Program of China (2021YFD1300800).