Supplementary Material for: Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

<b><i>Background/Aims:</i></b> Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. <b><i>Methods:</i></b> In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. <b><i>Results:</i></b> A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. <b><i>Conclusion:</i></b> <i>XLOC_046142, XLOC_004398</i> and <i>XLOC_015408</i> may target <i>MAPKAPK2, NR1D2</i> and <i>AKR1C4</i>, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. <i>XLOC_064871</i> and <i>XLOC_011001</i> may play a role in lipid metabolism-related disease via regulating <i>TRIB3</i> and <i>BRCA1</i>. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.