Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs

Abstract

In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs.

Global DNA Methylation, miRNA, and mRNA Profiles in Sheep Skeletal Muscle Promoted by Hybridization

“…12 Using results obtained from the longissimus dorsi muscle, Zhang et al found some genes, miRNAs, and lncRNA related to intramuscular fat deposition and bone development, and proposed the miRNA ssc-let-7a as the main modulator of fat deposition through the regulation of GALNT15 (N-acetylgalactosaminyltransferases 15), PPARG-C1A (PPARG coactivator 1 alpha), and FKBP5 (FKBP prolyl isomerase 5) genes. 13 Other studies have reported DNA methylation in the muscle of fetal and adult Hu sheep, highlighting ADIPOQ (adiponectin, C1Q and collagen domain containing), CCNA2 (cyclin A2), ITGA2 (integrin subunit alpha 2), and MYOG (myogenin) as mediators of muscle growth and metabolism. 14 Nevertheless, meat quality is a very complex trait, determined by multiple regulatory mechanisms, 15,16 such as epigenetic marks/factors, 17,18 miRNAs, 19 translation regulation, RNA/peptide degradation, and posttranslational modification.…”

“…Multiomics allows a comprehensive understanding of the systematic study of biology and can integrate genomics, epigenomics, transcriptomics, etc., to systematically analyze the mechanisms and phenotypes of complex life systems. − Zhan et al used transcriptomics and metabolomics and obtained 120 differentially expressed genes (DEGs) and 171 significantly changed metabolites that contributed to the content of intramuscular fat through fat accumulation and regulation of lipolysis in Enshi black pork . Using results obtained from the longissimus dorsi muscle, Zhang et al found some genes, miRNAs, and lncRNA related to intramuscular fat deposition and bone development, and proposed the miRNA ssc-let-7a as the main modulator of fat deposition through the regulation of GALNT15 (N-acetylgalactosaminyltransferases 15), PPARGC1A (PPARG coactivator 1 alpha), and FKBP5 (FKBP prolyl isomerase 5) genes . Other studies have reported DNA methylation in the muscle of fetal and adult Hu sheep, highlighting ADIPOQ (adiponectin, C1Q and collagen domain containing), CCNA2 (cyclin A2), ITGA2 (integrin subunit alpha 2), and MYOG (myogenin) as mediators of muscle growth and metabolism .…”