A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits

Abstract

Pork is the most popular meat in the world. Unfortunately, the selection pressure focused on high meat content led to a reduction in pork quality. The present study used RNA-seq technology to identify metabolic process genes related to pork quality traits and fat deposition. Differentially expressed genes (DEGs) were identified between pigs of Pulawska and Polish Landrace breeds for two the most important muscles (semimembranosus and longissimus dorsi). A total of 71 significant DEGs were reported: 15 for longissimus dorsi and 56 for semimembranosus muscles. The genes overexpressed in Pulawska pigs were involved in lipid metabolism (APOD, LXRA, LIPE, AP2B1, ENSSSCG00000028753 and OAS2) and proteolysis (CST6, CTSD, ISG15 and UCHL1). In Polish Landrace pigs, genes playing a role in biological adhesion (KIT, VCAN, HES1, SFRP2, CDH11, SSX2IP and PCDH17), actin cytoskeletal organisation (FRMD6, LIMK1, KIF23 and CNN1) and calcium ion binding (PVALB, CIB2, PCDH17, VCAN and CDH11) were transcriptionally more active. The present study allows for better understanding of the physiological processes associated with lipid metabolism and muscle fiber organization. This information could be helpful in further research aiming to estimate the genetic markers.

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

“…This result was consistent with the fact that in ammatory cell in ltration has been documented to commonly occur in adipose tissue and stimulate the activation of the immune defense system [50]. We also found that many pathways related to lipid metabolism (Cholesterol metabolism and Arachidonic acid metabolism) were signi cantly enriched for many DEMs, such as HABP2, CST6, DLK1, PLA2G4E and FOSL1 that have been reported to participate in lipid metabolism [51][52][53][54][55]. Based on the GO and KEGG analysis, we obtained DEMs expression pro les that affected the IMF deposition of sheep.…”

Gga-miR-3525 Targets PDLIM3 through the MAPK Signaling Pathway to Regulate the Proliferation and Differentiation of Skeletal Muscle Satellite Cells

“…A new PDLIM3 splice variant was identified in porcine skeletal muscle that is expressed only in heart and skeletal muscle, showing the highest expression in adult porcine skeletal muscle [25]. Piórkowska et al concluded that PDLIM3 is a candidate gene for pork quality through quantitative trait loci [26]. These results indicate that PDLIM3 plays important roles in maintaining muscle cell stability, cell differentiation, cell signal transduction, cell proliferation, and cytoskeletal structure integration and that it has a positive role in muscle development.…”

Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages

“…Gene activating transcription factor 3 (ATF3) and nitric oxide synthase 1 (NOS1) were DE between Iberian and Iberian and Duroc crossbred pigs [10]. Piórkowska et al reported that Parvalbumin (PVALB), calcium and integrin-binding family member 2 (CIB2), choline phosphotransferase 1 (CHPT1), transcription factor Dp-2 (TFDP2) and breast cancer anti-estrogen resistance protein 3 (BCAR3) were DE amid pigs of Polish Landrace and Pulawska breeds [12]. These genes were also DEGs in our study.…”

“…Xu et al uncovered a set of DE genes (DEGs), which are potentially associated with myofiber development in the skeletal muscle fiber phenotypes between Northeast Min pigs and the Changbaishan wild boar [8]. Seventy-one significant DEGs (15 for LDM and 56 for semimembranosus muscles) were found for the Pulawska and Polish Landrace breeds [12]. RNA sequencing (RNA-Seq) and miRNA sequencing were also used to find out the relation of transcriptome profiles of skeletal muscle in two pigs breeds at five developmental stages of gestation [13,14].…”

“…RNA sequencing (RNA-Seq) and miRNA sequencing were also used to find out the relation of transcriptome profiles of skeletal muscle in two pigs breeds at five developmental stages of gestation [13,14]. A total of 1317 and 691 DEGs were detected in TC and YK pigs and 23,30,12,6, and 30 breed-DE miRNA was identified between YK and TC at five different developmental stages. E1A binding protein P300 (EP300), cyclin-dependent kinase 14 (CDK14), insulin receptor substrate 1 (IRS1), tensin homolog (PTEN) and phosphatase, Myosin 9A, protein phosphatase 1 catalytic subunit gamma (PPP1CC) and miR-499-5p were identified as the important molecular markers for deciphering the developmental differences in two pigs breeds.…”