Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Abstract

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

Hypothalamic transcriptome analysis reveals male-specific differences in molecular pathways related to oxidative phosphorylation between Iberian pig genotypes

“…As found in other studies [ 38 , 124 ], differences tend to be more notable with the RNA-seq approach than with the Real-Time qPCR. However, the concordance correlation coefficient (CCC) showed an acceptable correlation between techniques (CCC in all samples = 0.73; CCC in females = 0.66; CCC in males = 0.60).…”

Transcriptome-metabolome analysis reveals how sires affect meat quality in hybrid sheep populations

“…Additionally, fatty acid metabolism strongly influences meat quality. Previous studies have found that the fatty acid composition and its metabolism in muscles are important factors influencing overall meat quality and consumer preference ( 15 , 33 – 35 ). In the present study, enrichment analysis of the muscle metabolomic data revealed several pathways related to fat metabolic processes ( Figures 4 , 6 ), including arachidonic acid metabolism and fatty acid biosynthesis.…”

“…Multi-omics techniques are widely used to analyze muscle tissue in sheep, pigs and cattle and have identified many genes involved in fatty acid metabolism (11)(12)(13)(14). RNA-seq and qRT-PCR have identified several candidate genes for lipid metabolism, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1, as main gene factors defining the processes influencing meat composition and quality (15).…”

Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics

“…In response to carbohydrate intake, glucose is taken by adipocytes through insulin-stimulated GLUT4 (see Figure 2 ). There are several published schematic representations of the pathways involved in de novo fatty acid synthesis [ 43 , 44 , 45 , 46 , 47 , 48 , 49 ]. A simplified pathway is shown in Figure 2 .…”

“…Poklukar et al [ 46 ] published a detailed review on the transcriptomic networks, hormones and enzymes modulating transcriptional regulation of adipogenesis in local and modern pig genotypes. Additionally, other studies have also revealed putative IMF accretion and fat metabolism-related genes [ 45 , 46 , 47 , 48 , 49 ], hormones, enzymes, transcription factors, and miRNAs [ 50 , 51 , 52 ] and their interaction with dietary nutrients [ 2 , 12 , 53 , 54 ] in pigs. Other findings evinced the possible association of genes influencing fat deposition and IMF accretion to the mitogen-activated protein kinase (MAPK) pathway regulating adipogenesis and lipogenesis [ 55 , 56 ].…”