Dissecting the Gene Expression Networks Associated with Variations in the Major Components of the Fatty Acid Semimembranosus Muscle Profile in Large White Heavy Pigs

Abstract

To date, high-throughput technology such as RNA-sequencing has been successfully applied in livestock sciences to investigate molecular networks involved in complex traits, such as meat quality. Pork quality depends on several organoleptic, technological, and nutritional characteristics, and it is also influenced by the fatty acid (FA) composition of intramuscular fat (IMF). To explore the molecular networks associated with different IMF FA compositions, the Semimembranosus muscle (SM) from two groups of Italian Large White (ILW) heavy pigs divergent for SM IMF content was investigated using transcriptome analysis. After alignment and normalization, the obtained gene counts were used to perform the Weighted Correlation Network Analysis (WGCNA package in R environment). Palmitic and palmitoleic contents showed association with the same gene modules, comprising genes significantly enriched in autophagy, mitochondrial fusion, and mitochondrial activity. Among the key genes related to these FAs, we found TEAD4, a gene regulating mitochondrial activity that seems to be a promising candidate for further studies. On the other hand, the genes comprised in the modules associated with the IMF contents of oleic, n-6, and n-3 polyunsaturated FAs (PUFAs) were significantly enriched in Mitogen-Activated Protein Kinase (MAPK) signaling, in agreement with previous studies suggesting that several MAPK players may have a primary role in regulating lipid deposition. These results give an insight into the molecular cascade associated with different IMF FA composition in ILW heavy pigs. Further studies are needed to validate the results and confirm whether some of the identified key genes may be effective candidates for pork quality.

Genome‐wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

“…Finally, Cinta Senese, Casertana, Mora Romagnola, and cosmopolitan breeds outlined ROHet islands on SSC2, SSC6, SSC14, and SSC15 that mapped genes and QTL linked to productive traits (Howard et al, 2015; Kim et al, 2021; Li et al, 2011; Qi et al, 2022; Zappaterra et al, 2021; Zhang et al, 2015). In particular, the heterozygosity‐rich segment, observed on SSC6 (54.2–55.9 Mb) in Duroc, Landrace, Large White, and Pietrain, correlates with QTL for average daily gain, daily feed intake, fat androstenone level, mean corpuscular haemoglobin concentration and meat colour, and partially overlapped a ROHet island detected by Ruan et al (2022) in a Duroc sample.…”

Using Machine Learning to Identify Biomarkers Affecting Fat Deposition in Pigs by Integrating Multisource Transcriptome Information

“…In addition, we also collected similar transcriptome data from 64 samples in the GEO database from four different sources (Table ), including adipose tissue samples of 24 Duroc × Gottingen minipigs and 16 Pulawska pigs and muscle tissue samples of 12 Italian Large White pigs and 12 Iberian pigs . The samples were screened and grouped according to their phenotypic information, including the obesity index, intramuscular fat content, and backfat thickness.…”

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

“…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 ]. However, studies on such mechanisms related to fat metabolism and pork quality traits, including IMF, are limited while existing few investigations remain elusive.…”

“…The literature suggests the indispensable role of miRNA in fat deposition and adipocyte differentiation [ 130 , 131 ]. Additionally, the use of miRNA sequence in investigating IMF content-related genes is uncovering differentially expressed genes (DEGs) associated with muscle growth and lipid deposition in pigs [ 56 ]. MiRNAs have the potential to down-regulate gene expression by blocking mRNA translation of certain genes.…”