Global analysis of the association between pig muscle fatty acid composition and gene expression using RNA-Seq

Abstract

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candidate genes, biological processes, and pathways involved in the modulation of intramuscular FA profile from longissimus dorsi muscle. FA profile by gas chromatography of methyl esters and gene expression by RNA-Seq were determined in 129 Iberian × Duroc backcrossed pigs. An association analysis between the muscle transcriptome and its FA profile was performed, followed by a concordance and functional analysis. Overall, a list of well-known (e.g., PLIN1, LEP, ELOVL6, SC5D, NCOA2, ACSL1, MDH1, LPL, LGALS12, TFRC, GOT1, and FBP1) and novel (e.g., TRARG1, TANK, ENSSSCG00000011196, and ENSSSCG00000038429) candidate genes was identified, either in association with specific or several FA traits. Likewise, several of these genes belong to biological processes and pathways linked to energy, lipid, and carbohydrate metabolism, which seem determinants in the modulation of FA compositions. This study can contribute to elucidate the complex relationship between gene expression and FA profile in pig muscle.

Identification of candidate regulatory genes for intramuscular fatty acid composition in pigs by transcriptome analysis

“…The experimental backcross population (25% Iberian and 75% Duroc, BC1_DU) used in this study is described in [ 9 ]. Briefly, it included 129 animals, which were raised under the standard, intensive conditions of production; and fed ad libitum with a cereal-based commercial diet and free access to water.…”

“…For complex phenotypes such as porcine IMF content and its FA composition, in a previous study based on a hierarchical clustering analysis [ 4 ], we have shown that lipogenic-related genes are in general positively correlated with MUFA, while the lipolytic-related genes are specifically positively correlated with PUFA. Likewise, by conducting RNA sequencing (RNA-Seq) experiments, several studies have reported numerous candidate genes with differential effects or global changes on intramuscular FA composition across several tissues, such as backfat, liver, and muscle [ 5 – 9 ]. Our research group has also identified links between the muscle transcriptome and its FA profile in Iberian × Duroc backcross (BC1_DU) pigs [ 9 ].…”

“…Likewise, by conducting RNA sequencing (RNA-Seq) experiments, several studies have reported numerous candidate genes with differential effects or global changes on intramuscular FA composition across several tissues, such as backfat, liver, and muscle [ 5 – 9 ]. Our research group has also identified links between the muscle transcriptome and its FA profile in Iberian × Duroc backcross (BC1_DU) pigs [ 9 ]. In that study, we used a univariate extended linear model and found that several candidate genes involved in carbohydrate and lipid metabolism were significantly associated with FA composition traits (mainly MUFA, PUFA, and FA ratios).…”

“…In the study reported here, we analyzed our existing muscle data (i.e., expression levels of genes and only individual FA phenotypes) of the BC1_DU population [ 9 ]. From a multivariate perspective and using a complementary integrative analysis, we investigated the gene expression of potential candidate genes and novel regulators for intramuscular FA composition.…”

A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

“…Functionally, as a coactivator of PPARγ, NCOA2 plays a pivotal role in regulating lipid metabolism and energy homeostasis [49]. Furthermore, it emerges as a key player in modulating intramuscular fatty acid composition in pigs [50,51]. In a different context, we observed BMPER as a differential gene situated within TAD unique to muscle when compared to adipose in Large White pigs.…”