Abstract
Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle (Longissimus dorsi) of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the Iberian breed. Expression genome-wide association studies (eGWAS) were performed between the muscle gene expression values, measured by real-time quantitative PCR, and the genotypes of 38,426 SNPs distributed along all chromosomes. The eGWAS identified 186 eSNPs located in ten Sus scrofa regions and associated with the expression of ACSM5, ACSS2, ATF3, DGAT2, FOS and IGF2 (FDR < 0.05) genes. Two expression quantitative trait loci (eQTLs) for IGF2 and ACSM5 were classified as cis-acting eQTLs, suggesting a mutation in the same gene affecting its expression. Conversely, ten eQTLs showed trans-regulatory effects on gene expression. When the eGWAS was performed for each backcross independently, only three common trans-eQTL regions were observed, indicating different regulatory mechanisms or allelic frequencies among the breeds. In addition, hotspot regions regulating the expression of several genes were detected. Our results provide new data to better understand the functional regulatory mechanisms of lipid metabolism genes in muscle.
Highlights
Studies on the traits that determine the quality of pork meat and their derived products have received increasing attention in recent years
We have identified differentially expressed (DE) genes in the muscle transcriptome among two groups of extreme animals for fatty acid (FA) composition in an Iberian x Landrace cross by RNA-Seq, reinforcing the view that variation in gene expression and its genetic basis may play an important role in the genetic determinism of these traits[16]
Genes over-expressed in females were implicated in transcriptional regulation and control (CREG1, LXRA, NFKB1, NCOA1, NCOA2, NCOA6, PPARG, PRKAA1, RXRG, SP1 and SREBP1c), FA β-oxidation (CROT, PXMP3 and SCD), lipid storage (ACSM5, DGAT2, HIF1AN and AQP7), cholesterol (ACSS2, ANGPT1 and SETD7) and the AKT pathway (IGF2, PIK3R1 and PLA2G12A)
Summary
Studies on the traits that determine the quality of pork meat and their derived products have received increasing attention in recent years. Pig breeding companies have produced commercial pigs that grow faster and have superior carcasses These carcasses have become leaner having less IMF and, producing a decrease in the meat quality according to consumers. The main goal of the present study was the identification of genomic variants regulating the expression in pig muscle of 45 candidate genes for lipid metabolism and fatty acid composition. To achieve this objective, an eGWAS study was conducted for 355 animals using gene expression data of 114 BC1_LD pigs (25% Iberian and 75% Landrace) previously generated in Puig-Oliveras et al (2016)[17], and re-analysed in the present study using the Sus Scrofa 11.2 genome assembly, and new expression data of 122 BC1_DU (25% Iberian and 75% Duroc) and 119 BC1_PI (25% Iberian and 75% Pietrain) pigs
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