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. 2025 Oct;56(5):e70051.
doi: 10.1111/age.70051.

Transcription factors and candidate functional SNPs associated with variation in fatty acid composition from skeletal muscle of pigs

Mariah C Durval  1   2 , Luiz F Brito  2 , Simara L Fanalli  1 , Artur O Rocha  2 , Lorena F Benfica  2 , Fernanda N Ciconello  3 , Camila S Oliveira  2   3 , Ingrid S Garcia  3 , Felipe A Oliveira Freitas  2   3 , Lucas E Nascimento  3 , Bruna P Martins da Silva  3 , Bárbara Silva-Vignato  3 , Aline S M Cesar  1   3
Affiliations

Transcription factors and candidate functional SNPs associated with variation in fatty acid composition from skeletal muscle of pigs

Mariah C Durval et al. Anim Genet. 2025 Oct.

Abstract

Pork is an essential source of fatty acids (FAs) in the human diet. Fatty acids are important for various biological processes and can impact transcription regulation. The primary objective of this study was to identify candidate functional single nucleotide polymorphisms (SNPs) and expression quantitative trait loci (eQTL) associated with FA composition variation, and transcription factors (TFs) related to lipid metabolism using SNP array genotyping and Longissimus lumborum muscle transcriptome of Large White pigs. A total of 105 378 unique SNPs were identified, including 74 955 originating from RNA-Seq data and 30 423 SNPs from the Porcine 50K SNP chip. These SNPs were tested for association with the skeletal muscle gene expression data (15 090 genes) using the matrixeqtl package. Genome-wide association studies were conducted to test the association of these SNPs with FA trait variation, resulting in 74 254 eQTL, including 15 558 cis- and 58 696 trans-eQTL. Furthermore, 23 eQTL hotspots were identified, along with four TFs related to lipid metabolism: EGR1, SP1, CREB3 and INSM. The analysis identified two SNPs significantly associated with oleic and linolenic acids in the skeletal muscle of pigs. Candidate genes previously reported to influence meat quality in pigs and human health were identified, including PITX3, NT5C2, FTL, GLIS1, API5 and HILPDA. Although these findings offer valuable insights into metabolic disease response and lipid metabolism, contributing to a better understanding of gene expression related to lipid metabolism, meat quality and FA composition in pigs, the limited sample size indicates that further validations using larger datasets are recommended.

Keywords: Longissimus lumborum; gene expression; lipid metabolism.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Variant annotation by the Ensembl variant effect predictor tool for cis‐expression quantitative trait loci (eQTL) (a) and trans‐eQTL (b).
FIGURE 2
FIGURE 2
(a) Percentage of quantitative trait loci (QTL) type for cis‐eQTL. (b) Percentage of QTL type for trans‐eQTL.
FIGURE 3
FIGURE 3
Histogram showing the number of genes regulated by each expression quantitative trait loci (eQTL) hotspot.
See this image and copyright information in PMC

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