Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs

Abstract

Background The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype of three SNP mutations in the stearoyl-coA desaturase (SCD) gene promoter associated with higher content of monounsaturated fatty acids in intramuscular fat. The second of these three SNPs (rs80912566, C > T) affected a putative retinol response element in the SCD promoter. The effect of dietary vitamin A restriction over intramuscular fat content is controversial as it depends on the pig genetic line and the duration of the restriction. This study aims to investigate changes in the muscle transcriptome in SCD rs80912566 TT and CC pigs fed with and without a vitamin A supplement during the fattening period. Results Vitamin A did not affect carcass traits or intramuscular fat content and fatty acid composition, but we observed an interaction between vitamin A and SCD genotype on the desaturation of fatty acids in muscle. As reported before, the SCD-TT pigs had more monounsaturated fat than the SCD-CC animals. The diet lacking the vitamin A supplement enlarged fatty acid compositional differences between SCD genotypes, partly because vitamin A had a bigger effect on fatty acid desaturation in SCD-CC pigs (positive) than in SCD-TT and SCD-TC animals (negative). The interaction between diet and genotype was also evident at the transcriptome level; the highest number of differentially expressed genes were detected between SCD-TT pigs fed with the two diets. The genes modulated by the diet with the vitamin A supplement belonged to metabolic and signalling pathways related to immunity and inflammation, transport through membrane-bounded vesicles, fat metabolism and transport, reflecting the impact of retinol on a wide range of metabolic processes. Conclusions Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content despite relevant changes in muscle gene expression, both in coding and non-coding genes. Vitamin A activated general pathways of retinol response in a SCD genotype-dependant manner, which affected the monounsaturated fatty acid content, particularly in SCD-CC pigs.

Identification of a missense variant in the porcine AGPAT gene family associated with intramuscular fat content through whole‐genome sequencing

“…Although GPAT4 was previously named AGPAT6 , we did not include it in our study because it is no longer considered a member of the AGPAT family and its ortholog showed no acylglycerol acyltransferase activity in humans (Chen et al, 2008 ). To determine gene expression of the members of the AGPAT family, we analyzed RNA‐Seq data from muscle semimembranosus of a subset of 40 pigs from one of the batches, obtained and processed as detailed by Solé et al ( 2022 ).…”

“…high resolution melt software v3.1 (Applied Biosystems, Thermo Scientific) was used for the analysis of melting data and sample genotyping. All pigs were also genotyped for SNPs in genes SCD (rs80912566, C>T, on SSC14) and LEPR (rs709596309, C>T, on SSC6) following the protocols described in Estany et al ( 2014 ), Solé et al ( 2022 ), and Ros‐Freixedes et al ( 2016 ) respectively. In a subset of 807 pigs, the genotype for DGAT2 (rs3472408443, G>A, on SSC9) was also available (Solé et al, 2021 ).…”

“…The results for AGPAT5 are consistent with the fact that this gene is the most expressed of the AGPAT gene family in skeletal muscle in pigs. Using data from a previous RNA-Seq experiment (Solé et al, 2022), we found that AGPAT5 and AGPAT2 are the most expressed genes in muscle semimembranosus in pig (Figure S2). Those results are also in line with previous gene expression data reported in pig skeletal muscle (Freeman et al, 2012).…”

Identification of a missense variant in the porcine AGPAT gene family that affects intramuscular fat content through whole-genome sequencing

“…High Resolution Melt software v3.1 (Applied Biosystems, Thermo Scientific) was used for the analysis of melting data and sample genotyping. All pigs were also genotyped for SNPs in genes SCD (rs80912566, C>T, on SSC14) and LEPR (rs709596309, C>T, on SSC6) following the protocols described in (Estany et al, 2014;Solé et al, 2022) and (Ros-Freixedes et al, 2016), respectively. In a subset of 807 pigs, the genotype for DGAT2 (ss7315407085, G>A, on SSC9) was also available (Solé et al, 2021).…”

“…The results for AGPAT5 are consistent with the fact that this gene is the most expressed of the AGPAT gene family in skeletal muscle in pigs. Using data from a previous RNA-Seq experiment (Solé et al, 2022), we found that AGPAT5 and AGPAT2 are the most expressed genes in muscle semimembranosus in pig (Supplementary Figure S1). Those results are also in line with previous gene expression data reported in pig skeletal muscle (Freeman et al, 2012).…”