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BackgroundBeef tenderness is a complex trait of economic importance for the beef industry. Understanding the epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs. However, little is known about epigenetic effects on Bos taurus muscle and their implications in tenderness, and no studies have been conducted in Bos indicus.ResultsComparing methylation profile of Bos indicus skeletal muscle with contrasting beef tenderness at 14 days after slaughter, we identified differentially methylated cytosines and regions associated with this trait. Interestingly, muscle that became tender beef had higher levels of hypermethylation compared to the tough group. Enrichment analysis of predicted target genes suggested that differences in methylation between tender and tough beef may affect signal transduction pathways, among which G protein signaling was a key pathway. In addition, different methylation levels were found associated with expression levels of GNAS, PDE4B, EPCAM and EBF3 genes. The differentially methylated elements correlated with EBF3 and GNAS genes overlapped CpG islands and regulatory elements. GNAS, a complex imprinted gene, has a key role on G protein signaling pathways. Moreover, both G protein signaling pathway and the EBF3 gene regulate muscle homeostasis, relaxation, and muscle cell-specificity.ConclusionsWe present differentially methylated loci that may be of interest to decipher the epigenetic mechanisms affecting tenderness. Supported by the previous knowledge about regulatory elements and gene function, the methylation data suggests EBF3 and GNAS as potential candidate genes and G protein signaling as potential candidate pathway associated with beef tenderness via methylation.

Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix–partial correlation information theory (AWM‐PCIT) approach. Beyond a simple list of candidate genes, AWM‐PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility‐associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower‐density genotypes. Sequence‐level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes—KDM5C, LRRK2, and PME—was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further. [ABSTRACT FROM AUTHOR]

Despite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factors governing fertility. Herein, we identified regulatory variants from RNA-Seq data associated with gene expression regulation in the uterine luminal epithelial cells of beef cows. We identified 4676 cis and 7682 trans eQTLs (expression quantitative trait loci) affecting the expression of 1120 and 2503 genes, respectively (FDR < 0.05). These variants affected the expression of transcription factor coding genes (71 cis and 193 trans eQTLs) and genes previously reported as differentially expressed between pregnant and nonpregnant cows. Functional over-representation analysis highlighted pathways related to metabolism, immune response, and hormone signaling (estrogen and GnRH) affected by eQTL-regulated genes (p-value ≤ 0.01). Furthermore, eQTLs were enriched in QTL regions for 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05). Our study provides novel insights into the genetic basis of reproductive processes in cattle. The underlying causal mechanisms modulating the expression of uterine genes warrant further investigation. [ABSTRACT FROM AUTHOR]

Reproductive inefficiency is a major cause for economic loss in cattle operations. However, the mechanisms underlying their ethology are still unknown. Herein, we aimed to identify genes and genetic variants underlying the uterine function and their role in female fertility. To this end, we performed a multi-tiered approach to identify endometrial differentially expressed genes (DEGs) from beef heifers classified as fertile (n = 7) or sub-fertile (n = 5). Further, we used public RNASeq data from uterine luminal epithelial cells from beef cows (n = 43) to identify genetic variants affecting the expression of genes (expression quantitative trait loci - eQTLs) involved with pregnancy outcomes. We identified 798 DEGs underlying pathways important for pregnancy establishment, including inflammatory response and G-protein coupled receptor (GPCR) signaling (P-value ≤ 0.01). Based on the eQTL mapping analysis, we identified 4,676 cis and 7,682 trans eQTLs (FDR ≤ 0.05). Interestingly, some of the eQTLs overlapped with 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05), including daughter pregnancy rate and non-return rate. Additionally, these eQTLs were modulating the expression of transcription factors and DEGs previously associated with pregnancy outcomes in beef cows. The integration of gene lists from both studies resulted in 16 common genes, including F2 and P2RX5. The F2 gene encodes for a coagulation factor that plays a role in smooth muscle contraction and is modulated by a unique family of GPCRs. The expression of purinergic receptors, such as P2RX5, have been proposed to be major facilitators of attachment and implantation through calcium ions. Functional over-representation analysis highlighted metabolism, immune response, and hormone (estrogen and GnRH) signaling pathways affected by eQTL-regulated genes (P-value < 0.01). Immune cells and regulatory pregnancy hormones, such as interferon tau and progesterone, are tightly regulated by each other and work cooperatively. GPCR signaling involves key regulatory hormones of the estrous cycle, specifically GnRH, LH, and FSH. Improper immune cell signaling, cyclicity, hormonal signaling, and smooth muscle contractions all affect the endometrium function, with potential downstream effects on pregnancy establishment and fertility. Dysregulation of these signaling pathways due to genetic variants could have detrimental effects, ultimately leading to failed pregnancy. Our findings provide novel insights into the genetic basis of reproductive processes in beef cattle. The molecular features and over-represented pathways could be used for identification of potential biomarkers for predicting pregnancy success. However, the underlying causal mechanisms modulating the expression of uterine genes warrant further investigation. [ABSTRACT FROM AUTHOR]

Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is an important source of fatty acids (FAs) in the human diet, as it is one of the most consumed meats worldwide. The effects of dietary inclusion of oils such as canola, fish, and soybean oils on pig gene expression are mostly unknown. Our objective was to evaluate FA composition, identify changes in gene expression in the liver of male pigs fed diets enriched with different FA profiles, and identify impacted metabolic pathways and gene networks to enlighten the biological mechanisms’ variation. Large White male pigs were randomly allocated to one of three diets with 18 pigs in each; all diets comprised a base of corn and soybean meal to which either 3% of soybean oil (SOY), 3% canola oil (CO), or 3% fish oil (FO) was added for a 98-day trial during the growing and finishing phases. RNA sequencing was performed on the liver samples of each animal by Illumina technology for differential gene expression analyses, using the R package DESeq2. The diets modified the FA profile, mainly in relation to polyunsaturated and saturated FAs. Comparing SOY vs. FO, 143 differentially expressed genes (DEGs) were identified as being associated with metabolism, metabolic and neurodegenerative disease pathways, inflammatory processes, and immune response networks. Comparing CO vs. SOY, 148 DEGs were identified, with pathways related to FA oxidation, regulation of lipid metabolism, and metabolic and neurodegenerative diseases. Our results help explain the behavior of genes with differential expression in metabolic pathways resulting from feeding different types of oils in pig diets. [ABSTRACT FROM AUTHOR]

Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation. [ABSTRACT FROM AUTHOR]

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle. [ABSTRACT FROM AUTHOR]

Simple Summary: Findings from the analysis of the pig transcriptome may help to better understand the biological mechanisms that can be modulated by the diet. Thus, the aim of this study was to identify the differentially expressed genes from the skeletal muscle and liver samples of pigs fed diets with two different levels of soybean oil (1.5 or 3%). The FA profile in the tissues was modified by the diet mainly related to monounsaturated (MUFA) and polyunsaturated (PUFA). This nutrigenomics study verified the effect of different levels of soybean oil in the pig diet on the transcriptome profile of skeletal muscle and liver, where the higher level of soybean oil added to the diet led to a higher expression of genes targeting biological processes related to lipid oxidation and consequently to metabolic diseases and inflammation. The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet. [ABSTRACT FROM AUTHOR]

Fatty acid (FA) content has a significant role in the quality and nutritional composition of beef. However, genetic and epigenetic mechanisms governing FA content in beef are not fully understood. Therefore, we identified putative regulatory genes potentially modulating FA content in Nelore cattle muscle that are also being epigenetically repressed. These genes are called discordantly regulated genes (DRGs). We used genome-wide expression data from muscle samples of Nelore steers, which were selected based on contrasting levels of five specific fatty acids. Our study cohort comprised 15 muscle samples per contrasting group, sourced from an experimental breeding herd, born between 2009 and 2011 and assayed on feedlot at the Brazilian Agricultural Research Corporation (EMBRAPA/Brazil). These animals were sired by 34 unrelated bulls representing prominent genealogies prevalent in Brazil during that period. We identified 48 unique DRGs associated with the content of at least one FA. There were 24 DRGs for conjugated linoleic acid (CLA), 32 for oleic acid (OA), 26 for palmitic acid (PA), 22 for eicosapentaenoic acid (EPA) and 22 for docosahexaenoic acid (DHA). These DRGs have crucial roles in developmental and differentiation processes, aligning with expectations for genes under epigenetic regulation. Notably, 10 DRGs were identified as common regulators across all five FAs (COMP, HOXC10, LBX1, PAX7, PITX2, SIM2, SOX17, TBX15, TBX3 and ZIC4); five DRGs were previously published differentially expressed genes for CLA, 25 were annotated as known bovine transcription factors and one as a known bovine transcription cofactor, further supporting their regulatory potential. To investigate genetic variants associated with epigenetically regulated genomic regions linked to FA traits, we conducted association tests with SNPs proximal to the transcription start sites (TSS) of DRGs. For that we considered a window of 10 kb for each side, and the previously published genetic estimated breeding value for the fatty acids in the study. We identified a significant SNP, rs110498194, associated with CLA (FDR < 0.05). This SNP is within an intron of the PITX2 gene, located 7,537 bp downstream of its TSS. PITX2 is a DRG for all five FA and is a known bovine transcription factor. To validate the presence of epigenetic elements within the genomic region associated with CLA, we examined two bovine muscle samples from the FAANG project using the UCSC Genome Browser. We identified ATAC-Seq and ChIP-Seq peaks for CTCF, H3K27ac, H3K27me3, H3K4me1 and H3K4me3, indicating active epigenetic regulation in these genomic regions. Despite the limitations in our predictions, stemming from the enrichment of cell differentiation related processes and reliance on human-based data, our findings highlight candidate genes implicated in the regulation of fatty acid content in bovine muscle, potentially repressed by epigenetic mechanisms and a SNP involved in this regulation for CLA. [ABSTRACT FROM AUTHOR]

Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3 , FEZF2 , and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle. [ABSTRACT FROM AUTHOR]

Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p -value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1 , ELK3 , ETS1 , FLI1 , and TCF4 , were identified with binding sites in at least one hub gene. Gene expression of CCDC80 , FBLN5 , SERPINF1 , and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle. [ABSTRACT FROM AUTHOR]

[Display omitted] • Transcription factors and miRNA co-regulate gene expression in reproductive tissues. • Transcription factors and miRNA have a predicted influence over spermatogenesis and male fertility. • Genes involved in contrary regulations were associated with spermatogenesis, sexual reproduction and sperm motility. Spermatogenesis is highly conserved among mammalians, but its gene expression and regulatory profile are not entirely known. As transcription factors (TFs) and miRNAs are crucial for gene expression regulation, identifying genes negatively regulated by miRNAs and positively regulated by TFs in the testis and epididymis can provide a deeper understanding of gene expression and regulatory patterns. To do this, we used expression data coming from RNA-Seq and miRNA-Seq experiments made with biopsies from testicular parenchyma, head of the epididymis, and tail of the epididymis of four Brahman bulls. We identified miRNA differentially expressed (DE) by comparing the three distinct tissues. A co-expression analysis combined with a regulatory impact factor approach identified miRNAs and TFs with regulatory impact over gene expression regulation in the Bos indicus tissues studied. We identified 116 DE miRNAs, 206 miRNAs and 237 TFs with a significant regulatory impact on mRNA patterns in the tissues' comparisons. bta-miR-196b was the only DE miRNA for all tissue comparisons and it may be a regulator of spermatogenesis through its links with adipogenesis and insulin biosynthesis. DE genes and TFs involved in contrary regulations between the epididymis head and testis parenchyma were associated with spermatogenesis, sexual reproduction, and sperm motility. Our results provide possible mechanisms, governed by the contrary effect of miRNA and TF, leading to the differential expression between the studied tissues. We have demonstrated that our predictions of miRNAs and TFs co-regulations over target DE genes can retrieve known regulatory mechanisms and predict new ones that merit further validation. [ABSTRACT FROM AUTHOR]

Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5 , and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected. [ABSTRACT FROM AUTHOR]

Female fertility significantly affects the efficiency of cow-calf production. Despite the collective efforts to understand the complex regulation of reproductive traits, causative genes and/or mutations have yet to be reported. Using omics technologies, such as gene expression, may unveil potential regulatory mechanisms and provide opportunities that link genotype to phenotype. Among them, expression quantitative trait loci (eQTL) are a powerful tool to identify biological mechanisms and potential markers for improving fertility. This study aimed to identify eQTLs underlying fertility-related traits and their co-localization with previously annotated QTLs. RNA-Seq from uterine epithelial cells (GSE171577) from crossbreed cows (n = 18 non-pregnant - NP and n = 25 pregnant - P) were used for gene expression analysis and SNP calling. Raw data quality control was performed, and read mapping was carried out using STAR. Genes were normalized to counts per million (CPM) and then the CPM values were log2 transformed using edgeR. Next, uniquely mapped reads were used for variant detection using the GATK software. Significant eQTLs were compared with the Animal Genome cattle database (QTLdb) to identify overlapping QTL regions. After quality control, 43 samples, 203,404 SNPs, and 15,029 genes were used for eQTL analysis. Using an additive linear model from the Matrix eQTL R-package, we identified 3,989 cis- and 7,683 trans-eQTLs for 1,120 and 2,503 genes, respectively (FDR < 0.05). A total of 50 cis-eQTLs were previously reported as differentially expressed genes, including CD37, CXCL3, PILRA, and PPP6R1 genes. The QTLs from QTLdb overlapping with our eQTLs were associated with traits such as age at puberty, conception rate, fertility index, and luteal activity (FDR < 0.05). Additionally, QTLs for production traits, such as milk production and body weight gain, were over-represented by the eQTLs we have identified. Significant biological processes underlying cis-regulated genes retrieved from ShinyGO were related to antigen processing and presentation. Likewise, trans-eQTLs genes were involved with transcription cisregulatory region binding and transcription regulator activity. Our study provides novel regulatory and potential causative genetic variants, biological pathways, and genes underlying fertility in cows. Annotation and co-localization of detected eQTLs retrieved genomic regions previously reported as QTLs for production and reproduction-related traits. Further investigation, however, is required to untangle the mechanisms modulating gene expression and its effects on fertilityrelated traits. [ABSTRACT FROM AUTHOR]

BACKGROUND: Individuals with bronchiectasis exhibit colonization and infection of the respiratory system, with a consequent alteration of the macroscopic appearance of secretions, which ranges from mucoid to purulent. Purulence is related to the structural conformation, rheological profile, and transport indexes of mucus. We analyzed and compared the transport properties of respiratory secretions with mucoid appearance versus those with purulent appearance in patients with bronchiectasis and in subjects without lung disease. METHODS: In a simulated cough machine we assessed the mucociliary transport and contact angle of 32 mucoid and 19 purulent samples from subjects with bronchiectasis, and 21 samples from subjects without lung disease. RESULTS: Mucociliary transport was lower in the mucoid samples (0.78 ± 0.22) and in the purulent samples (0.73 ± 0.22) than in the samples from subjects without lung disease (1 ± 0.19). The purulent samples had less displacement in the simulated cough machine (7.57 ± 3 cm) than did the mucoid samples (23 ± 15 cm) or the samples from subjects without lung disease (34 ± 8.4 cm), as did the mucoid samples compared to the samples from subjects without lung disease. The purulent samples had a higher contact angle (25 ± 6.1°) than the mucoid samples (17 ± 7.8°) or the samples from subjects without lung disease (10 ± 2.5°), as did the mucoid samples compared to the samples from subjects without lung disease. CONCLUSIONS: Respiratory secretions in individuals with bronchiectasis have poor transport properties, which manifest as reduced mucociliary transport, reduced mucus transport by cough, and higher contact angle. These features were more accentuated in the purulent samples. This simple classification can be used by therapists to plan treatments, and by researchers to obtain more homogeneity between groups of subjects. [ABSTRACT FROM AUTHOR]

The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.