Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome

Identification of trait-associated microRNA modules in liver transcriptome of pig fed with PUFAs-enriched supplementary diet

Dietary lipids provide energy, are cellular structural components, and are involved in physiological processes. Lipids are the dietary source in supplementary diet experiments in pigs. This study aims to investigate the dietary effects of PUFAs on the hepatic transcriptome and physiological pathways of two diets on two pig breeds. Polish Landrace (PL: n = 6) and six PLxDuroc (PLxD: n = 6) pigs were fed with a normal diet (n = 3) or PUFAs-enriched healthy diet (n = 3), and the hepatic miRNA profiles were studied for weighted gene co-expression network analysis biological interactions between gene networks and metabolic pathways of DE miRNA genes. The study identified trait-associated modules that were significantly associated with four phenotypic traits in the dietary groups of PL and PLxD: meat colour (a*), shoulder subcutaneous fat thickness, conductivity 24 h post-mortem (PE24), and ashes. Trait-wise, a large set of co-expressed miRNAs of porcine liver were identified in these trait-associated significant modules (9, 7, 2, and 8) in PL and PLxD. Each module is represented by a module eigengene (ME). Forty-four miRNAs out of 94 miRNAs interacted with 6719 statistically significant target genes with a target score > 90. The GO/pathway analysis showed association with pathways including regulation of metallopeptidase activity, sebaceous gland development, collagen fibril organization, WNT signalling, epithelial tube morphogenesis, etc. The study showed the differences in miRNA expression between the dietary groups of PL and PLxD breeds. Hub genes of discovered miRNA clusters can be considered predicted miRNA genes associated with PE24, meat colour, shoulder subcutaneous fat thickness, and ashes. Discovered target genes for miRNA clusters play significant roles in biological functions such as (i) muscle and body growth development, (ii) different cellular processes and developments, (iii) system development, and (iv) metabolic processes.

Untargeted lipidomics reveals unique lipid signatures of extracellular vesicles from porcine colostrum and milk

Extracellular vesicles (EV) are membranous vesicles considered as significant players in cell-to-cell communication. Milk provides adequate nutrition, transfers immunity, and promotes neonatal development, and milk EV are suggested to play a crucial role in these processes. Milk samples were obtained on days 0, 7, and 14 after parturition from sows receiving either a standard diet (ω-6:ω-3 = 13:1) or a test diet enriched in ω-3 (ω-6:ω-3 = 4:1). EV were isolated using ultracentrifugation coupled with size exclusion chromatography, and characterized by nanoparticle tracking analysis, transmission electron microscopy, and assessment of EV markers via Western blotting. The lipidome was determined following a liquid chromatography-quadrupole time-of-flight mass spectrometry approach. Here, we show that different stages of lactation (colostrum vs mature milk) have a distinct extracellular vesicle lipidomic profile. The distinct lipid content can be further explored to understand and regulate milk EV functionalities and primordial for enabling their diagnostic and therapeutic potential.

Effect of Dietary Supplementation of Durvillaea Antarctica Meal on Production and Meat Quality Traits of Lambs

Worldwide, there are reports indicating that sheep raised in insular systems spontaneously consume seaweed. In the southern hemisphere, there exists Durvillaea antarctica, a brown seaweed that possesses minerals and fatty acids that could improve some aspects of sheep production and meat quality, respectively. However, the consumption of this algae in lambs has been scarcely studied. The objective of this study was to evaluate the effects of dietary inclusion of Durvillaea antarctica meal on the growth performance, blood profile, and meat quality of fattening lambs. Thirty Araucana Creole lambs were housed and allocated to three pens. One pen served as a control, while the remaining two were supplemented with diets containing 5% and 10% Durvillaea antarctica meal. After 9 weeks, the animals were slaughtered. The dietary treatments did not significantly affect body weight and blood biochemical parameters. However, changes were observed in meat quality traits, including increased redness and reduced luminosity in the loin for the high inclusion treatment, in addition to slight alterations in pH and lower lipid oxidation in lambs' meat fed Durvillaea antarctica. Furthermore, the meat from lambs supplemented with Durvillaea antarctica exhibited increased levels of linoleic acid and arachidonic acid, along with higher monounsaturated fatty acid content and a reduced omega-3/omega-6 ratio. This study shows that Durvillaea antarctica can be used to feed lambs without impairing growth or production parameters, which has been little studied. It is possible that this brown seaweed could be considered a natural additive to improve the quality and nutritional value of lamb meat. The effect of this seaweed on other ruminant models could be addressed in future studies.

Preliminary investigation on the impact of salty and sugary former foods on pig liver and plasma profiles using OMICS approaches

Replacing cereals with food leftovers could reduce feed-food competition and keep nutrients and energy in the food chain. Former food products (FFPs) are industrial food leftovers no more intended for human but still suitable as alternative and sustainable feedstuffs for monogastric. In this study, omics approaches were applied to evaluate the impact of dietary FFPs on pig liver proteome and plasma peptidome. Thirty-six Swiss Large White male castrated pigs were randomly assigned to three dietary treatments [control (CTR), 30% CTR replaced with salty FFP (SA), 30% CTR replaced with sugary FFP (SU)] from the start of the growing phase (22.4 ± 1.7 kg) until slaughtering (110 ± 3 kg). The low number of differentially regulated proteins in each comparison matrix (SA/SU vs. CTR) and the lack of metabolic interaction indicated a marginal impact on hepatic lipid metabolism. The plasma peptidomics investigation showed low variability between the peptidome of the three dietary groups and identified three possible bioactive peptides in the SA group associated with anti-hypertension and vascular homeostasis regulation. To conclude, the limited modulation of liver proteome and plasma peptidome by the SA and SU diets strenghtened the idea of reusing FFPs as feed ingredients to make pig production more sustainable.

RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids

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.

The effects of dietary essential fatty acid ratios and linoleic acid level in grow-finish pigs

The objective of this study was to investigate the effects of dietary linoleic acid level and the ratio of linoleic acid:linolenic acid (LA:ALA) on the growth performance, expression of genes associated with lipid metabolism, and inflammatory status of grow-finish pigs. A total of 300 growing pigs (body weight [BW] = 41.1 ± 6.3 kg) were randomly assigned to either a high (30 g/kg; HLA) or low (15 g/kg; LLA) dietary linoleic acid level with a high (23:1; HR), moderate (13:1; MR) or low (4:1; LR) dietary LA:ALA in a 2 × 3 factorial design. Diets were fed across three 28-d phases and were balanced for dietary metabolizable energy. Pigs were housed five pigs per pen in single-sex pens. Blood samples were collected on days 0, 21, 42, and 84, and synovial fluid was collected from the hock joint on days 0 and 84 for inflammatory marker analysis. Data were analyzed as repeated measures using PROC MIXED (SAS 9.4) with initial BW as a covariate, pen as the experimental unit, and LA level, LA:ALA, sex, phases, and their interactions as fixed effects. Compared to HLA, LLA pigs tended to have increased BW at days 56 and 84 (P = 0.088). There was no effect of LA × LA:ALA for growth performance. For the overall days 0 to 84 growth period, pigs fed HR had increased ADG compared to MR, with pigs receiving LR performing intermediate of MR and HR. Gilts receiving HR diets had increased day 84 BW compared to gilts receiving the low and moderate LA:ALA (P = 0.006), which was a result of improved overall days 0 to 84 ADG compared to gilts receiving the MR diets (P = 0.023). Barrows fed LR had improved BW on day 56 compared to MR and HR and higher final BW compared to HR, with MR performing intermediately (P = 0.006). This was a result of greater days 0 to 84 ADG (P = 0.023). Overall, C-reactive protein (CRP), tumor necrosis factor-α (TNFα), and interleukin-6 were reduced in the plasma of pigs over time (P ≤ 0.037). Across all treatments, CRP and TNFα were reduced in the hock and carpus synovial fluid on day 84 vs. day 0 (P ≤ 0.049). In conclusion, LA:ALA ratios utilized in this study can be fed at varying linoleic acid levels without impacting growth or inflammation. Additionally, LA:ALA ratios can differentially impact the growth of gilts and barrows.

Nutritional significance and health benefits of omega-3, -6 and -9 fatty acids in animals

The balance between omega-3 (ω-3), omega-6 (ω-6) and omega-9 (ω-9) fatty acids (FAs) is very important because these types of oils constitute essential components for the formation of the cell membrane, also they are precursors for a large number of substances in the body. One of the most important strategies for improving the increment of polyunsaturated FAs in poultry and animal meat is the dietary administration of these FAs. Additionally, the different sources of ω-3 or 6 in the diet improve the performance, public health and physiological aspects including anti-oxidative properties and immunity. ω-3 FAs have anti-inflammatory characteristics due to their ability to reduce cytokines liberation. High-level of ω-6 FAs is always associated with an increased incidence of dangerous disorders like depression and heart disease. These FAs showed a tremendous series of beneficial impacts like improved cholesterol levels and a decreased occurrence of coronary heart diseases. This article includes some information on the use of ω-3, ω-6 and ω-9 FAs in animal and human diets. These oils are vital for the physiological and health aspects, and the information mentioned here will improve our understanding of the functions and roles of these FAs in the body.

Low n-6/n-3 Gestation and Lactation Diets Influence Early Performance, Muscle and Adipose Polyunsaturated Fatty Acid Content and Deposition, and Relative Abundance of Proteins in Suckling Piglets

Elevated omega-6 (n-6) and omega-3 (n-3) polyunsaturated fatty acids (PUFAs) ratios in swine diets can potentially impose a higher risk of inflammatory and metabolic diseases in swine. A low ratio between the two omega PUFAs has beneficial effects on sows' and piglets' production performance and immunity status. At present, there are few studies on how sow nutrition directly affects the protein and fat deposition in suckling piglets. Two groups of sows were fed diets with high or low n-6/n-3 polyunsaturated ratios of 13:1 (SOY) and 4:1 (LIN), respectively, during gestation and lactation. Longissimus dorsi muscle and adipose tissue from newborn piglets, nourished only with sow's milk, were subjected to fatty acid profiling by gas chromatography-mass spectrometry (GC-MS) and to proteomics assays based on nano-liquid chromatography coupled to high-resolution tandem mass spectrometry (nLC-HRMS). Fatty acid profiles on both muscle and adipose tissues resembled the magnitude of the differences between fatty acid across diets. Proteomic analysis revealed overabundance of 4 muscle and 11 adipose tissue proteins in SOY compared to LIN in both piglet tissues. The detected overabundance of haptoglobin, an acute-phase protein, and the stimulation of protein-coding genes and proteins related to the innate immune response and acute inflammatory response could be associated with the pro-inflammatory role of n-6 PUFAs.

Dietary Supplementation of Inorganic, Organic, and Fatty Acids in Pig: A Review

Simple Summary

The role of acids in pig feed strategies has changed from feed acidifier and preservative to growth promoter and antibiotics substitute. Since the 2006 European banning of growth promoters in the livestock sector, several feed additives have been tested with the goal of identifying molecules with the greatest beneficial antimicrobial, growth-enhancing, or disease-preventing abilities. These properties have been identified among various acids, ranging from inexpensive inorganic acids to organic and fatty acids, and these have been widely used in pig production. Acids are mainly used during the weaning period, which is considered one of the most critical phases in pig farming, as well as during gestation, lactation, and fattening. Such supplementation generally yields improved growth performance and increased feed efficiency; these effects are the consequences of different modes of action acting on the microbiome composition, gut mucosa morphology, enzyme activity, and animal energy metabolism.

Abstract

Reduction of antibiotic use has been a hot topic of research over the past decades. The European ban on growth-promoter use has increased the use of feed additivities that can enhance animal growth performance and health status, particularly during critical and stressful phases of life. Pig farming is characterized by several stressful periods, such as the weaning phase, and studies have suggested that the proper use of feed additives during stress could prevent disease and enhance performance through modulation of the gastrointestinal tract mucosa and microbiome. The types of feed additive include acids, minerals, prebiotics, probiotics, yeast, nucleotides, and phytoproducts. This review focuses on commonly used acids, classified as inorganic, organic, and fatty acids, and their beneficial and potential effects, which are widely reported in the bibliography. Acids have long been used as feed acidifiers and preservatives, and were more recently introduced into feed formulated for young pigs with the goal of stabilizing the stomach pH to offset their reduced digestive capacity. In addition, some organic acids represent intermediary products of the tricarboxylic acid cycle (TCA), and thus could be considered an energy source. Moreover, antimicrobial properties have been exploited to modulate microbiota populations and reduce pathogenic bacteria. Given these potential benefits, organic acids are no longer seen as simple acidifiers, but rather as growth promoters and potential antibiotic substitutes owing to their beneficial action on the gastrointestinal tract (GIT).

3'quant mRNA-Seq of Porcine Liver Reveals Alterations in UPR, Acute Phase Response, and Cholesterol and Bile Acid Metabolism in Response to Different Dietary Fats

Animal fats are considered to be unhealthy, in contrast to vegetable fats, which are rich in unsaturated fatty acids. However, the use of some fats, such as coconut oil, is still controversial. In our experiment, we divided experimental animals (domestic pigs) into three groups differing only in the type of fat used in the diet: group R: rapeseed oil (n = 5); group B: beef tallow (n = 5); group C: coconut oil (n = 6). After transcriptomic analysis of liver samples, we identified 188, 93, and 53 DEGs (differentially expressed genes) in R vs. B, R vs. C, and B vs. C comparisons, respectively. Next, we performed a functional analysis of identified DEGs with String and IPA software. We observed the enrichment of genes engaged in the unfolded protein response (UPR) and the acute phase response among genes upregulated in B compared to R. In contrast, cholesterol biosynthesis and cholesterol efflux enrichments were observed among genes downregulated in B when compared to R. Moreover, activation of the UPR and inhibition of the sirtuin signaling pathway were noted in C when compared to R. The most striking difference in liver transcriptomic response between C and B was the activation of the acute phase response and inhibition of bile acid synthesis in the latest group. Our results suggest that excessive consumption of animal fats leads to the activation of a cascade of mutually propelling processes harmful to the liver: inflammation, UPR, and imbalances in the biosynthesis of cholesterol and bile acids via altered organelle membrane composition. Nevertheless, these studies should be extended with analysis at the level of proteins and their function.

Effects of dietary n-6/n-3 polyunsaturated fatty acids ratio on growth performance, apparent digestibility, blood lipid profiles, fecal microbiota, and meat quality in finishing pigs

The effects of dietary omega-6 (n-6) to omega-3 (n-3) polyunsaturated fatty acid (PUFA) ratios on growth performance, digestibility, blood lipid profiles, fecal microbial counts, and meat quality in finishing pigs were examined by using linseed and fish oil. A total of 140 crossbred finishing pigs [(Landrace × Yorkshire) × Duroc] were used in a 10 wk trial. Pigs were blocked based on body weight (BW) and sex and randomly allotted to four dietary treatments formulated to have n-6/n-3 ratios of 5/1, 10/1, 15/1, and 17/1 (control). Throughout the experiment, BW, average daily gain, and average daily feed intake were significantly (P < 0.05) increased with a decreased ratio of n-6/n-3 PUFA. Energy digestibility and fecal Lactobacillus count showed a linear (P < 0.05) increase in week 10. The high-density lipoprotein cholesterol and blood triglyceride concentrations increased (P < 0.1) during week 10. However, low-density lipoprotein cholesterol was reduced (P < 0.05) linearly during week 5 and week 10 with a reduction in dietary n-6/n-3 ratio. This study provides a basis for future research on altering n-6/n-3 ratio by using linseed oil and refined fish oil in finishing pigs.

Suplementação com óleos ricos em ácidos graxos poli-insaturados na dieta de leitões na fase de creche: efeitos no desempenho, na resposta inflamatória, no perfil lipídico e no “status” oxidativo

RESUMO Nos sistemas de produção, os produtos naturais vêm se destacando na substituição a produtos sintéticos, dentre eles podemos ressaltar os óleos vegetais ricos em ácido graxos poli-insaturados (PUFA), que são conhecidos, popularmente, por seus efeitos benéficos. Dessa forma, o objetivo com este trabalho foi avaliar os efeitos da suplementação dos óleos de pequi (Caryocar brasiliense) e girassol (Helianthus annus) sobre parâmetros fisiológicos em leitões na fase de creche. Foram utilizados 180 leitões alojados em granja comercial, distribuídos em três grupos (n=60) conforme suplementação alimentar: óleo de pequi, óleo de girassol e controle negativo. Amostras de sangue e o peso dos animais foram obtidos nos intervalos de quatro trocas de rações da fase de creche para avaliação do desempenho, da resposta inflamatória, do perfil lipídico e do “status” oxidativo. Os parâmetros fisiológicos mensurados demonstraram que os óleos interferiram positivamente na resposta inflamatória sistêmica, por meio dos leucócitos totais e da relação neutrófilo/linfócito (P<0,05); no equilíbrio oxidante-antioxidante, por mensuração de óxido nítrico e do malondialdeído (P<0,05); e no metabolismo lipídico, com a avaliação de colesterol total e triglicérides (P<0,05). Por outro lado, esses óleos vegetais interferiram no ganho de peso e no consumo de ração (P<0,05). Assim, concluí-se que a suplementação com óleos de pequi e girassol melhora a saúde dos animais, mas tem impacto negativo no desempenho zootécnico de leitões na fase de creche.

Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness

Fat deposition is very important in pig production, and its mechanism is not clearly understood. MicroRNAs (miRNAs) play critical roles in fat deposition and energy metabolism. In the current study, we investigated the mRNA and miRNA transcriptome in the livers of Landrace pigs with extreme backfat thickness to explore miRNA-mRNA regulatory networks related to lipid deposition and metabolism. A comparative analysis of liver mRNA and miRNA transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. We identified differentially expressed genes from RNA-seq data using a Cufflinks pipeline. Seventy-one differentially expressed genes (DEGs), including twenty-eight well annotated on the porcine reference genome genes, were found. The upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (FASN), glucokinase (GCK), phosphoglycerate dehydrogenase (PHGDH), and apolipoprotein A4 (APOA4). Cytochrome P450, family 2, subfamily J, polypeptide 34 (CYP2J34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. Moreover, 13 differentially expressed miRNAs were identified. Seven miRNAs were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. Based on comprehensive analysis of the transcriptome of both mRNAs and miRNAs, an important regulatory network, in which six DEGs could be regulated by differentially expressed miRNAs, was established for fat deposition. The negative correlate in the regulatory network including, miR-545-5p and GRAMD3, miR-338 and FASN, and miR-127, miR-146b, miR-34c, miR-144 and THBS1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. Based on liver mRNA and miRNA transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed miRNAs, and established an important miRNA-mRNA regulatory network. This study provides new insights into the molecular mechanisms that determine fat deposition in pigs.

Nutrigenomics in livestock-recent advances

The study of the effects of nutrients on genome functioning, in terms of gene transcription, protein levels, and epigenetic mechanisms, is referred to as nutrigenomics. Nutrigenomic studies in farm animals, as distinct from rodents, are limited by the high cost of keeping livestock, their long generational distance, and ethical aspects. Yet farm animals, and particularly pigs, can serve as valuable animal models for human gastrological diseases, since they possess similar size, physiology, and nutritional habits and can develop similar pathological states. In livestock, the effects of dietary modifications have mostly been studied with reference to effective breeding and their influence on production traits and animal health. The majority of such studies have looked at the impact of various sources and quantities of fat and protein, supplementation with microelements, and plant-derived additives. The period of life of the animal—whether prenatal, neonatal, or mature—is typically considered when a modified diet is used. This review presents a summary of recent nutrigenomic studies in livestock.

A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals

Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.

Negative effects on newborn piglets caused by excess dietary tryptophan in the morning in sows

BACKGROUND

This study investigated the effect of dynamic feeding models of dietary tryptophan on sows' performance during late pregnancy.

RESULTS

The average piglet birth weight and live farrowing rate from sows consuming a high-low tryptophan diet (0.39% Trp in the morning and 0.13% Trp in the afternoon) were decreased compared with those fed a 2×tryptophan diet (0.26% Trp in the morning and afternoon). Compared with the 2×tryptophan group, sow serum kynurenic acid and the newborn liver n-6:n-3 polyunsaturated fatty acid ratio were significantly higher, and sow serum taurine and newborn serum taurine, phosphoserine, cysteine and proline were lower in the high-low tryptophan diet group. Eighty-eight genes were differentially expressed in newborn piglets' livers between the 2×tryptophan and high-low groups. Genes related to cytotoxic effector regulation (major histocompatibility complex class I proteins), NADH oxidation, reactive oxygen species (ROS) metabolism and tissue development were differentially expressed between these two groups.

CONCLUSION

Together, the results provide information on new biomarkers in serum or liver and provide novel insights into variations in the fetal liver during exogenous stimulus response and biological processes of ROS metabolism in fetuses during late pregnancy caused by a single excessive tryptophan ingestion daily in the morning. © 2018 Society of Chemical Industry.

Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations

Supplementing pig diets with n-3 polyunsaturated fatty acids (n-3 PUFA) may produce meat products with an increased n-3 fatty acid content, and the combined antioxidants addition could prevent lipid oxidation in the feed. However, to date, the effects of these bioactive compounds at the molecular level in porcine skeletal muscle are mostly unknown. This study aimed to analyse changes in the Longissimus thoracis transcriptome of 35 pigs fed three diets supplemented with: linseed (L); linseed, vitamin E and Selenium (LES) or linseed and plant-derived polyphenols (LPE). Pigs were reared from 80.8 ± 5.6 kg to 151.8 ± 9.9 kg. After slaughter, RNA-Seq was performed and 1182 differentially expressed genes (DEGs) were submitted to functional analysis. The L vs LES comparison did not show differences, while L vs LPE showed 1102 DEGs and LES vs LPE 80 DEGs. LPE compared to the other groups showed the highest number of up-regulated genes involved in preserving muscle metabolism and structure. Results enlighten that the combined supplementation of bioactive lipids (n-3 PUFA from linseed) with plant extracts as a source of polyphenols increases, compared to the only addition of linseed, the expression of genes involved in mRNA metabolic processes and transcriptional regulation, glucose uptake and, finally, in supporting muscle development and physiology. These results improve the knowledge of the biological effect of bioactive compounds in Longissimus thoracis muscle, and sustain the growing interest over their use in pig production.

Next-Generation Sequencing Identifies Polyunsaturated Fatty Acid Responsive Genes in the Juvenile Rat Cerebellum

Dietary n-3 polyunsaturated fatty acids (PUFA) influence postnatal brain growth and development. However, little data exist regarding the impacts of dietary n-3 PUFA in juvenile animals post weaning, which is a time of rapid growth. We tested the hypothesis that depleting dietary n-3 PUFA would result in modifications to the cerebellar transcriptome of juvenile rats. To test this hypothesis, three week old male rats (an age that roughly corresponds to an 11 month old child in brain development) were fed diets containing either soybean oil (SO) providing 1.1% energy from α-linolenic acid (ALA; 18:3n-3; ALA-sufficient) or corn oil (CO) providing 0.13% energy from ALA (ALA-deficient) for four weeks. Fatty acids (FAs) in the cerebellum were analyzed and revealed a 4-fold increase in n-6 docosapentaenoic acid (DPA; 22:5n-6), increases in arachidonic acid (AA; 20:4n-6) and docosatetraenoic acid (DTA; 22:4n-6), but no decrease in docosahexaenoic acid (DHA; 22:6n-3), in animals fed CO versus SO. Transcript abundance was then characterized to identify differentially expressed genes (DEGs) between the two diets. Upper quartile (UQ) scaling and transcripts per million (TPM) data normalization identified 100 and 107 DEGs, respectively. Comparison of DEGs from the two normalization methods identified 70 genes that overlapped, with 90% having abundance differences less than 2-fold. Nr4a3, a transcriptional activator that plays roles in neuroprotection and learning, was elevated over 2-fold from the CO diet. These data indicate that expression of Nr4a3 in the juvenile rat cerebellum is responsive to dietary n-3 PUFA, but additional studies are needed clarify the neurodevelopmental relationships between n-3 PUFA and Nr4a3 and the resulting impacts.

Effect of diets supplemented with linseed alone or combined with vitamin E and selenium or with plant extracts, on Longissimus thoracis transcriptome in growing-finishing Italian Large White pigs

Background

Supplementing farm animals diet with functional ingredients may improve the nutritional quality of meat products. Diet composition has been also demonstrated to influence the gene expression with effect on biological processes and pathways. However, the knowledge on the effect of nutrients at the molecular level is scant. In particular, studies on the effects of antioxidants and polyphenols dietary supplementation have been investigated mainly in rodents, and only scarcely in farm animals so far. RNA-Seq with next-generation sequencing is increasingly the method of choice for studying changes in the transcriptome and it has been recently employed also in pig nutrigenomics studies to identify diet-induced changes in gene expression. The present study aimed to investigate the effect of diets enriched with functional ingredients (linseed, vitamin E and plant extracts) on the transcriptome of pig Longissimus thoracis to elucidate the role of these compounds in influencing genes involved in muscle physiology and metabolism compared to a standard diet.

Results

Eight hundred ninety-three significant differentially expressed genes (DEGs) (FDR adjusted P-value ≤ 0.05) were detected by RNA-Seq analysis in the three diet comparisons (D2-D1, D3-D1, D4-D1). The functional analysis of DEGs showed that the diet enriched with n-3 PUFA from linseed (D2) mostly downregulated genes in pathways and biological processes (BPs) related to muscle development, contraction, and glycogen metabolism compared to the standard diet. The diet supplemented with linseed and vitamin E/Selenium (D3) showed to mostly downregulate genes linked to oxidative phosphorylation. Only few genes involved in extracellular matrix (ECM) organization were upregulated by the D3. Finally, the comparison D4-D1 showed that the diet supplemented with linseed and plant extracts (D4) upregulated the majority of genes compared to D1 that were involved in a complex network of pathways and BPs all connected by hub genes. In particular, IGF2 was a hub gene connecting protein metabolism, ECM organization, immune system and lipid biosynthesis pathways.

Conclusion

The supplementation of pig diet with n-3 PUFA from linseed, antioxidants and plant-derived polyphenols can influence the expression of a relevant number of genes in Longissimus thoracis muscle that are involved in a variety of biochemical pathways linked to muscle function and metabolism.

Effect of dietary polyunsaturated fatty acid and antioxidant supplementation on the transcriptional level of genes involved in lipid and energy metabolism in swine

Porcine fat traits depend mostly on the interaction between nutritional and genetic factors. However, the pathways and biological processes influenced by this interaction are still poorly known in pigs, although they can have a huge impact on meat quality traits. The present research provides new knowledge insight into the effect of four diets (D1 = standard diet; D2 = linseed supplementation; D3 = linseed, vitamin E and selenium supplementation; D4 = linseed and plant-derived polyphenols supplementation) on the expression of 24 candidate genes selected for their role in lipid and energy metabolism. The data indicated that 10 out of 24 genes were differentially expressed among diets, namely ACACA, ADIPOQ, ADIPOR1, CHREBP (MLXPL), ELOVL6, FASN, G6PD, PLIN2, RXRA and SCD. Results from the univariate analysis displayed an increased expression of ACACA, ADIPOQ, ADIPOR1, CHREBP, ELOVL6, FASN, PLIN2, RXRA and SCD in D4 compared to D2. Similarly, ACACA, ADIPOQ, ADIPOR1, ELOVL6 and SCD were highly expressed in D4 compared to D3, while no differences were observed in D2-D3 comparison. Moreover, an increased expression of G6PD and ELOVL6 genes in D4 compared to D1 was observed. Results from the multivariate analysis confirmed that D2 was not different from D3 and that ACACA, SCD and FASN expression made D4 different from D2 and D3. Comparing D4 and D1, the expression levels of ELOVL6 and ACACA were the most influenced. This research provides evidence that the addition of both n-3 PUFA and polyphenols, derived from linseed, grape-skin and oregano supplementation in the diets, stimulates the expression of genes involved in lipogenesis and in oxidative processes. Results evidenced a greater effect on gene expression of the diet added with both plant extracts and n-3 PUFA, resulting in an increased expression of genes coding for fatty acid synthesis, desaturation and elongation in pig Longissimus thoracis muscle.

Longissimus dorsi muscle transcriptomic analysis of Yunling and Chinese simmental cattle differing in intramuscular fat content and fatty acid composition

Intramuscular fat (IMF) content and fatty acid (FA) composition vary significantly across beef cattle breeds, which play an important role in taste and nutritional value. However, the molecular mechanisms underlying these phenotypic differences remain unknown. The present study compared meat quality traits between Yunling cattle and Chinese Simmental cattle. Yunling cattle showed a lower IMF content and proportion of monounsaturated fatty acids (MUFA), as well as higher proportions of saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), and short-chain fatty acids (sc-FA) in the longissimus dorsi (LD) muscle than Chinese Simmental cattle. To further identify the candidate genes and pathways responsible for these phenotypic differences, the transcriptome of LD muscle from the two breeds were measured using RNA-seq. A total of 1347 differentially expressed genes were identified. The major metabolic pathways that were differentially modulated were lipolysis and glycometabolism. Yunling cattle showed a higher expression of lipolysis genes (ALDH9A1, ACSL5, ACADM, ACAT2, ACOT2) and a lower expression of genes related to glycometabolism (PGM1, GALM, PGM1, GPI, LDHA). This research identified candidate genes and pathways for IMF content and FA composition in the LD muscle of beef cattle, which may facilitate the design of new selection strategies to improve meat quality.

RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population

Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108–44,901,729 uniquely mapped reads, which covered 74.15% of the current annotated transcripts including 18964 mRNA transcripts, across all the six thigh muscle tissue samples. Of these, we revealed 274 differentially expressed genes (DEGs) with a highly significant correlation with polyunsaturated fatty acids percentage between the comparison groups based on the ratio of PUFA/SFA. Gene ontology and pathway analysis indicated that the DEGs were enriched in particular biological processes affecting fatty acids metabolism, biosynthesis of unsaturated fatty acids (USFAs), and cell junction-related pathways. Integrated interpretation of differential gene expression and formerly reported quantitative trait loci (QTL) demonstrated that FADS2, DCN, FRZB, OGN, PRKAG3, LHFP, CHCHD10, CYTL1, FBLN5, and ADGRD1 are the most promising candidate genes affecting polyunsaturated fatty acids percentage.

A porcine gluteus medius muscle genome-wide transcriptome analysis: dietary effects of omega-6 and omega-3 fatty acids on biological mechanisms

Background

The level of omega-6 and omega-3 polyunsaturated fatty acids can affect many cellular systems and function via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate changes in the muscle transcriptome and the biological functions regulated by increased consumption of omega-3 and omega-6 fatty acids in the pig gluteus medius muscle.

Results

The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content. Next-generation sequencing (NGS) was used to generate the muscle tissue transcriptome database pointing differentially expressed genes (DEG). Comparative expression analyses identified 749 genes significantly differing at least in the twofold of change between two groups of animals fed with divergent level of omega-3 and omega-6 fatty acids. The expression of 219 genes was upregulated, and the expression of 530 genes was downregulated in the group of pigs supplemented with omega-3 and omega-6 fatty acids in relation to control group pigs. Results of RNA-seq indicated a role of fatty acid in the regulation of the expression of genes which are essential for muscle tissue development and functioning. Functional analysis revealed that the identified genes were important for a number of biological processes including inflammatory response, signaling, lipid metabolism, and homeostasis.

Conclusions

Summarizing, obtained results provide strong evidence that omega-6 and omega-3 fatty acids regulate fundamental metabolic processes in muscle tissue development and functioning.

Electronic supplementary material

The online version of this article (doi:10.1186/s12263-017-0552-8) contains supplementary material, which is available to authorized users.