Identification of Differentially Expressed miRNAs in Porcine Adipose Tissues and Evaluation of Their Effects on Feed Efficiency

Feed efficiency (FE) is a very important trait affecting the economic benefits of pig breeding enterprises. Adipose tissue can modulate a variety of processes such as feed intake, energy metabolism and systemic physiological processes. However, the mechanism by which microRNAs (miRNAs) in adipose tissues regulate FE remains largely unknown. Therefore, this study aimed to screen potential miRNAs related to FE through miRNA sequencing. The miRNA profiles in porcine adipose tissues were obtained and 14 miRNAs were identified differentially expressed in adipose tissues of pigs with extreme differences in FE, of which 9 were down-regulated and 5 were up-regulated. GO and KEGG analyses indicated that these miRNAs were significantly related to lipid metabolism and these miRNAs modulated FE by regulating lipid metabolism. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) of five randomly selected DEMs was used to verify the reliability of miRNA-seq data. Furthermore, 39 differentially expressed target genes of these DEMs were obtained, and DEMs-target mRNA interaction networks were constructed. In addition, the most significantly down-regulated miRNAs, ssc-miR-122-5p and ssc-miR-192, might be the key miRNAs for FE. Our results reveal the mechanism by which adipose miRNAs regulate feed efficiency in pigs. This study provides a theoretical basis for the further study of swine feed efficiency improvement.

Short Communication: Beta-adrenergic agonists alter oxidative phosphorylation in primary myoblasts

Beta-adrenergic agonists (β-AAs) are widely used supplements in beef and pork production to improve feed efficiency and increase lean muscle mass, yet little is known about the molecular mechanism by which β-AAs achieve this outcome. Our objective was to identify the influence of ractopamine HCl and zilpaterol HCl on mitochondrial respiratory activity in muscle satellite cells isolated from crossbred beef steers (N = 5), crossbred barrows (N = 2), Yorkshire-cross gilts (N = 3), and commercial weather lambs (N = 5). Real-time measurements of oxygen consumption rates (OCRs) were recorded using extracellular flux analyses with a Seahorse XFe24 analyzer. After basal OCR measurements were recorded, zilpaterol HCl, ractopamine HCl, or no β-AA was injected into the assay plate in three technical replicates for each cell isolate. Then, oligomycin, carbonyl cyanide-p-trifluoromethoxyphenylhydrazone, and rotenone were injected into the assay plate sequentially, each inducing a different cellular state. This allowed for the measurement of OCR at these states and for the calculation of the following measures of mitochondrial function: basal respiration, non-mitochondrial respiration, maximal respiration, proton leak, adenosine triphosphate (ATP)-linked respiration, and spare respiratory capacity. Incubation of bovine cells with either zilpaterol HCl or ractopamine HCl increased maximal respiration (P = 0.046) and spare respiratory capacity (P = 0.035) compared with non-supplemented counterparts. No difference (P > 0.05) was observed between zilpaterol HCl and ractopamine HCl for maximal respiration and spare respiratory capacity in bovine cell isolates. No measures of mitochondrial function (basal respiration, non-mitochondrial respiration, maximal respiration, proton leak, ATP-linked respiration, and spare respiratory capacity) were altered by β-AA treatment in ovine or porcine cells. These findings indicate that β-AAs in cattle may improve the efficiency of oxidative metabolism in muscle satellite cells by modifying mitochondrial respiratory activity. The lack of response by ovine and porcine cells to β-AA incubation also demonstrates differing physiological responses to β-AA across species, which helps to explain the variation in its effectiveness as a growth supplement.

Genes Involved in Feed Efficiency Identified in a Meta-Analysis of Rumen Tissue from Two Populations of Beef Steers

In cattle, the rumen is an important site for the absorption of feed by-products released by bacterial fermentation, and variation in ruminal function plays a role in cattle feed efficiency. Studies evaluating gene expression in the rumen tissue have been performed prior to this. However, validating the expression of genes identified in additional cattle populations has been challenging. The purpose of this study was to perform a meta-analysis of the ruminal transcriptome of two unrelated populations of animals to identify genes that are involved in feed efficiency across populations. RNA-seq data from animals with high and low residual feed intake (RFI) from a United States population of cattle (eight high and eight low RFI) and a Canadian population of cattle (nine high and nine low RFI) were analyzed for differences in gene expression. A total of 83 differentially expressed genes were identified. Some of these genes have been previously identified in other feed efficiency studies. These genes included ATP6AP1, BAG6, RHOG, and YPEL3. Differentially expressed genes involved in the Notch signaling pathway and in protein turnover were also identified. This study, combining two unrelated populations of cattle in a meta-analysis, produced several candidate genes for feed efficiency that may be more robust indicators of feed efficiency than those identified from single populations of animals.

Review: Implication of redox imbalance in animal health and performance at critical periods, insights from different farm species

The process of oxidative stress occurs all over the production chain of animals and food products. This review summarises insights obtained in different farm species (pigs, ruminants, poultry, and fishes) to underpin the most critical periods for the venue of oxidative stress, namely birth/hatching and weaning/start-feeding phase. Common responses between species are also unravelled in periods of high physiological demands when animals are facing dietary deficiencies in specific nutrients, suggesting that nutritional recommendations must consider the modulation of responses to oxidative stress for optimising production performance and quality of food products. These conditions concern challenges such as heat stress, social stress, and inflammation. The magnitude of the responses is partly dependent on the prior experience of the animals before the challenge, reinforcing the importance of nutrition and other management practices during early periods to promote the development of antioxidant reserves in the animal. When these practices also improved the performance and health of the animal, this further confirms the central role played by oxidative stress in physiologically and environmentally induced perturbations. Difficulties in interpreting responses to oxidative stress arise from the fact that the indicators are only partly shared between studies, and their modulations may also be challenge-specific. A consensus about the best indicators to assess pro-oxidative and antioxidant pathways is of huge demand to propose a synthetic index measurable in a non-invasive way and interpretable along the productive life of the animals.

Identification of Key Pathways Associated With Residual Feed Intake of Beef Cattle Based on Whole Blood Transcriptome Data Analyzed Using Gene Set Enrichment Analysis

We applied whole blood transcriptome analysis and gene set enrichment analysis to identify pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, whole blood samples were collected from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.

Evaluation of the Links between Lamb Feed Efficiency and Rumen and Plasma Metabolomic Data

Feed efficiency is one of the keystones that could help make animal production less costly and more environmentally friendly. Residual feed intake (RFI) is a widely used criterion to measure feed efficiency by regressing intake on the main energy sinks. We investigated rumen and plasma metabolomic data on Romane male lambs that had been genetically selected for either feed efficiency (line rfi−) or inefficiency (line rfi+). These investigations were conducted both during the growth phase under a 100% concentrate diet and later on under a mixed diet to identify differential metabolite expression and to link it to biological phenomena that could explain differences in feed efficiency. Nuclear magnetic resonance (NMR) data were analyzed using partial least squares discriminant analysis (PLS-DA), and correlations between metabolites’ relative concentrations were estimated to identify relationships between them. High levels of plasma citrate and malate were associated with genetically efficient animals, while high levels of amino acids such as L-threonine, L-serine, and L-leucine as well as beta-hydroxyisovalerate were associated with genetically inefficient animals under both diets. The two divergent lines could not be discriminated using rumen metabolites. Based on phenotypic residual feed intake (RFI), efficient and inefficient animals were discriminated using plasma metabolites determined under a 100% concentrate diet, but no discrimination was observed with plasma metabolites under a mixed diet or with rumen metabolites regardless of diet. Plasma amino acids, citrate, and malate were the most discriminant metabolites, suggesting that protein turnover and the mitochondrial production of energy could be the main phenomena that differ between efficient and inefficient Romane lambs.

Differences in Liver microRNA profiling in pigs with low and high feed efficiency

Feed cost is the main factor affecting the economic benefits of pig industry. Improving the feed efficiency (FE) can reduce the feed cost and improve the economic benefits of pig breeding enterprises. Liver is a complex metabolic organ which affects the distribution of nutrients and regulates the efficiency of energy conversion from nutrients to muscle or fat, thereby affecting feed efficiency. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate feed efficiency through the modulation of gene expression at the post-transcriptional level. In this study, we analyzed miRNA profiling of liver tissues in High-FE and Low-FE pigs for the purpose of identifying key miRNAs related to feed efficiency. A total 212~221 annotated porcine miRNAs and 136~281 novel miRNAs were identified in the pig liver. Among them, 188 annotated miRNAs were co-expressed in High-FE and Low-FE pigs. The 14 miRNAs were significantly differentially expressed (DE) in the livers of high-FE pigs and low-FE pigs, of which 5 were downregulated and 9 were upregulated. Kyoto Encyclopedia of Genes and Genomes analysis of liver DE miRNAs in high-FE pigs and low-FE pigs indicated that the target genes of DE miRNAs were significantly enriched in insulin signaling pathway, Gonadotropin-releasing hormone signaling pathway, and mammalian target of rapamycin signaling pathway. To verify the reliability of sequencing results, 5 DE miRNAs were randomly selected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR results of miRNAs were confirmed to be consistent with sequencing data. DE miRNA data indicated that liver-specific miRNAs synergistically acted with mRNAs to improve feed efficiency. The liver miRNAs expression analysis revealed the metabolic pathways by which the liver miRNAs regulate pig feed efficiency.

How much energetic trade-offs limit selection? Insights from livestock and related laboratory model species

Trade-offs between life history traits are expected to occur due to the limited amount of resources that organisms can obtain and share among biological functions, but are of least concern for selection responses in nutrient-rich or benign environments. In domestic animals, selection limits have not yet been reached despite strong selection for higher meat, milk or egg yields. Yet, negative genetic correlations between productivity traits and health or fertility traits have often been reported, supporting the view that trade-offs do occur in the context of nonlimiting resources. The importance of allocation mechanisms in limiting genetic changes can thus be questioned when animals are mostly constrained by their time to acquire and process energy rather than by feed availability. Selection for high productivity traits early in life should promote a fast metabolism with less energy allocated to self-maintenance (contributing to soma preservation and repair). Consequently, the capacity to breed shortly after an intensive period of production or to remain healthy should be compromised. We assessed those predictions in mammalian and avian livestock and related laboratory model species. First, we surveyed studies that compared energy allocation to maintenance between breeds or lines of contrasting productivity but found little support for the occurrence of an energy allocation trade-off. Second, selection experiments for lower feed intake per unit of product (i.e. higher feed efficiency) generally resulted in reduced allocation to maintenance, but this did not entail fitness costs in terms of survival or future reproduction. These findings indicate that the consequences of a particular selection in domestic animals are much more difficult to predict than one could anticipate from the energy allocation framework alone. Future developments to predict the contribution of time constraints and trade-offs to selection limits will be insightful to breed livestock in increasingly challenging environments.

Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = -0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

Proteomic Analysis of Liver from Finishing Beef Cattle Supplemented with a Rumen-Protected B-Vitamin Blend and Hydroxy Trace Minerals

Simple Summary

Greater metabolic needs in high-producing beef cattle might lead to mineral and vitamin deficiency. Previous studies have shown the benefits of B-vitamin and trace mineral supplementation in animal performance of ruminants; however, little is known about the effects of supplementing finishing beef cattle with rumen-protected forms on the liver metabolism. Therefore, the aim of the present study was to determinate the impact of rumen-protected B-vitamin blend and hydroxy trace mineral supplementation on the hepatic proteome of finishing steers. This study reports the first evidence indicating that the supplementation of these micronutrients induces protein changes concerning oxidative metabolism and responses to oxidative stress in the liver tissue.

Abstract

Vitamin B and trace minerals are crucial molecular signals involved in many biological pathways; however, their bioavailability is compromised in high-producing ruminant animals. So far, studies have mainly focused on the effects of these micronutrients on animal performance, but their use in a rumen-protected form and their impact on liver metabolism in finishing beef cattle is poorly known. We used a shotgun proteomic approach combined with biological network analyses to assess the effects of a rumen-protected B-vitamin blend, as well as those of hydroxy trace minerals, on the hepatic proteome. A total of 20 non-castrated Nellore males with 353 ± 43 kg of initial body weight were randomly assigned to one of the following treatments: CTRL—inorganic trace minerals without supplementation of a protected vitamin B blend, or SUP—supplementation of hydroxy trace minerals and a protected vitamin B blend. All animals were fed the same amount of the experimental diet for 106 days, and liver biopsies were performed at the end of the experimental period. Supplemented animals showed 37 up-regulated proteins (p < 0.10), and the enrichment analysis revealed that these proteins were involved in protein folding (p = 0.04), mitochondrial respiratory chain complex I (p = 0.01) and IV (p = 0.01), chaperonin-containing T-complex 2 (p = 0.01), glutathione metabolism (p < 0.01), and other aspects linked to oxidative-stress responses. These results indicate that rumen-protected vitamin B and hydroxy trace mineral supplementation during the finishing phase alters the abundance of proteins associated with the electron transport chain and other oxidation–reduction pathways, boosting the production of reactive oxygen species, which appear to modulate proteins linked to oxidative-damage responses to maintain cellular homeostasis.

Novel Observations of Peroxiredoxin-2 Profile and Protein Oxidation in Skeletal Muscle From Pigs of Differing Residual Feed Intake and Health Status

This study’s objective was to determine the impact of a dual respiratory and enteric bacterial health challenge on the antioxidant protein peroxiredoxin-2 (Prdx-2) profile and protein oxidation in the skeletal muscle of pigs from 2 lines that were divergently selected for residual feed intake (RFI). The hypotheses were that (1) differences exist in the Prdx-2 profile between 2 RFI lines and infection status and (2) muscle from less efficient high-RFI and health-challenged pigs have greater cellular protein oxidation. Barrows (50 ± 7 kg, N = 24) from the 11th generation of the high-RFI (n = 12) and low-RFI (n = 12) Iowa State University lines were used. Pigs (n = 6 per line) were inoculated with Mycoplasma hyopneumoniae and Lawsonia intracellularis (MhLI) on day 0 post infection to induce a respiratory and enteric health challenge. Uninoculated pigs served as controls (n = 6 per line). Necropsy was at 21 d post infection. Sarcoplasmic protein oxidation, various forms of Prdx-2, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) content were determined. Neither RFI line nor infection status significantly affected protein carbonylation. Under nonreducing conditions, MhLI pigs had a greater amount of a slower-migrating GAPDH band (P = 0.017), indicating oxidative modification. Regardless of health status, the low-RFI pigs had less total Prdx-2 (P = 0.035), Prdx-2 decamer (P = 0.0007), and a higher ratio of hyperoxidized peroxiredoxin relative to Prdx-2 (P = 0.028) than the high-RFI pigs. The increased pool of active Prdx-2 in high-RFI pigs suggests greater oxidative stress in muscle in high- versus low-RFI pigs. The increase in oxidized GAPDH seen in muscle from MhLI pigs—particularly the high-RFI MhLI pigs—may be a response to the greater oxidative stress in the high-RFI MhLI. This work suggests that antioxidant proteins are important in growth and health-challenge situations.

Lawsonia intracellularis infected enterocytes lack sucrase-isomaltase which contributes to reduced pig digestive capacity

Lawsonia intracellularis is endemic to swine herds worldwide, however much is still unknown regarding its impact on intestinal function. Thus, this study aimed to characterize the impact of L. intracellularis on digestive function, and how vaccination mitigates these impacts. Thirty-six L. intracellularis negative barrows were assigned to treatment groups (n  =  12/trt): (1) nonvaccinated, L. intracellularis negative (NC); (2) nonvaccinated, L intracellularis challenged (PC); and (3) L. intracellularis challenged, vaccinated (Enterisol^® Ileitis, Boehringer Ingelheim) 7 weeks pre-challenge (VAC). On days post-inoculation (dpi) 0 PC and VAC pigs were inoculated with L. intracellularis. From dpi 19–21 fecal samples were collected for apparent total tract digestibility (ATTD) and at dpi 21, pigs were euthanized for sample collection. Post-inoculation, ADG was reduced in PC pigs compared with NC (41%, P  <  0.001) and VAC (25%, P  <  0.001) pigs. Ileal gross lesion severity was greater in PC pigs compared with NC (P  =  0.003) and VAC (P  =  0.018) pigs. Dry matter, organic matter, nitrogen, and energy ATTD were reduced in PC pigs compared with NC pigs (P  ≤  0.001 for all). RNAscope in situ hybridization revealed abolition of sucrase-isomaltase transcript in the ileum of PC pigs compared with NC and VAC pigs (P  <  0.01). Conversely, abundance of stem cell signaling markers Wnt3, Hes1, and p27^Kip1 were increased in PC pigs compared with NC pigs (P  ≤  0.085). Taken together, these data demonstrate that reduced digestibility during L. intracellularis challenge is partially driven by abolition of digestive machinery in lesioned tissue. Further, vaccination mitigated several of these effects, likely from lower bacterial burden and reduced disease severity.

Genetic relationship between purebred and synthetic pigs for growth performance using single step method

Objective

The objective of this study was to estimate the genetic correlation (r_pc) of growth performance between purebred (Duroc and Korean native) and synthetic (WooriHeukDon) pigs using a single-step method.

Methods

Phenotypes of 15,902 pigs with genotyped data from 1,792 pigs from a nucleus farm were used for this study. We estimated the r_pc of several performance traits between WooriHeukDon and purebred pigs: day of target weight (DAY), backfat thickness (BF), feed conversion rate (FCR), and residual feed intake (RFI). The variances and covariances of the studied traits were estimated by an animal multi-trait model that applied the Bayesian inference.

Results

r_pc within traits was lower than 0.1 for DAY and BF, but high for FCR and RFI; in particular, r_pc for RFI between Duroc and WooriHeukDon pigs was nearly 1. Comparison between different traits revealed that RFI in Duroc pigs was associated with different traits in WooriHeukDon pigs. However, the most of r_pc between different traits were estimated with low or with high standard deviation.

Conclusion

The results indicated that there were substantial differences in r_pc of traits in the synthetic WooriHeukDon pigs, which could be caused by these pigs having a more complex origin than other crossbred pigs. RFI was strongly correlated between Duroc and WooriHeukDon pigs, and these breeds might have similar single nucleotide polymorphism effects that control RFI. RFI is more essential for metabolism than other growth traits and these metabolic characteristics in purebred pigs, such as nutrient utilization, could significantly affect those in synthetic pigs. The findings of this study can be used to elucidate the genetic architecture of crossbred pigs and help develop new breeds with target traits.

Brachyspira hyodysenteriae Infection Reduces Digestive Function but Not Intestinal Integrity in Growing Pigs While Disease Onset Can Be Mitigated by Reducing Insoluble Fiber

Swine dysentery (SD) induced by Brachyspira hyodysenteriae manifests as mucohemorrhagic diarrhea in pigs, but little is known about the changes that occur to the gastrointestinal tract during this disease. It is thought that dietary fibers alter disease pathogenesis, although the mechanisms of action are unclear. Thus, the objectives of this study were to characterize intestinal integrity, metabolism, and function in pigs during SD and determine if replacing insoluble fiber with fermentable fibers mitigates disease. Thirty-six B. hyodysenteriae-negative gilts [24.3 ± 3.6 kg body weight (BW)] were assigned to one of three treatment groups: (1) B. hyodysenteriae negative, control diet (NC); (2) B. hyodysenteriae challenged, control diet (PC); and (3) B. hyodysenteriae challenged, highly fermentable fiber diet (RS). The NC and PC pigs were fed the same control diet, containing 20% corn distillers dried grains with solubles (DDGS). The RS pigs were fed a diet formulated with 5% sugar beet pulp and 5% resistant potato starch. On days post inoculation (dpi) 0 and 1, pigs were inoculated with B. hyodysenteriae or sham. Pigs were euthanized for sample collection after onset of SD. The challenge had high morbidity, with 100% of PC and 75% of RS pigs developing clinical SD. The timing of onset of clinical SD differed due to treatment, with RS pigs having a delayed onset (dpi 9) of clinical SD compared with dpi 7 for PC pigs. Colon transepithelial resistance was increased and macromolecule permeability was reduced in PC pigs compared with NC pigs (P < 0.01). Minimal changes in ileal permeability, mitochondrial function, or volatile fatty acids (VFAs) were observed. Total VFA concentrations were lower in the colon and cecum in both PC and RS pigs compared to NC pigs (both P < 0.05), but iso-acids were higher (both P < 0.05). Total tract digestibility of dry matter (DM), organic matter (OM), nitrogen (N), and gross energy (GE) was lower in PC pigs compared with both NC and RS pigs (both P < 0.001). These data indicate that SD reduces digestive function but does not reduce ex vivo intestinal integrity. Further, replacement of insoluble fiber with highly fermentable fibers mitigated and delayed the onset of SD.

Piceatannol Ameliorates Hepatic Oxidative Damage and Mitochondrial Dysfunction of Weaned Piglets Challenged with Diquat

Simple Summary

In our experiment, piglets in two challenged groups were orally administrated either piceatannol or another vehicle solution, and then injected with diquat, a bipyridyl herbicide that can cause a large amount of reactive oxygen species in animal bodies and is widely used to cause oxidative stress, to investigate the effects of piceatannol on hepatic redox status, mitochondrial function and the underlying mechanism. A control group was given neither piceatannol supplementation nor diquat injection. Results showed that piceatannol could improve hepatic redox status, preserve mitochondrial function, and prevent excessive apoptosis of liver cells. In addition, piceatannol might exert its protective effects through a classic antioxidant signaling pathway named Nrf2. Our findings indicated that piceatannol might be an appropriate candidate for further development as an antioxidant food supplement to minimize the risk of oxidative stress in young animals.

Abstract

The liver is an organ that produces large amounts of reactive oxygen species (ROS). Human infants or piglets are prone to oxidative damage due to their uncompleted development of the antioxidant system, causing liver disease. Piceatannol (PIC) has been found to have significant antioxidant effects. The aim of this experiment was to investigate the effects of PIC on the liver in piglets experiencing oxidative stress caused by diquat (DQ). After weaning, 54 male piglets (Duroc × [Landrace × Yorkshire]) were selected and randomly divided into three treatment groups: the CON group, the DQ-CON group, and the DQ-PIC group. The two challenged groups were injected with DQ and then orally administrated either PIC or another vehicle solution, while the control group was given sterile saline injections and an orally administrated vehicle solution. Compared to the results of the CON group, DQ increased the percentage of apoptosis cells in the liver, also decreased the amount of reduced glutathione (GSH) and increased the concentration of malondialdehyde (MDA). In addition, the adenosine triphosphate (ATP) production, activities of mitochondrial complex I, II, III, and V, and the protein expression level of sirtuin 1 (SIRT1) were inhibited by DQ. Furthermore, PIC supplementation inhibited the apoptosis of hepatic cells caused by DQ. PIC also decreased MDA levels and increased the amount of GSH. Piglets given PIC supplementation exhibited increased activities of mitochondrial complex I, II, III, and V, the protein expression level of SIRT1, and the ATP production in the liver. In conclusion, PIC affected the liver of piglets by improving redox status, preserving mitochondrial function, and preventing excessive apoptosis.

Impact of Up- and Downregulation of Metabolites and Mitochondrial Content on pH and Color of the Longissimus Muscle from Normal-pH and Dark-Cutting Beef

Limited knowledge is currently available on the biochemical basis for the development of dark-cutting beef. The objective of this research was to determine the metabolite profile and mitochondrial content differences between normal-pH and dark-cutting beef. A gas chromatography-mass spectrometer-based nontargeted metabolomic approach indicated downregulation of glycolytic metabolites, including glucose-1- and 6-phosphate and upregulation of tricarboxylic substrates such as malic and fumaric acids occurred in dark-cutting beef when compared to normal-pH beef. Neurotransmitters such as 4-aminobutyric acid and succinate semialdehyde were upregulated in dark-cutting beef than normal-pH beef. Immunohistochemistry indicated a more oxidative fiber type in dark-cutting beef than normal-pH beef. In support, the mitochondrial protein and DNA content were greater in dark-cutting beef. This increased mitochondrial content, in part, could influence oxygen consumption and myoglobin oxygenation/appearance of dark-cutting beef. The current results demonstrate that the more tricarboxylic metabolites and mitochondrial content in dark-cutting beef impact muscle pH and color.

Integrative Analysis of Metabolomic and Transcriptomic Profiles Uncovers Biological Pathways of Feed Efficiency in Pigs

Feed efficiency (FE) is an economically important trait. Thus, reliable predictors would help to reduce the production cost and provide sustainability to the pig industry. We carried out metabolome-transcriptome integration analysis on 40 purebred Duroc and Landrace uncastrated male pigs to identify potential gene-metabolite interactions and explore the molecular mechanisms underlying FE. To this end, we applied untargeted metabolomics and RNA-seq approaches to the same animals. After data quality control, we used a linear model approach to integrate the data and find significant differently correlated gene-metabolite pairs separately for the breeds (Duroc and Landrace) and FE groups (low and high FE) followed by a pathway over-representation analysis. We identified 21 and 12 significant gene-metabolite pairs for each group. The valine-leucine-isoleucine biosynthesis/degradation and arginine-proline metabolism pathways were associated with unique metabolites. The unique genes obtained from significant metabolite-gene pairs were associated with sphingolipid catabolism, multicellular organismal process, cGMP, and purine metabolic processes. While some of the genes and metabolites identified were known for their association with FE, others are novel and provide new avenues for further research. Further validation of genes, metabolites, and gene-metabolite interactions in larger cohorts will elucidate the regulatory mechanisms and pathways underlying FE.

Effect of a dual enteric and respiratory pathogen challenge on swine growth, efficiency, carcass composition, and pork quality1

The objective of this study was to determine the influence of a dual respiratory and enteric pathogen challenge on growth performance, carcass composition, and pork quality of high and low feed efficient pigs. Pigs divergently selected for low and high residual feed intake (RFI, ~68 kg) from the 11th generation of Iowa State University RFI project were used to represent high and low feed efficiency. To elicit a dual pathogen challenge, half of the pigs (n = 12/line) were inoculated with Mycoplasma hyopneumoniae (Mh) and Lawsonia intracellularis (MhLI) on days post-inoculation (dpi) 0. Pigs in a separate room of the barn were not inoculated and used as controls (n = 12/RFI line). Pigs were weighed and feed intake was recorded to calculate ADG, ADFI, and G:F for the acclimation period (period 1: dpi -21 to 0), during peak infection (period 2: dpi 0 to 42), and during the remaining growth period to reach market weight (period 3: dpi 42 to harvest). At ~125 kg, pigs were harvested using standard commercial procedures. Carcasses were evaluated for composition (weight, fat free lean, loin eye area, 10th rib fat depth) and meat quality (pH decline, temperature decline, Hunter L, a, and b, subjective color and marbling, star probe, drip loss, cook loss, proximate composition, and desmin degradation). Challenged pigs had lesser ADFI than controls during period 2 (P < 0.05), but had greater ADG and G:F during period 3 (P < 0.05). Selection for feed efficiency did not result in a differential response to MhLI (P > 0.05). Loin chops from the less feed efficient, high RFI pigs, had greater drip loss, greater cook loss, lesser moisture content, greater Hunter L values, and greater Hunter b values (P < 0.05) than loin chops from low RFI pigs. Infection status did not significantly affect carcass composition or pork quality traits (P > 0.05). These results indicate that a MhLI challenge early in growth did not significantly affect ultimate carcass composition or meat quality traits. Selection for greater feed efficiency in pigs did not affect their response to pathogenic challenge.

Dietary pomegranate peel improves milk quality of lactating ewes: Emphasis on milk fat globule membrane properties and antioxidative traits

Concentrated pomegranate peel extract (CPE) was supplemented to ewes, and milk yield and fat content-fatty acid (FA) and phospholipid (PL) composition-were monitored. CPE-fed ewes had higher milk yield, and fat, protein and lactose contents than controls. Milk PL content-20% higher in the CPE-supplemented group-was regulated by treatment and not by total fat content; milk phosphatidylethanolamine and phosphatidylcholine increased by 22 and 26%, respectively, in CPE-supplemented vs. control ewes. Milk saturated FA concentration was higher, and total polyunsaturated and monounsaturated FA content lower in the CPE vs. control group, regardless of milk total fat content. CPE supplementation increased milk antioxidant capacity, suggesting antioxidant transfer from dietary source to milk, increasing stability and nutritive value. Our study provides first evidence for milk quality improvement in terms of antioxidants and PL enrichment without compromising total milk fat, suggesting strategies to improve dairy animals' milk composition without compromising total production.

Tissue-specific responses of antioxidant pathways to poor hygiene conditions in growing pigs divergently selected for feed efficiency

BACKGROUND

Poor hygiene of housing induces a systemic inflammatory response. Because inflammation and oxidative stress are processes that can sustain each other, the ways pigs are able to activate their antioxidant defenses are critical for production performance and health during periods when the immune system is solicited. Selection for production performance can also influence reactive oxygen species (ROS) production and expression levels of genes involved in cellular response to oxidative stress in different tissues. To establish the extent by which poor hygiene and selection for feed efficiency affected redox status, pigs divergently selected for residual feed intake (RFI) were housed in poor or good hygiene during 6 weeks. At the end, blood was collected in all pigs, and half of them were killed for tissue sampling. The remaining pigs were reared in good hygiene conditions during a recovery period of 7-8 weeks.

RESULTS

At week 6, poor hygiene was associated with a lower total antioxidant capacity assessed by plasma ferric reducing ability in all pigs, and with greater plasma levels of hydrogen peroxides in the high RFI pigs (less efficient). Adipose tissue of high RFI pigs exhibited higher activities of catalase and glutathione reductase, and greater thiobarbituric acid reactive substances (TBARS) concentrations when compared with the low RFI pigs (more efficient). Poor hygiene conditions activated the antioxidant enzymes activities (glutathione reductase, superoxide dismutase and catalase) in adipose tissue of both lines, but led to higher ROS production by mature adipocytes isolated from the high RFI pigs only. In liver and muscle, there were only minor changes in antioxidant molecules due to genetics and hygiene conditions. After the resilience period, adipose tissue of pigs previously challenged by poor hygiene maintained higher antioxidant enzyme activities, and for the high RFI line, displayed higher TBARS concentrations.

CONCLUSIONS

Pigs selected for improved feed efficiency showed a lower susceptibility to oxidative stress induced by poor hygiene conditions. This could led to a lower inflammatory response and less impaired growth when these pigs are facing sanitary challenges during the production period.

Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs

BACKGROUND

Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, and potential predictors of FE in a Duroc pig population.

RESULTS

We applied an association weight matrix (AWM) approach to analyse the results from genome-wide association studies (GWAS) for nine FE associated and production traits using 31K SNPs by defining residual feed intake (RFI) as the target phenotype. The resulting co-association network was formed by 829 SNPs. Additive effects of this SNP panel explained 61% of the phenotypic variance of RFI, and the resulting phenotype prediction accuracy estimated by cross-validation was 0.65 (vs. 0.20 using pedigree-based best linear unbiased prediction and 0.12 using the 31K SNPs). Sixty-eight transcription factor (TF) genes were identified in the co-association network; based on the lossless approach, the putative main regulators were COPS5, GTF2H5, RUNX1, HDAC4, ESR1, USP16, SMARCA2 and GTF2F2. Furthermore, gene expression data of the gluteus medius muscle was explored through differential expression and multivariate analyses. A list of candidate genes showing functional and/or structural associations with FE was elaborated based on results from both AWM and gene expression analyses, and included the aforementioned TF genes and other ones that have key roles in metabolism, e.g. ESRRG, RXRG, PPARGC1A, TCF7L2, LHX4, MAML2, NFATC3, NFKBIZ, TCEA1, CDCA7L, LZTFL1 or CBFB. The most enriched biological pathways in this list were associated with behaviour, immunity, nervous system, and neurotransmitters, including melatonin, glutamate receptor, and gustation pathways. Finally, an expression GWAS allowed identifying 269 SNPs associated with the candidate genes' expression (eSNPs). Addition of these eSNPs to the AWM panel of 829 SNPs did not improve the accuracy of genomic predictions.

CONCLUSIONS

Candidate genes that have a direct or indirect effect on FE-related traits belong to various biological processes that are mainly related to immunity, behaviour, energy metabolism, and the nervous system. The pituitary gland, hypothalamus and thyroid axis, and estrogen signalling play fundamental roles in the regulation of FE in pigs. The 829 selected SNPs explained 61% of the phenotypic variance of RFI, which constitutes a promising perspective for applying genetic selection on FE relying on molecular-based prediction.

Impact of porcine reproductive and respiratory syndrome virus on muscle metabolism of growing pigs1

Porcine reproductive and respiratory syndrome (PRRS) virus is one of the most economically significant pig pathogens worldwide. However, the metabolic explanation for reductions in tissue accretion observed in growing pigs remains poorly defined. Additionally, PRRS virus challenge is often accompanied by reduced feed intake, making it difficult to discern which effects are virus vs. feed intake driven. To account for this, a pair-fed model was employed to examine the effects of PRRS challenge and nutrient restriction on skeletal muscle and liver metabolism. Forty-eight pigs were randomly selected (13.1 ± 1.97 kg BW) and allotted to 1 of 3 treatments (n = 16 pigs/treatment): 1) PRRS naïve, ad libitum fed (Ad), 2) PRRS-inoculated, ad libitum fed (PRRS+), and 3) PRRS naïve, pair-fed to the PRRS-inoculated pigs' daily feed intake (PF). At days postinoculation (dpi) 10 and 17, 8 pigs per treatment were euthanized and tissues collected. Tissues were assayed for markers of proteolysis (LM only), protein synthesis (LM only), oxidative stress (LM only), gluconeogenesis (liver), and glycogen concentrations (LM and liver). Growth performance, feed intake, and feed efficiency were all reduced in both PRRS+ and PF pigs compared with Ad pigs (P < 0.001). Furthermore, growth performance and feed efficiency were additionally reduced in PRRS+ pigs compared with PF pigs (P < 0.05). Activity of most markers of LM proteolysis (μ-calpain, 20S proteasome, and caspase 3/7) was not increased (P > 0.10) in PRRS+ pigs compared with Ad pigs, although activity of m-calpain was increased in PRRS+ pigs compared with Ad pigs (P = 0.025) at dpi 17. Muscle reactive oxygen species production was not increased (P > 0.10) in PRRS+ pigs compared with Ad pigs. However, phosphorylation of protein synthesis markers was decreased in PRRS+ pigs compared with both Ad (P < 0.05) and PF (P < 0.05) pigs. Liver gluconeogenesis was not increased as a result of PRRS; however, liver glycogen was decreased (P < 0.01) in PRRS+ pigs compared with Ad and PF pigs at both time points. Taken together, this work demonstrates the differential impact a viral challenge and nutrient restriction have on metabolism of growing pigs. Although markers of skeletal muscle proteolysis showed limited evidence of increase, markers of skeletal muscle synthesis were reduced during PRRS viral challenge. Furthermore, liver glycogenolysis seems to provide PRRS+ pigs with glucose needed to fuel the immune response during viral challenge.

Responsiveness of swine divergently selected for feed efficiency to exogenous adrenocorticotropic hormone and glucose challenges

Increasing the feed efficiency of lean tissue gains is an important goal for improving sustainable pork production and profitability for swine producers. To study feed efficiency, genetic selection based on residual feed intake (RFI) was used to create two divergent lines. Low-RFI pigs consume less feed for equal weight gain compared with their less-efficient, high-RFI counterparts. As cortisol and insulin are important energy control and growth regulators, our objective was to evaluate the role of the adrenocorticotropic hormone (ACTH)-cortisol and the glucose-insulin axes in pigs divergently selected for RFI. Adrenocorticotropic hormone (0.2 IU/kg BW)-stimulated cortisol and non-esterified fatty acids (NEFA) concentrations and intravenous glucose tolerance test (IVGTT; 0.25 g/kg BW)-stimulated glucose, insulin, and NEFA concentrations were assessed in six low-RFI and six high-RFI gilts (68 ± 5.2 kg). Before the ACTH challenge, low-RFI gilts tended to have less baseline plasma cortisol (P = 0.08) but no difference in NEFA concentrations (P = 0.63) compared with high-RFI gilts. After the ACTH challenge, low-RFI gilts had less cortisol (P = 0.04) and NEFA concentrations (P = 0.05) compared with high-RFI gilts. Glucose, insulin, and NEFA concentrations did not differ between genetic lines before the IVGTT. After glucose infusion, low-RFI gilts had greater insulin concentrations (P = 0.003) but did not differ in glucose or NEFA concentrations compared with high-RFI gilts. These results indicate that genetic selection for reduced RFI (improved feed efficiency) resulted in less stress responsiveness and an increase in insulin after glucose infusion. These data have implications for identifying and selecting more feed efficient pigs and for understanding the physiological mechanisms underlying feed efficiency.

Correlations between mitochondrial respiration activity and residual feed intake after divergent genetic selection for high- and low- oxygen consumption in mice

The aims of the present study were to identify the differences between two mouse lines (high (H)- and low (L)-oxygen consumption) in terms of mitochondrial respiratory activity when GMP (glutamate, malate, and pyruvate) and succinic acid are used as substrates and to examine the relationship between mitochondrial respiration activity and feed efficiency in both lines. The average daily feed intake, feed conversion ratio (FCR), and residual feed intake (RFI) were significantly higher in the H than the L line. The correlation between FCR and RFI was significant (r = 0.60, p < 0.05). RFI was effective as an indicator of feed efficiency. When succinic acid was used as a substrate, mitochondrial respiration states 2-4, ACR, and proton leak were significantly higher in the H than the L line. When GMP was used as a substrate, respiration states 3 and 4 in the H line were significantly higher than those in the L line, and there were significant positive correlations between FCR and RFI and mitochondrial respiration states 2-4. The results indicated that selection for high or low OC changed the basal metabolic rates estimated from liver mitochondrial respiration activity and feed efficiency.

Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle

Improving nutrient utilization efficiency is essential for livestock, given the current scenario of increasing demand for animal protein and sustainable resource use. In this context, understanding the biology of feed efficiency (FE) in beef cattle allows the development of markers for identification and selection of best animals for animal production. Thus, 98 young Nellore bulls were evaluated for FE and at the end of the experiment liver samples from six High Feed Efficient (HFE) and six Low Feed Efficient (LFE) animals were collected for protein extraction, digestion and analysis by HPLC-MS/MS. Data were analyzed for differential abundant proteins (DAPs), protein networks, and functional enrichment. Serum endotoxin was also quantified. We found 42 DAPs and 3 protein networks significantly related to FE. The main pathways associated with FE were: microbial metabolism; biosynthesis of fatty acids, amino acids and vitamins; glycolysis/gluconeogenesis; xenobiotic metabolism and; antigen processing and presentation. Serum endotoxins were significantly higher in LFE animals supporting the results. Therefore, the findings presented here confirmed the altered hepatic metabolism and pronounced hepatic inflammation in LFE animals supporting that the increased bacterial load is at least in part responsible for the hepatic lesions and inflammation in LFE animals.

Machine learning applied to transcriptomic data to identify genes associated with feed efficiency in pigs

BACKGROUND

To date, the molecular mechanisms that underlie residual feed intake (RFI) in pigs are unknown. Results from different genome-wide association studies and gene expression analyses are not always consistent. The aim of this research was to use machine learning to identify genes associated with feed efficiency (FE) using transcriptomic (RNA-Seq) data from pigs that are phenotypically extreme for RFI.

METHODS

RFI was computed by considering within-sex regression on mean metabolic body weight, average daily gain, and average backfat gain. RNA-Seq analyses were performed on liver and duodenum tissue from 32 high and 33 low RFI pigs collected at 153 d of age. Machine-learning algorithms were used to predict RFI class based on gene expression levels in liver and duodenum after adjusting for batch effects. Genes were ranked according to their contribution to the classification using the permutation accuracy importance score in an unbiased random forest (RF) algorithm based on conditional inference. Support vector machine, RF, elastic net (ENET) and nearest shrunken centroid algorithms were tested using different subsets of the top rank genes. Nested resampling for hyperparameter tuning was implemented with tenfold cross-validation in the outer and inner loops.

RESULTS

The best classification was obtained with ENET using the expression of 200 genes in liver [area under the receiver operating characteristic curve (AUROC): 0.85; accuracy: 0.78] and 100 genes in duodenum (AUROC: 0.76; accuracy: 0.69). Canonical pathways and candidate genes that were previously reported as associated with FE in several species were identified. The most remarkable pathways and genes identified were NRF2-mediated oxidative stress response and aldosterone signalling in epithelial cells, the DNAJC6, DNAJC1, MAPK8, PRKD3 genes in duodenum, and melatonin degradation II, PPARα/RXRα activation, and GPCR-mediated nutrient sensing in enteroendocrine cells and SMOX, IL4I1, PRKAR2B, CLOCK and CCK genes in liver.

CONCLUSIONS

ML algorithms and RNA-Seq expression data were found to provide good performance for classifying pigs into high or low RFI groups. Classification was better with gene expression data from liver than from duodenum. Genes associated with FE in liver and duodenum tissue that can be used as predictive biomarkers for this trait were identified.

Diquat-induced oxidative stress increases intestinal permeability, impairs mitochondrial function, and triggers mitophagy in piglets

In the present study, we investigated the influence of diquat-induced oxidative stress on intestinal barrier, mitochondrial function, and the level of mitophagy in piglets. Twelve male Duroc × Landrace × Yorkshire 35-d-old pigs (weaned at 21 d of age), with an average body of 9.6 kg, were allotted to two treatments of six piglets each including the challenged group and the control group. The challenged pigs were injected with 100 mg/kg bodyweight diquat and control pigs injected with 0.9% (w/v) NaCl solution. The results showed that diquat injection decreased ADFI and ADG. Diquat decreased (P < 0.05) the activities of superoxide dismutase and glutathione peroxidase and increased (P < 0.05) the malondialdehyde concentrations. The lower (P < 0.05) transepithelial electrical resistance and higher (P < 0.05) paracellular permeability of fluorescein isothiocyanatedextran 4 kDa were found in diquat challenged piglets. Meanwhile, diquat decreased (P < 0.05) the protein abundance of claudin-1, occluding, and zonula occludens-1 in jejunum compared with the control group. Diquat-induced mitochondrial dysfunction, as demonstrated by increased (P < 0.05) reactive oxygen species production and decreased (P < 0.05) membrane potential of intestinal mitochondria. Diquat-injected pigs revealed a decrease (P < 0.05) of mRNA abundance of genes related to mitochondrial biogenesis and functions, PPARg coactivator-1α, mammalian-silencing information regulator-1, nuclear respiratory factor-1, mt transcription factor A, mt single-strand DNA-binding protein, mt polymerase r, glucokinase, citrate synthase, ATP synthase, and cytochrome coxidase subunit I and V in the jejunum. Diquat induced an increase (P < 0.05) in expression of mitophagy-related proteins, phosphatase and tensin homologue deleted on chromosome 10-induced putative kinase, and Parkin in the intestinal mitochondria, as well as an enhancement of the ratio of light chain 3-II (LC3-II) to LC3-I content in the jejunal mucosa. These results suggest that oxidative stress disrupted the intestinal barrier, caused mitochondrial dysfunction, and triggered mitophagy.

Role of AMPK signalling pathway during compensatory growth in pigs

Background

The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during compensatory growth following a feed restriction period. A RNA-Seq experiment was performed with a total of 24 females belonging to a Duroc commercial line. Half of the animals received either a restricted (RE) or ad libitum (AL) diet during the first fattening period (60–125 d of age). After that, all gilts were fed ad libitum for a further ~30 d until the age of ~155 d, when animals were slaughtered and samples of gluteus medius muscle were harvested to perform RNA-Seq analyses and intramuscular fat content determination.

Results

During the period following food restriction, RE animals re-fed ad libitum displayed compensatory growth, showed better feed conversion rate and tended to deposit more subcutaneous fat than AL fed animals. Animals were slaughtered in the phase of accelerated growth, when RE animals had not completely compensated the performance of AL group, showing lower live and carcass weights. At intramuscular level, RE gilts showed a higher content of polyunsaturated fatty acids during the compensatory growth phase. The comparison of RE and AL expression profiles allowed the identification of 86 (ǀlog₂Fold-Changeǀ > 1, p_adj < 0.05) differentially expressed (DE) genes. A functional categorization of these DE genes identified AMPK Signaling as the most significantly enriched canonical pathway. This kinase plays a key role in the maintenance of energy homeostasis as well as in the activation of autophagy. Among the DE genes identified as components of AMPK Signaling pathway, five out of six genes were downregulated in RE pigs.

Conclusions

Animals re-fed after a restriction period exhibited a less oxidative metabolic profile and catabolic processes in muscle than animals fed ad libitum. The downregulation of autophagy observed in the skeletal muscle of pigs undergoing compensatory growth may constitute a mechanism to increase muscle mass thus ensuring an accelerated growth rate. These results reveal that the downregulation of AMPK Signaling plays an important role in compensatory growth in pigs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5071-5) contains supplementary material, which is available to authorized users.

Metabolic adaptation of pigs to a Mycoplasma hyopneumoniae and Lawsonia intracellularis dual challenge

Respiratory and enteric pathogens such as Mycoplasma hyopneumoniae (Mh) and Lawsonia intracellularis (LI) reduce lean accretion and feed efficiency (FE) in growing pigs. However, the metabolic mechanism by which this occurs is still unknown. Therefore, the primary aim of this study was to examine the metabolic adaptation of pigs presented with a dual Mh and LI challenge (MhLI). A secondary objective was to examine if selection for high FE, modeled by selection for low residual feed intake (RFI), alters molecular response to disease. Using a 2 × 2 factorial design, 6 littermate pairs from a high RFI (HRFI) and 6 littermate pairs from a low RFI (LRFI) line (barrows, 66 ± 2 kg BW) were selected, with 1 pig from each pair assigned to individual pens in either the challenge or the nonchallenge (control) rooms (n = 6 barrows per line/challenge). On days post inoculation (dpi) 0, MhLI pigs were inoculated intragastrically with LI and intratracheally with Mh. Pig and feeder weights were recorded at dpi 0, 7, 14, and 21. On dpi 21, pigs were euthanized and tissues and blood were collected. Markers of oxidative stress, skeletal muscle metabolism and proteolysis, and liver gluconeogenesis were evaluated to determine the effects of MhLI, RFI line, and their interaction. The interaction of line and challenge was not significant (P > 0.05) for any measure. Overall, MhLI pigs had lower ADG (38%, P < 0.001), ADFI (25%, P < 0.001), and G:F (19%, P = 0.012) compared with controls. As expected, LRFI pigs had lower ADFI (P = 0.028) for the same ADG, giving them greater G:F (P = 0.021) than HRFI pigs. Challenged pigs had greater reactive oxygen species (ROS) production in the LM and liver (P < 0.10) but did not have greater skeletal muscle proteolysis. Liver gluconeogenesis was also not upregulated (P > 0.05) due to MhLI. These results provide further evidence that selection for LRFI does not negatively affect response to disease. In addition, these results suggest that postabsorptive metabolic functions are altered due to MhLI challenge. The MhLI challenge induced mitochondrial dysfunction, evident by greater ROS production, and caused pigs to favor glycolytic energy generation. However, skeletal muscle proteolysis and liver gluconeogenesis were not upregulated during MhLI challenge. These data suggest that during mild disease stress, pigs can meet energy demands without reliance on nutrient mobilization and gluconeogenesis.

Impact of Mycoplasma hyopneumoniae and Lawsonia intracellularis on the performance of pigs divergently selected for feed efficiency

Feed efficiency (FE) is a valuable trait, yet how genetic selection for enhanced FE affects other processes such as response to disease is unknown. Disease from endemic respiratory and enteric pathogens such as Mycoplasma hyopneumoniae (Mh) and Lawsonia intracellularis (LI) are common in swine production. Therefore, the aim of this study was to examine if pigs selected for high vs. low FE based on residual feed intake (RFI) respond differently to a dual respiratory and enteric challenge. Pigs selected for low RFI (LRFI, high FE) are considered more FE compared to their high RFI (HRFI, low FE) selected counterparts. Using a 2 × 2 factorial design, 25 littermate pairs from the HRFI and 25 littermate pairs from the LRFI line (barrows, 50 ± 7 kg BW) were selected, with one pig from each pair assigned to individual pens in either the challenge or the nonchallenge (control) rooms (n = 25 barrows/line/challenge). On days post inoculation (dpi) 0, the challenged pigs were inoculated with LI and Mh (MhLI). Feed intake, BW, fecal swabs, and serum samples were collected and recorded weekly for 42 d. On dpi -2 and 47, 14 littermate pairs (n = 7 barrows/line/challenge) were utilized for initial and final body composition scans using dual-energy X-ray absorptiometry to calculate longitudinal whole body tissue accretion rates for lean, protein, fat, and bone mineral content. Serum antibody levels and fecal shedding of LI were used to confirm infection. Control pigs remained negative by all measures during the 6-wk trial and MhLI inoculated pigs were confirmed positive via serological antibody responses by dpi 14 for LI and Mh. There were no interactions between RFI line and challenge status for any overall performance parameter (P > 0.05). The 6-wk MhLI challenge resulted in a 17% reduction in ADG, a 12% reduction in ADFI, and a 7% reduction in G:F vs. Controls (P < 0.05). In addition, compared to the Control pigs, MhLI challenge reduced lean, protein, and lipid accretion rates by 16% (P < 0.05). Genetic selection for high FE resulted in decreased ADFI and increased G:F (P < 0.01), but did not impact ADG or tissue accretion vs. low FE pigs. Collectively, these results demonstrate that a dual enteric and respiratory pathogen challenge reduced ADG, ADFI, G:F, and tissue accretion in growing pigs. Further, there was no evidence that selection for enhanced FE based on RFI index affects response to disease.

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs

This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern. Four modules, one in liver (with 444 co-expressed genes) and three in duodenum (gathering 37, 126 and 41 co-expressed genes), were significantly associated with FE indicators. Intra-module analyses revealed tissue-specific candidate genes; 12 of these genes were also identified as DE between individuals with high and low RFI. Pathways enriched by the list of genes showing DE and/or belonging to FE co-expressed modules included response to oxidative stress, inflammation, immune response, lipid metabolism and thermoregulation. Low overlapping between genes identified in duodenum and liver tissues was observed but heat shock proteins were associated to FE in both tissues. Our results suggest tissue-specific rather than common transcriptome regulatory processes associated with FE in pigs.

Effects of Muscle-Specific Oxidative Stress on Cytochrome c Release and Oxidation-Reduction Potential Properties

Mitochondria play a significant role in beef color. However, the role of oxidative stress in cytochrome c release and mitochondrial degradation is not clear. The objective was to determine the effects of display time on cytochrome c content and oxidation-reduction potential (ORP) of beef longissimus lumborum (LL) and psoas major (PM) muscles. PM discolored by day 3 compared with LL. On day 0, mitochondrial content and mitochondrial oxygen consumption were greater in PM than LL. However, mitochondrial content and oxygen consumption were lower (P < 0.05) in PM than LL by day 7. Conversely, cytochrome c content in sarcoplasm was greater on days 3 and 7 for PM than LL. There were no significant differences in ORP for LL during display, but ORP increased for PM on day 3 when compared with day 0. The results suggest that muscle-specific oxidative stress can affect cytochrome c release and ORP changes.

Review: divergent selection for residual feed intake in the growing pig

This review summarizes the results from the INRA (Institut National de la Recherche Agronomique) divergent selection experiment on residual feed intake (RFI) in growing Large White pigs during nine generations of selection. It discusses the remaining challenges and perspectives for the improvement of feed efficiency in growing pigs. The impacts on growing pigs raised under standard conditions and in alternative situations such as heat stress, inflammatory challenges or lactation have been studied. After nine generations of selection, the divergent selection for RFI led to highly significant (P<0.001) line differences for RFI (-165 g/day in the low RFI (LRFI) line compared with high RFI line) and daily feed intake (-270 g/day). Low responses were observed on growth rate (-12.8 g/day, P<0.05) and body composition (+0.9 mm backfat thickness, P=0.57; -2.64% lean meat content, P<0.001) with a marked response on feed conversion ratio (-0.32 kg feed/kg gain, P<0.001). Reduced ultimate pH and increased lightness of the meat (P<0.001) were observed in LRFI pigs with minor impact on the sensory quality of the meat. These changes in meat quality were associated with changes of the muscular energy metabolism. Reduced maintenance energy requirements (-10% after five generations of selection) and activity (-21% of time standing after six generations of selection) of LRFI pigs greatly contributed to the gain in energy efficiency. However, the impact of selection for RFI on the protein metabolism of the pig remains unclear. Digestibility of energy and nutrients was not affected by selection, neither for pigs fed conventional diets nor for pigs fed high-fibre diets. A significant improvement of digestive efficiency could likely be achieved by selecting pigs on fibre diets. No convincing genetic or blood biomarker has been identified for explaining the differences in RFI, suggesting that pigs have various ways to achieve an efficient use of feed. No deleterious impact of the selection on the sow reproduction performance was observed. The resource allocation theory states that low RFI may reduce the ability to cope with stressors, via the reduction of a buffer compartment dedicated to responses to stress. None of the experiments focussed on the response of pigs to stress or challenges could confirm this theory. Understanding the relationships between RFI and responses to stress and energy demanding processes, as such immunity and lactation, remains a major challenge for a better understanding of the underlying biological mechanisms of the trait and to reconcile the experimental results with the resource allocation theory.

Only 7% of the variation in feed efficiency in veal calves can be predicted from variation in feeding motivation, digestion, metabolism, immunology, and behavioral traits in early life

High interindividual variation in growth performance is commonly observed in veal calf production and appears to depend on milk replacer (MR) composition. Our first objective was to examine whether variation in growth performance in healthy veal calves can be predicted from early life characterization of these calves. Our second objective was to determine whether these predictions differ between calves that are fed a high- or low-lactose MR in later life. A total of 180 male Holstein-Friesian calves arrived at the facilities at 17 ± 3.4 d of age, and blood samples were collected before the first feeding. Subsequently, calves were characterized in the following 9 wk (period 1) using targeted challenges related to traits within each of 5 categories: feeding motivation, digestion, postabsorptive metabolism, behavior and stress, and immunology. In period 2 (wk 10–26), 130 calves were equally divided over 2 MR treatments: a control MR that contained lactose as the only carbohydrate source and a low-lactose MR in which 51% of the lactose was isocalorically replaced by glucose, fructose, and glycerol (2:1:2 ratio). Relations between early life characteristics and growth performance in later life were assessed in 117 clinically healthy calves. Average daily gain (ADG) in period 2 tended to be greater for control calves (1,292 ± 111 g/d) than for calves receiving the low-lactose MR (1,267 ± 103 g/d). Observations in period 1 were clustered per category using principal component analysis, and the resulting principal components were used to predict performance in period 2 using multiple regression procedures. Variation in observations in period 1 predicted 17% of variation in ADG in period 2. However, this was mainly related to variation in solid feed refusals. When ADG was adjusted to equal solid feed intake, only 7% of the variation in standardized ADG in period 2, in fact reflecting feed efficiency, could be explained by early life measurements. This indicates that >90% of the variation in feed efficiency in later life could not be explained by early life characterization of the calves. It is speculated that variation in health status explains a substantial portion of variation in feed efficiency in later life. Significant relations between fasting plasma glucose concentrations, fecal pH, drinking speed, and plasma natural antibodies in early life (i.e., not exposed to the lactose replacer) and feed efficiency in later life depended on MR composition. These measurements are therefore potential tools for screening calves in early life on their ability to cope with MR varying in lactose content.

Strategies towards Improved Feed Efficiency in Pigs Comprise Molecular Shifts in Hepatic Lipid and Carbohydrate Metabolism

Due to the central role of liver tissue in partitioning and metabolizing of nutrients, molecular liver-specific alterations are of considerable interest to characterize an efficient conversion and usage of feed in livestock. To deduce tissue-specific and systemic effects on nutrient metabolism and feed efficiency (FE) twenty-four animals with extreme phenotypes regarding residual feed intake (RFI) were analyzed. Transcriptome and fatty acid profiles of liver tissue were complemented with measurements on blood parameters and thyroid hormone levels. Based on 803 differentially-abundant probe sets between low- and high-FE animals, canonical pathways like integrin signaling and lipid and carbohydrate metabolism, were shown to be affected. Molecular alterations of lipid metabolism show a pattern of a reduced hepatic usage of fatty acids in high-FE animals. Complementary analyses at the systemic level exclusively pointed to increased circulating triglycerides which were, however, accompanied by considerably lower concentrations of saturated and polyunsaturated fatty acids in the liver of high-FE pigs. These results are in accordance with altered muscle-to-fat ratios usually ascribed to FE animals. It is concluded that strategies to improve FE might favor a metabolic shift from energy storage towards energy utilization and mobilization.

Relationships between the genes expressed in the mesenteric adipose tissue of beef cattle and feed intake and gain

Mesenteric fat, a depot within the visceral fat, accumulates in cattle during maturation and finishing and may be a potential source of production inefficiency. The aim of this study was to determine whether the genes expressed in the mesenteric fat of steers were associated with body weight gain and feed intake. Sixteen steers chosen by their rank of distance from the bivariate mean for gain and feed intake were used for this study. Mesenteric fat was obtained and evaluated for differences in gene expression. A total of 1831 genes were identified as differentially expressed among steers with variation in feed intake and gain. Many of these genes were involved with metabolic processes such as proteolysis, transcription and translation. In addition, the Gene Ontology annotations including transport and localization were both over-represented among the differentially expressed genes. Pathway analysis was also performed on the differentially expressed genes. The superoxide radical degradation pathway was identified as over-represented based on the differential expression of the genes GPX7, SOD2 and TYRP1, suggesting a potential role for oxidative stress or inflammatory pathways among low gain-high intake animals. GPX7 and SOD2 were in lower transcript abundance, and TYRP1 was higher in transcript abundance among the low gain-high feed intake animals. The retinoate biosynthesis pathway was also enriched due to the differential expression of the genes AKR1C3, ALDH8A1, RDH8, RDH13 and SDR9C7. These genes were all more highly expressed in the low gain-high intake animals. The glycerol degradation and granzyme A signaling pathways were both associated with gain. Three glycerol kinase genes and the GZMA gene were differentially expressed among high vs. low gain animals. Mesenteric fat is a metabolically active tissue, and in this study, genes involved in proteolysis, transcription, translation, transport immune function, glycerol degradation and oxidative stress were differentially expressed among beef steers with variation in body weight gain and feed intake.

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs

BACKGROUND

Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI).

RESULTS

Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines.

CONCLUSIONS

Non-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.

Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs

Feed efficiency (FE) is essential for pig production. In this study, 300 significantly differentially expressed (DE) transcripts, including 232 annotated genes, 28 cis-natural antisense transcripts (cis-NATs), and 40 long noncoding RNAs (lncRNAs), were identified between the liver of Yorkshire pigs with extremely high and low FE. Among these transcripts, 25 DE lncRNAs were significantly correlated with 125 DE annotated genes at a transcriptional level. These DE genes were enriched primarily in vitamin A (VA), fatty acid, and steroid hormone metabolism. VA metabolism is regulated by energy status, and active derivatives of VA metabolism can regulate fatty acid and steroid hormones metabolism. The key genes of VA metabolism (CYP1A1, ALDH1A2, and RDH16), fatty acid biosynthesis (FASN, SCD, CYP2J2, and ANKRD23), and steroid hormone metabolism (CYP1A1, HSD17B2, and UGT2B4) were significantly upregulated in the liver of high-FE pigs. Previous study with the same samples indicated that the mitochondrial function and energy expenditure were reduced in the muscle tissue of high-FE pigs. In conclusion, VA metabolism in liver tissues plays important roles in the regulation of FE in pigs by affecting energy metabolism, which may mediate fatty acid biosynthesis and steroid hormone metabolism. Furthermore, our results identified novel transcripts, such as cis-NATs and lncRNAs, which are also involved in the regulation of FE in pigs.

Ruminal expression of the NQO1, RGS5, and ACAT1 genes may be indicators of feed efficiency in beef steers

Ruminal genes differentially expressed in crossbred beef steers from USMARC with variation in gain and feed intake were identified in a previous study. Several of the genes identified with expression patterns differing between animals with high gain-low feed intake and low gain-high feed intake were evaluated in a separate, unrelated population of Angus × Hereford beef steers from the University of Wyoming that was classified to differ in residual feed intake (RFI). Of the 17 genes tested, two were differentially expressed by RFI class in the Angus × Hereford animals. These genes included NAD(P)H dehydrogenase, quinone 1 (NQO1; P = 0.0009) and regulator of G-protein signaling 5 (RGS5; P = 0.01). A third gene, acetyl-CoA acetyltransferase 1 (ACAT1; P = 0.06), displayed a trend toward association with RFI. These data suggest that some of the genes identified in a previous rumen transcriptome discovery study may have utility for identifying or selecting for animals with superior feed efficiency phenotypes across cattle breeds and populations.

Association of mitochondrial function and sperm progressivity in slow- and fast-growing roosters

The objectives of the current study were to investigate the activity of the electron transport chain (ETC) complexes, adenosine triphosphate (ATP), and reactive oxygen species (ROS) in the sperm mitochondria of 2 Iranian slow- and fast-growing chickens, namely native and Aryan strains. In this study, semen of 133 roosters was analyzed by computer-assisted sperm analysis (CASA). The roosters were categorized by sperm progressivity, as a low or high sperm motility phenotype. Mitochondrial complex I (NADH ubiquinone oxidoreductase), II (succinate dehydrogenase), III (ubiquinol cytochrome C reductase), IV (cytochrome C oxidase) activity, ATP, and ROS production in sperm were assayed. As a result, Aryan roosters with high progressive motility levels (HPL) had the greatest progressivity. Progressive motility was significant in in both strains (Aryan and native; P = 0.020) and motility levels (high and low; P = 0.007). The highest activity of complexes I was observed in Aryan with HPL roosters (P = 0.004). Native roosters with HPLs demonstrated higher complex activities I compared with Aryan and native roosters with low progressive motility levels (LPL) (P = 0.004). Significant differences were observed not only in the mitochondrial amounts of ATP of the strains (P = 0.000) but also between HPL and LPL (P = 0.003). The highest mitochondrial amounts of ATP was found in Aryan roosters with HPL (P = 0.021). Native roosters with LPL had the highest concentration of mitochondrial ROS (P = 0.033). The Aryan roosters with HPL, on the other hand, indicated less concentration of the mitochondrial ROS compared with Aryan having LPL and native roosters with HPL and LPL (P = 0.033). A significant difference was observed in the mitochondrial ROS between the strains (P = 0.004) and between HPL and LPL (P = 0.000). There was positive relationship between progressivity and each of mitochondrial complexes and ATP (r = 0.71, 0.62, 0.90 and 0.65 respectively). Based on our results, the sperm progressivity largely depends on the whole energy production originating in the mitochondrial compartment. Therefore, the deficiency in the function of mitochondria in the sperm and energy production could be responsible for low progressive motility.

Profile of the Spleen Transcriptome in Beef Steers with Variation in Gain and Feed Intake

We have previously identified components of the immune system contributing to feed intake and gain in both the rumen and small intestine of beef steers. In this study, we examined the spleen, a major lymphatic organ near the digestive tract, to determine whether it was also influencing individual feed efficiency status through immune responses. Animals (n = 16) that were divergent for gain and intake were selected for tissue sampling. The spleen transcriptomes were evaluated by microarray. A total of 1216 genes were identified as differentially expressed. Genes were over-represented in Kyoto encyclopedia of genes and genomes (KEGG) pathways including biological regulation, protein folding, cell communication, immune systems process, response to stress, and RNA metabolic process. Several stress response or heat shock genes including HSPH1, HSPA1A, HSPA4, DNAJB4, DNAJA4, etc., were identified as a stress response functional gene cluster in the low gain-low intake animals. These genes were up-regulated amongst the low gain-low intake animals compared to all other groups. Canonical pathways associated with the differentially expressed genes included the coagulation system, extrinsic prothrombin activation, protein ubiquitination, unfolded protein response, and aldosterone signaling in epithelial cells. An analysis of expressed copy number variable (CNV) genes in the spleen produced some of the same genes and gene families that were differentially expressed. Our data suggests the splenic contribution to some of the underlying variation among gain and intake within this group of animals may be a result of immune function and stress response. In addition, some of the differences in immune response functions may be related to gene copy number.

Relationship between antioxidant capacity, oxidative stress, and feed efficiency in beef steers

Feed efficiency (FE) can vary between individuals but sources of variation are not well characterized. Oxidative stress is among the biological mechanisms believed to contribute to variation. The objective of this study was to evaluate the relationship between FE, antioxidant activity, and oxidative stress in feedlot steers representing phenotypic extremes for FE. Crossbred beef steers ( = 181) fed 70-d growing phase (GP) whole-shell corn-based (G-Corn) or rye baleage and soybean hull-based (G-Rough) diets in GrowSafe bunks at the University of Missouri were shipped to Iowa State University where the 12 most feed efficient (HFE) and 12 least feed efficient (LFE) steers from each diet (n = 48; 467 kg [SD 51]) were selected for evaluation. Steers received diets similar to GP diets, and 3 d after arrival, blood was sampled to evaluate antioxidant activity and oxidative stress markers for the GP following transit. Steers were transitioned to finishing phase (FP) cracked corn-based (F-Corn) or dried distillers' grains and soybean hull-based (F-Byp) diets, and on FP d 97, blood samples for the FP were collected. Data for the GP were analyzed as a 2 × 2 factorial, and data for the FP were analyzed as a 2 × 2 × 2 factorial using PROC MIXED of SAS. No GP diet × FP diet, FP diet × FE group, or 3-way interactions were noted ( ≥ 0.11) for FP measures. Steers fed the G-Rough diet had greater ( = 0.04) GP plasma protein carbonyl concentrations. During the GP, HFE steers had greater ( ≤ 0.04) protein carbonyl and ratio of oxidized:reduced blood lysate glutathione concentrations than LFE steers. There were GP diet × FE group interactions ( ≤ 0.03) during the GP and FP. During the GP, total blood lysate superoxide dismutase (SOD) activity was greater ( ≤ 0.03) in G-Rough/LFE steers than in G-Rough/HFE and G-Corn/LFE steers; G-Corn/HFE steers were intermediate. The G-Rough/LFE steers had greater ( < 0.04) glutathione peroxidase (GPX) activity than other groups and greater ( = 0.03) plasma malondialdehyde concentrations than G-Corn/LFE steers. During the FP, the G-Rough/LFE steers had greater ( ≤ 0.04) GPX activity than G-Rough/HFE and G-Corn/LFE steers; G-Corn/HFE steers were intermediate. The F-Byp diet had greater ( < 0.01) protein carbonyl than the F-Corn diet, and no other FP diet effects were noted ( ≥ 0.3) for any FP measures. The GP diet and FE groups had stronger relationships with antioxidant activity and oxidative stress markers measured for the GP than for the FP. Overall, antioxidant activity may play a role in FE as LFE steers, driven largely by G-Rough/LFE steers, had greater SOD activity and GPX activity than HFE steers, potentially using a greater proportion of energy otherwise available for tissue accretion.

Composition and quality characteristics of carcasses from pigs divergently selected for residual feed intake on high- or low-energy diets

The objective was to determine the extent to which feeding low-energy, high-fiber (LEHF) and high-energy, low-fiber (HELF) diets impacts meat quality and carcass composition of pigs divergently selected for residual feed intake (RFI). Two experiments were conducted in the divergently selected Iowa State University RFI lines: Exp. 1 evaluated carcasses of generation (G) 8 pigs fed on commercial feeders; Exp. 2 evaluated composition, pork quality, sensory, and postmortem proteolysis of pigs fed on electronic single-space feeders in G 8 and 9. Pigs (N = 177) in Exp. 1 were randomly assigned a pen (mixed sex and line; N = 8). Groups (n = 3) of pigs were slaughtered at a mean BW of 121.5 kg. Pigs in Exp. 2 (G8: n = 158; G9: n = 157) were randomly assigned to 1 of 6 pens of each diet per G. Pigs from G8 were slaughtered at a mean BW of 122.5 kg and G9 at a mean of 128.4 kg. Data were analyzed using the mixed procedure of SAS. Fixed effects were line, diet, sex, and all appropriate interactions. Random effects were group, pen, litter, and sire and covariate of off-test BW. For Exp. 2, G was added as a fixed effect and sensory day was added as a random effect when applicable. In Exp. 1, carcasses from low RFI (LRFI) pigs were leaner and had less fat depth (P < 0.01). Carcasses from pigs fed the LEHF diet had a lighter HCW and greater estimated percent lean than pigs fed HELF diet (P < 0.01). In Exp. 2, LRFI pigs on the HELF diet had the greatest loin depth (P < 0.01). Chops from HRFI pigs had greater drip loss, color scores, lean tissue a*, and percent lipid and lesser percent moisture than LRFI ( P< 0.05). Chops from pigs on the LEHF diet had lesser muscle L* values and greater percent moisture than chops from pigs fed the HELF diet (P < 0.05). Chops from LRFI pigs were juicer than those from HRFI pigs (P < 0.05). Protein extracted at d 2 postmortem from LRFI pigs on the LEHF diet had a greater 38 kDa desmin degradation product than protein from LRFI pigs fed the HELF diet (P < 0.05). Day 5 postmortem extracted protein from HRFI pigs had greater 38 kDa desmin degradation product than LRFI (P = 0.05). Pigs fed LEHF (P < 0.01) had adipose with a greater iodine value than adipose from HELF fed pigs. Pork sensory quality from pigs differentially selected for residual feed intake was not influenced by energy content of the diet the pigs were fed.

FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves

Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1-3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 (FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; A<G substitution), in the promoter region of the gene, was significantly associated with all three RFIs. As the three RFI classes reflect changing diets and ages with concomitant RFI phenotypic consistency, the above polymorphisms and in particular FABP4_5, might be considered possible markers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation.

Divergent selection for residual feed intake affects the transcriptomic and proteomic profiles of pig skeletal muscle

Improving feed efficiency is a relevant strategy to reduce feed cost and environmental waste in livestock production. Selection experiments on residual feed intake (RFI), a measure of feed efficiency, previously indicated that low RFI was associated with lower feed intake, similar growth rate, and greater lean meat content compared with high RFI. To gain insights into the molecular mechanisms underlying these differences, 24 Large White females from 2 lines divergently selected for RFI were examined. Pigs from a low-RFI ("efficient") and high-RFI ("inefficient") line were individually fed ad libitum from 67 d of age (27 kg BW) to slaughter at 115 kg BW (n = 8 per group). Additional pigs of the high-RFI line were feed restricted to the daily feed intake of the ad libitum low-RFI pigs (n = 8) to investigate the impact of selection independently of feed intake. Global gene and protein expression profiles were assessed in the LM collected at slaughter. The analyses involved a porcine commercial microarray and 2-dimensional gel electrophoresis. About 1,000 probes were differentially expressed (P < 0.01) between RFI lines. Only 10% of those probes were also affected by feed restriction. Gene functional classification indicated a greater expression of genes involved in protein synthesis and a lower expression of genes associated with mitochondrial energy metabolism in the low-RFI pigs compared with the high-RFI pigs. At the protein level, 11 unique identified proteins exhibited a differential abundance (P < 0.05) between RFI lines. Differentially expressed proteins were generally not significantly affected by feed restriction. Mitochondrial oxidative proteins such as aconitase hydratase, ATP synthase subunit α, and creatine kinase S-type had a lower abundance in the low-RFI pigs, whereas fructose-biphosphate aldolase A and glyceraldehyde-3-phosphate dehydrogenase, 2 proteins involved in glycolysis, had a greater abundance in those pigs compared with high-RFI pigs. Antioxidant proteins such as superoxide dismutase and glutathione peroxidase 3 at the mRNA level and peroxiredoxin-6 at the protein level were also less expressed in LM of the most efficient pigs, likely related to lower oxidative molecule production. Collectively, both the transcriptomic and proteomic approaches revealed a lower oxidative metabolism in muscle of the low-RFI pigs and all these modifications were largely independent of differences in feed intake.

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

Background

Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. An increasingly accepted measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. Additionally, to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs, which is costly and time-consuming. Thus, convenient and predictive biomarkers for RFI that can be measured at an early age are greatly desired. In this study, we aimed to explore whether differences exist in the global gene expression profiles of peripheral blood of 35 to 42 day-old pigs with extremely low (more efficient) and high RFI (less efficient) values from two lines that were divergently selected for RFI during the grow-finish phase, to use such information to explore the potential molecular basis of RFI differences, and to initiate development of predictive biomarkers for RFI.

Results

We identified 1972 differentially expressed genes (DEGs) (q ≤ 0.15) between the low (n = 15) and high (n = 16) RFI groups of animals by using RNA sequencing technology. We validated 24 of 37 selected DEGs by reverse transcription-quantitative PCR (RT-qPCR) in a joint analysis of 24 (12 per line) of the 31 samples already used for RNA-seq plus 24 (12 per line) novel samples from the same contemporary group of pigs. Using an analysis of the 24 novel samples alone, only nine of the 37 selected DEGs were validated. Genes involved in small molecule biosynthetic process, antigen processing and presentation of peptide antigen via major histocompatibility complex (MHC) class I, and steroid biosynthetic process were overrepresented among DEGs that had higher expression in the low versus high RFI animals. Genes known to function in the proteasome complex or mitochondrion were also significantly enriched among genes with higher expression in the low versus high RFI animals. Alternatively, genes involved in signal transduction, bone mineralization and regulation of phosphorylation were overrepresented among DEGs with lower expression in the low versus high RFI animals. The DEGs significantly overlapped with genes associated with disease, including hyperphagia, eating disorders and mitochondrial diseases (q < 1E-05). A weighted gene co-expression network analysis (WGCNA) identified four co-expression modules that were differentially expressed between the low and high RFI groups. Genes involved in lipid metabolism, regulation of bone mineralization, cellular immunity and response to stimulus were overrepresented within the two modules that were most significantly differentially expressed between the low and high RFI groups. We also found five of the DEGs and one of the co-expression modules were significantly associated with the RFI phenotype of individual animals (q < 0.05).

Conclusions

The post-weaning blood transcriptome was clearly different between the low and high RFI groups. The identified DEGs suggested potential differences in mitochondrial and proteasomal activities, small molecule biosynthetic process, and signal transduction between the two RFI groups and provided potential new insights into the molecular basis of RFI in pigs, although the observed relationship between the post-weaning blood gene expression and RFI phenotype measured during the grow-finish phase was not strong. DEGs and representative genes in co-expression modules that were associated with RFI phenotype provide a preliminary list for developing predictive biomarkers for RFI in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2395-x) contains supplementary material, which is available to authorized users.