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

Adipose Tissue Inflammation: Linking Physiological Stressors to Disease Susceptibility

The study of adipose tissue (AT) is enjoying a renaissance. White, brown, and beige adipocytes are being investigated in adult animals, and the critical roles of small depots like perivascular AT are becoming clear. But the most profound revision of the AT dogma has been its cellular composition and regulation. Single-cell transcriptomic studies revealed that adipocytes comprise well under 50% of the cells in white AT, and a substantial portion of the rest are immune cells. Altering the function of AT resident leukocytes can induce or correct metabolic syndrome and, more surprisingly, alter adaptive immune responses to infection. Although the field is dominated by obesity research, conditions such as rapid lipolysis, infection, and heat stress impact AT immune dynamics as well. Recent findings in rodents lead to critical questions that should be explored in domestic livestock as potential avenues for improved animal resilience to stressors, particularly as animals age.

Performance and antioxidant traits of broiler chickens fed with diets containing rapeseed or flaxseed oil and optimized quercetin

This study evaluated the effect of quercetin (Q) added to feed mixtures, at concentrations directly optimized for the peroxidability of dietary rapeseed (RO) and flaxseed oil (FLO), on performance and selected biomarkers of oxidative stress of broiler chickens. Ninety-six one-day-old Ross 308 broiler chicken males were randomly assigned to four groups (six replicates per treatment, four birds per cage, n = 24 per group): Group RO received diets containing rapeseed oil (RO) and group FLO received diets containing flaxseed oil (FLO); Group RO_Q and group FLO_Q received these same diets containing RO or FLO oils, supplemented with optimized quercetin (Q). Blood, pectoral muscles, and liver samples of chickens were collected after 35 days to determine: (1) the global indicators of antioxidant capacity: ferric reducing antioxidant power (FRAP), antiradical activity (DPPH·/ABTS·+), total antioxidant status (TAS), and glutathione peroxidase (GSH-Px); (2) the activity of the antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD); and (3) the concentration of malondialdehyde (MDA). Data showed that the FLO diet did not affect the final performance parameters in relation to RO, but the optimized Q tended to improve the total body weight gain and the final body weight of broiler chickens (P = 0.10). The antioxidant traces analyzed in the blood (GSH-Px), plasma (FRAP, ABTS·+, DPPH·, TAS), serum (DPPH·), and pectoral muscles (SOD, CAT) of chickens were not altered by either Oil or Q factor. FLO supplementation increased MDA content in the liver of chickens (P < 0.05) and increased liver CAT activity, which was not improved by optimized Q. Meanwhile, the Oil × Q interaction suggests that optimized Q could reduce the liver burden and negative effects of oxidized lipid by-products associated with FLO diets. Our results indicate that optimizing the addition of natural polyphenols to feed may be a valuable alternative to the application of polyphenolic antioxidants in animal nutrition, allowing for an economical use of the antioxidant additives when customized to the peroxidability of fat sources, which is line to the conception of sustainable development covering 'The European Green Deal' and 'Farm to Fork Strategy'.

Increased dietary Trp, Thr, and Met supplementation improves growth performance and protein deposition of salmonella-challenged growing pigs under poor housing conditions

Highly intensified rearing conditions and precarious sanitary management predispose pigs to immune system activation, altered amino acid (AA) metabolism, and decreased growth performance. Thus, the main objective of this study was to evaluate the effects of increased dietary tryptophan (Trp), threonine (Thr), and methionine + cysteine (Met + Cys) supplementation on performance, body composition, metabolism, and immune responses of group-housed growing pigs under challenging sanitary conditions. A hundred and twenty pigs (25.4 ± 3.7 kg) were randomly assigned to a 2 × 2 factorial arrangement, consisting of two sanitary conditions (SC, good [GOOD] or salmonella-challenge and poor housing condition [Salmonella Typhimurium (ST) + POOR]) and two diets, control (CN) or supplemented with AA (Trp, Thr, and Met + Cys:Lys ratios 20% higher than those of the CN diet [AA>+]). Pigs were followed during the growing phase (25-50 kg) and the trial lasted 28 d. The ST + POOR SC pigs were challenged with Salmonella Typhimurium and raised in a poor housing condition. The ST + POOR SC increased rectal temperature, fecal score, serum haptoglobin, and urea concentration (P < 0.05) and decreased serum albumin concentration (P < 0.05) compared with GOOD SC. Body weight, average daily feed intake, average daily gain (ADG), feed efficiency (G:F), and protein deposition (PD) were greater in GOOD SC than in ST + POOR SC (P < 0.01). However, pigs housed in ST + POOR SC fed with AA+ diet had lower body temperature (P < 0.05), increased ADG (P < 0.05) and nitrogen efficiency (P < 0.05), and a tendency for improved PD and G:F (P < 0.10) compared with CN diet fed pigs. Regardless of the SC, pigs fed AA+ diet had lower serum albumin (P < 0.05) and tended to decrease serum urea levels (P < 0.10) compared with CN diet. The results of this study suggest that the ratio of Trp, Thr, and Met + Cys to Lys for pigs are modified by sanitary conditions. Furthermore, supplementation of diets with a blend of Trp, Thr, and Met + Cys improves performance, especially under salmonella-challenge and poor housing conditions. Dietary tryptophan, threonine, and methionine supplementation can modulate immune status and influence resilience to sanitary challenges.

Hygiene of housing conditions and proinflammatory signals alter gene expressions in porcine adipose tissues and blood cells

Adipose tissue is an organ with metabolic, endocrine and immune functions. In this tissue, the expressions of genes associated with several metabolic pathways, including lipid metabolism, have been shown to be affected by genetic selection for feed efficiency, an important trait to consider in livestock. We hypothesized that the stimulation of immune system caused by poor hygiene conditions of housing impacts the molecular and cellular features of adipose tissue and that the impact may differ between pigs that diverge in feed efficiency. At the age of 12 weeks, Large White pigs from two genetic lines divergent for residual feed intake (RFI) were housed in two contrasting hygiene conditions (good vs poor). After six weeks of exposure, pigs were slaughtered (n = 36). Samples of blood, subcutaneous (SCAT) and perirenal (PRAT) adipose tissues were collected for cell response and gene expression investigations. The decrease in the relative weight of PRAT was associated with a decline in mRNA levels of FASN, ME, LCN2 and TLR4 (P < 0.05) in pigs housed in poor conditions compared with pigs housed in good conditions for both RFI lines. In SCAT, the expressions of only two key genes (PPARG and TLR4) were significantly affected by the hygiene of housing conditions. Besides, the mRNA levels of both LCN2 and GPX3 were influenced by the RFI line (P < 0.05). Because we suspected an effect of poor hygiene at the cellular levels, we investigated the differentiation of stromal vascular cells isolated from SCAT in vitro in the absence or presence of a pro-inflammatory cytokine, Tumor Necrosis Factor-α (TNF-α). The ability of these cells to differentiate in the absence or presence of TNF-α did not differ among the four groups of animals (P > 0.05). We also investigated the expressions of genes involved in the immune response and lipid metabolism in whole blood cells cultured in the absence and presence of LPS. The hygiene conditions had no effect but, the relative expression of the GPX3 gene was higher (P < 0.001) in high RFI than in low RFI pigs while the expressions of IL-10 (P = 0.027), TGFβ1 (P = 0.023) and ADIPOR2 (P = 0.05) genes were lower in high RFI than in low RFI pigs. Overall, the current study indicates that the hygiene of housing had similar effects on both RFI lines on the expression of genes in adipose tissues and on the features of SCAT adipose cells and whole blood cells in response to TNF-α and LPS. It further demonstrates that the number of genes with expression impacted by housing conditions was higher in PRAT than in SCAT. It suggests a depot-specific response of adipose tissue to the current challenge.

Proteomic analysis of adipose tissue revealing differentially abundant proteins in highly efficient mid-lactating dairy cows

The improvement of nutrient utilization efficiency in dairy cows represents an important task in view of the current rising demand for animal products and sustainable resource usage. In this perspective, the identification of appropriate markers to identify the most efficient animals for dairy production becomes a crucial factor. Residual feed intake (RFI), which represents the difference between predicted and actual intake, is used to define the efficiency of cows. In this study, subcutaneous adipose tissue (AT) was collected from five high efficient (HEF) and five low efficient (LEF) mid-lactation Holstein dairy cows, that represented subgroups of the 20% lowest RFI values (HEF) and highest 20% RFI values (LEF), out of a cohort of 155 cows that were examined for feed efficiency at the individual dairy barn at Volcani Institute, Israel. Adipose samples were examined for proteomic analysis by nano-LC/MS–MS and gene expression by RT-PCR. A total of 101 differential proteins (P ≤ 0.05 and fold change ± 1.5) and two protein networks related to feed efficiency were found between HEF and LEF cows. Among the enriched top canonical pathways, FAT10 signaling, EIF2 signaling, Sirtuin signaling, Acute phase response signaling, Protein ubiquitination and mTOR signaling pathways were related to feed efficiency in AT. Furthermore, abundance of transferrin (TF; FC = 78.35, P = 0.02) enriched pathways, including mTOR signaling, LXR/RXR and FXR/RXR activation was found in AT of HEF cows. Relative mRNA expression of RBM39, which is involved in energy metabolism, was decreased in AT of HEF versus LEF. The relationship found between the AT proteins and/or metabolic pathways and the feed efficiency demonstrates that AT may reflect metabolic adaptations to high efficiency, and suggests that these proteins together with their metabolic mechanisms are suitable candidates as biomarkers to identify efficient cows for dairy production.

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.

Improving maternal welfare during gestation has positive outcomes on neonatal survival and modulates offspring immune response in pigs

Improving the housing of pregnant sows by giving them more space and access to deep straw had positive effects on their welfare, influenced their maternal behavior and improved the survival of their offspring. The present study aimed at determining whether these effects were actually due to environmental enrichment and whether the provision of straw pellets and wood can partly mimic the effects of straw bedding during gestation. Three graded levels of enrichment were used, that were, collective conventional pens on slatted floor (C, n = 26), the same pens with manipulable wood materials and distribution of straw pellets after the meals (CE, n = 30), and larger pens on deep straw litter (E, n = 27). Sows were then housed in identical farrowing crates from 105 days of gestation until weaning. Decreased stereotypies, blood neutrophils, and salivary cortisol, and increased behavioral investigation indicated that health and welfare of sows during gestation were improved in the E environment compared with the C environment. The CE sows responded as C or E sows depending on the trait. Piglet mortality rate in the first 12 h after birth was lower in E and CE litters than in C litters, but enrichment level during gestation had only small effects on lactating sow behavior and milk composition postpartum. On days 2 and 3 of lactation, E sows interrupted less often their nursing sequences than C and CE sows. On day 2, milk from both E and CE sows contained more minerals than that from C sows. In one-day-old piglets, the expression levels of genes encoding toll-like receptors (TLR2, TLR4) and cytokines (interleukin-1, -6 and -10) in whole blood after 20-h culture, were greater in E piglets than in CE or C piglets. In conclusion, housing sows in an enriched environment during gestation improved early neonatal survival, probably via moderate and cumulative positive effects on sow behavior, milk composition, and offspring innate immune response. The gradation in the effects observed in C, CE and E housing environment reinforced the hypothesis of a causal relationship between maternal environmental enrichment, sow welfare and postnatal piglet traits.

Poor hygiene of housing conditions influences energy metabolism in a muscle type-dependent manner in growing pigs differing in feed efficiency

The ability of pigs to cope with inflammatory challenges may by modified by selection for residual feed intake (RFI), a measure of feed efficiency. In the current study, we evaluated skeletal muscle metabolic responses to degraded hygiene conditions in pigs divergently selected for RFI. At 82 d of age, low RFI and high RFI pigs were housed in either poor or good hygiene conditions. After a 6-week challenge, the poor hygiene conditions induced a decrease in growth performance (P < 0.001) and in plasma IGF-I concentrations (P < 0.003) in both lines. In the slow-twitch oxidative semispinalis muscle, poor hygiene conditions induced a shift towards a more oxidative metabolism and an activation of the AMPK pathway in pigs of both RFI lines. In the fast-twitch glycolytic longississimus muscle, poor hygiene conditions were associated to a less glycolytic metabolism in the HRFI line only. Poor hygiene conditions also increased the protein level of lipidation of microtubule-associated protein 1 light-chain 3β (LC3-II) in both RFI lines, suggesting an activation of the autophagy pathway. Altogether, the data revealed muscle-type specific metabolic adaptations to poor hygiene conditions, which may be related to different strategies to fuel the activated immune system.

Exploration of early social behaviors and social styles in relation to individual characteristics in suckling piglets

Social behavior is a key component of pig welfare on farms, but little is known on the development of social behaviors in piglets. This study aimed to explore social behaviors and identify early social styles in suckling piglets. Social behaviors of 68 piglets from 12 litters were scored continuously for 8 h per day at 21 and 42 days of age, and were included in a Hierarchical Clustering on Principal Components analysis to identify clusters of pigs with similar social styles. Social nosing represented 78% of all social interactions given. Three social styles were identified: low-solicited inactive animals (inactive), active animals (active), and highly-solicited avoiders (avoiders). Belonging to a cluster was independent of age, but was influenced by sex, with females being more represented in the ‘inactive’ cluster, and males in the ‘active’ cluster, whereas both sexes were equally represented in the ‘avoider’ cluster. Stability of piglets’ allocation to specific clusters over age was high in the ‘inactive’ (59%) and ‘active’ (65%) clusters, but low in the ‘avoider’ cluster (7%). Haptoglobin and growth rate were higher in ‘active’ than ‘inactive’ pigs, and intermediate in ‘avoiders’. Our findings suggest the existence of transient social styles in piglets, likely reflective of sexual dimorphism or health status.

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.

Analysis of merged whole blood transcriptomic datasets to identify circulating molecular biomarkers of feed efficiency in growing pigs

Background

Improving feed efficiency (FE) is an important goal due to its economic and environmental significance for farm animal production. The FE phenotype is complex and based on the measurements of the individual feed consumption and average daily gain during a test period, which is costly and time-consuming. The identification of reliable predictors of FE is a strategy to reduce phenotyping efforts.

Results

Gene expression data of the whole blood from three independent experiments were combined and analyzed by machine learning algorithms to propose molecular biomarkers of FE traits in growing pigs. These datasets included Large White pigs from two lines divergently selected for residual feed intake (RFI), a measure of net FE, and in which individual feed conversion ratio (FCR) and blood microarray data were available. Merging the three datasets allowed considering FCR values (Mean = 2.85; Min = 1.92; Max = 5.00) for a total of n = 148 pigs, with a large range of body weight (15 to 115 kg) and different test period duration (2 to 9 weeks). Random forest (RF) and gradient tree boosting (GTB) were applied on the whole blood transcripts (26,687 annotated molecular probes) to identify the most important variables for binary classification on RFI groups and a quantitative prediction of FCR, respectively. The dataset was split into learning (n = 74) and validation sets (n = 74). With iterative steps for variable selection, about three hundred’s (328 to 391) molecular probes participating in various biological pathways, were identified as important predictors of RFI or FCR. With the GTB algorithm, simpler models were proposed combining 34 expressed unique genes to classify pigs into RFI groups (100% of success), and 25 expressed unique genes to predict FCR values (R² = 0.80, RMSE = 8%). The accuracy performance of RF models was slightly lower in classification and markedly lower in regression.

Conclusion

From small subsets of genes expressed in the whole blood, it is possible to predict the binary class and the individual value of feed efficiency. These predictive models offer good perspectives to identify animals with higher feed efficiency in precision farming applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07843-4.

Identification of blood immune and metabolic indicators explaining the variability of growth of pigs under contrasted sanitary conditions

Background

Health and growth of pigs are affected by the hygiene of housing. Lower growth performance observed in poor hygiene of housing conditions is explained by reduced feed intake and metabolic changes caused by the activation of body defences. In a previous experiment, we reported contrasted average values of body weight gain, concentrations of circulating metabolites, redox and immune indicators in blood of pigs housed in good or poor hygiene conditions during the growing period. This study addressed inter-individual variability in these responses to determine whether a particular blood profile explains average daily gain (ADG) of the pig.

Results

The data originated from 160 growing pigs, half of which subjected to a hygiene challenge for 6 weeks (W0 to W6) and the others housed in good hygiene conditions. Pigs originated from two lines divergently selected for residual feed intake (RFI). Individual body weights were recorded during this period, and relative ADG (rADG_W0-W6) was calculated as the ADG corrected by the initial body weight measured at W0. Blood samples were taken before (W0) and 3 weeks (W3) after the beginning of the challenge. The analysed dataset consisted of 51 metabolites and indicators of immune and inflammatory responses measured on 136 pigs having no missing value for any variables, when calculated as the differences W3 minus W0 in circulating concentrations. An algorithm tested all possible linear regression models and then selected the best ones to explain rADG_W0-W6. Six variables were identified across the best models and correlated with rADG_W0-W6 with a goodness of fit (adjusted R²) of about 67%. They were changes in haptoglobin, global antioxidant capacity of plasma (Biological Antioxidant Power or BAP), free fatty acids, and 3 amino acids: leucine, tryptophan, and 1-methylhistidine. The effects of housing conditions and RFI lines were comprised in the variables of the selected models and none of these conditions improved accuracy of the predictive models, leading to genericity of the pinpointed metabolic changes in relation to variability of ADG.

Conclusions

This approach allows us to identify blood variables, whose changes in blood concentrations correlated to ADG under contrasted sanitary conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02872-3.

Association of residual feed intake with growth performance, carcass traits, meat quality, and blood variables in native chickens

Improving feed efficiency is a primary goal in poultry breeding strategies. Residual feed intake (RFI) in chickens typically calculated during the growing period is a measure of feed efficiency that is independent of the level of production. The objective of this study was to evaluate phenotypic correlations of growth performance, carcass traits, meat quality, and blood variables with RFI in growing native chickens. A total of 1,008 chickens were selected for the experiment to derive RFI. After the RFI measurement period of 42 d, 25 chickens with low RFI values, 25 chickens with medium RFI values, and 25 chickens with high RFI values were selected. The RFI was significantly positively correlated with feed conversion ratio and average daily feed intake, while it was not significantly correlated with initial body weight (BW), final BW, average daily body weight gain, and metabolic BW0.75. The abdominal fat weight and yield of high RFI group were significantly greater than those of medium and low RFI groups, and the abdominal fat yield was significantly positively correlated with RFI. Moreover, the plasma insulin-like growth factor 1 (IGF-1) content of low RFI group was significantly greater than those of high and medium RFI groups. The plasma concentrations of adrenocorticotropic hormone, triiodothyronine (T3), and cortisol of high RFI birds were significantly greater than that of low RFI birds. RFI was significantly positively correlated with plasma concentrations of T3 and cortisol, while it was significantly negatively correlated with plasma concentration of IGF-1. In addition, the serum levels of glucose and triglyceride of high RFI birds were significantly lower than that of low RFI birds. The serum low-density lipoprotein cholesterol (LDL-C) content of high RFI group was significantly greater than that of medium and low RFI groups, and it was significantly positively correlated with RFI. Our data suggested that selection of chickens with low RFI values may be beneficial to reduce fat deposition in native chickens without affecting the meat quality. Circulating IGF-1, T3, cortisol, and LDL-C concentrations can be used as indirect selection indicators of feed efficiency in native chickens. The effect of IGF-1, T3, cortisol, and LDL-C on feed efficiency of native chickens should be carefully examined and validated in future breeding programs.

Genetic parameter estimates for plasma oxidative status traits in slaughter pigs

The aim of the present study was to assess the effect of sex and to estimate genetic parameters for several traits related to plasma oxidative status in slaughter pigs, i.e., ferric reducing ability of plasma (FRAP), concentrations of α-tocopherol and malondialdehyde (MDA), and glutathione peroxidase (GPx) activity. Blood samples were collected at slaughter from 477 Piétrain × (Landrace × Large White intercross) pigs of 2 performance test stations. Heritabilities (±SE) of plasma oxidative status traits as well as their phenotypic and additive genetic correlations with animal performance traits were estimated with multiple-trait REML animal models using VCE software. Results displayed no significant difference between barrows and gilts for FRAP and α-tocopherol in plasma. However, gilts had a significantly higher concentration of MDA and lower GPx activity compared with barrows. Heritability estimates were high for GPx (0.55 ± 0.05), and medium to low for α-tocopherol (0.30 ± 0.06), FRAP (0.22 ± 0.05), and MDA (0.15 ± 0.04). Estimated additive genetic and phenotypic correlations between these four traits were generally low, except for a negative additive genetic correlation between FRAP and GPx of -0.45 (±0.23). Additive genetic correlations between plasma oxidative status traits and animal performance traits were also generally absent or low with maximum values of ~0.3. Parameter estimates in this study have to be interpreted with caution because of the small size of the dataset. Nevertheless, it may be concluded that there is considerable additive genetic variance for plasma oxidative status traits in slaughter pigs. More research is warranted on the genetic determination of oxidative stress in farm animals and its relevance in breeding programs.

Identification of key genes and pathways associated with feed efficiency of native chickens based on transcriptome data via bioinformatics analysis

BACKGROUND

Improving feed efficiency is one of the important breeding targets for poultry industry. The aim of current study was to investigate the breast muscle transcriptome data of native chickens divergent for feed efficiency. Residual feed intake (RFI) value was calculated for 1008 closely related chickens. The 5 most efficient (LRFI) and 5 least efficient (HRFI) birds were selected for further analysis. Transcriptomic data were generated from breast muscle collected post-slaughter.

RESULTS

The differently expressed genes (DEGs) analysis showed that 24 and 325 known genes were significantly up- and down-regulated in LRFI birds. An enrichment analysis of DEGs showed that the genes and pathways related to inflammatory response and immune response were up-regulated in HRFI chickens. Moreover, Gene Set Enrichment Analysis (GSEA) was also employed, which indicated that LRFI chickens increased expression of genes related to mitochondrial function. Furthermore, protein network interaction and function analyses revealed ND2, ND4, CYTB, RAC2, VCAM1, CTSS and TLR4 were key genes for feed efficiency. And the 'phagosome', 'cell adhesion molecules (CAMs)', 'citrate cycle (TCA cycle)' and 'oxidative phosphorylation' were key pathways contributing to the difference in feed efficiency.

CONCLUSIONS

In summary, a series of key genes and pathways were identified via bioinformatics analysis. These key genes may influence feed efficiency through deep involvement in ROS production and inflammatory response. Our results suggested that LRFI chickens may synthesize ATP more efficiently and control reactive oxygen species (ROS) production more strictly by enhancing the mitochondrial function in skeletal muscle compared with HRFI chickens. These findings provide some clues for understanding the molecular mechanism of feed efficiency in birds and will be a useful reference data for native chicken breeding.