Identification of Important Proteins and Pathways Affecting Feed Efficiency in DLY Pigs by iTRAQ-Based Proteomic Analysis.
ABSTRACT: Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ?1.2 or ?0.84; p ? 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs.
Project description:Feed cost accounts for approximately 65-75% of overall commercial pork production costs. Therefore, improving the feed efficiency of pig production is important. In this study, 12 individuals with either extremely high (HE) or low (LE) feed efficiency were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs. After the pigs were slaughtered, we collected small intestine mucosal tissue. Next, RNA sequencing (RNA-seq) analysis was used to reveal the presence and quantity of genes expressed between these extremely HE- and LE-groups. We found 433 significantly differentially expressed genes (DEGs) between the HE- and LE-groups. Of these, 389 and 44 DEGs were upregulated and downregulated in the HE-group, respectively. An enrichment analysis showed that the DEGs were mainly enriched in functions related to apical plasma membrane composition, transporter activity, transport process and hormone regulation of digestion and absorption. Protein network interaction and gene function analyses revealed that SLC2A2 was an important candidate gene for FE in pigs, which may give us a deeper understanding of the mechanism of feed efficiency. Furthermore, some significant DEGs identified in the current study could be incorporated into artificial selection programs for increased feeding efficiency in pigs.
Project description:Feed efficiency (FE) is an important trait in the porcine industry. Therefore, understanding the molecular mechanisms of FE is vital for the improvement of this trait. In this study, 6 extreme high-FE and 6 low-FE pigs were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) in the liver tissues of the 12 individuals, and 507 DEGs were identified between high-FE pigs (HE- group) and low-FE pigs (LE- group). A gene ontology (GO) enrichment and pathway enrichment analysis were performed and revealed that glycolytic metabolism and lipid synthesis-related pathways were significantly enriched within DEGs; all of these DEGs were downregulated in the HE- group. Moreover, Weighted gene co-expression analysis (WGCNA) revealed that oxidative phosphorylation, thermogenesis, and energy metabolism-related pathways were negatively related to HE- group, which might result in lower energy consumption in higher efficiency pigs. These results implied that the higher FE in the HE- group may be attributed to a lower glycolytic, energy consumption and lipid synthesizing potential in the liver. Furthermore, our findings suggested that the inhibition of lipid synthesis and glucose metabolic activity in the liver may be strategies for improving the FE of DLY pigs.
Project description:Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.
Project description:Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs.
1000-01-01 | S-EPMC5366906 | BioStudies
Project description:RNA-seq of small intestine tissues in divergent feed efficiency DLY pigs
| PRJNA553821 | ENA
Project description:RNA-seq of small intestine tissues in divergent feed efficiency DLY pigs
Project description:Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs (P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia-Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome.
Project description:BACKGROUND:Improving feed efficiency (FE) is a major challenge in pig production. This complex trait is characterized by a high variability. Therefore, the identification of predictors of FE may be a relevant strategy to reduce phenotyping efforts in breeding and selection programs. The aim of this study was to investigate the suitability of expressed muscle genes in prediction of FE traits in growing pigs. The approach considered different transcriptomics experiments to cover a large range of FE values and identify reliable predictors. RESULTS:Microarrays data were obtained from longissimus muscles of two lines divergently selected for residual feed intake (RFI). Pigs (n?=?71) from three experiments belonged to generations 6 to 8 of selection, were fed either a diet with a standard composition or a diet rich in fiber and lipids, received feed ad libitum or at restricted level, and weighed between 80 and 115?kg at slaughter. For each pig, breeding value for RFI was estimated (RFI-BV), and feed conversion ratio (FCR) and energy-based feed conversion ratio (FCRe) were calculated during the test periods. Gradient boosting algorithms were used on the merged muscle transcriptomes to identify very important predictors of FE traits. About 20,405 annotated molecular probes were commonly expressed in longissimus muscle across experiments. Six to 267 expressed muscle genes covering a variety of biological processes were found as important predictors for RFI-BV (R2?=?0.63-0.65), FCR (R2?=?0.61-0.70) and FCRe (R2?=?0.49-0.52). The error of prediction was less than 8% for FCR. Altogether, 56 predictors were common to RFI-BV and FCR. Expression levels of 24 target genes were further measured by qPCR. Linear regression confirmed the good accuracy of combining mRNA levels of these genes to fit FE traits (RFI-BV: R2?=?0.73, FRC: R2?=?0.76; FCRe: R2?=?0.75). Stepwise regression procedure highlighted 10 genes (FKBP5, MUM1, AKAP12, FYN, TMED3, PHKB, TGF, SOCS6, ILR4, and FRAS1) in a linear combination predicting FCR and FCRe. In addition, FKBP5 and expression levels of five other genes (IGF2, SERINC3, CSRNP3, EZR and RPL16) significantly contributed to RFI-BV. CONCLUSION:It was possible to identify few genes expressed in muscle that might be reliable predictors of feed efficiency.
Project description:Feed efficiency (FE) is an indicator of efficiency in converting energy from feed into a tissue that is of major environmental and economic significance.This study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE.
Project description:Feed efficiency (FE) appears to vary even within closely related pigs, and may be partly affected by the diversity in the composition and function of gut microbes. To investigate the components and functional differences of gut microbiota of low and high FE pigs, high throughput sequencing and de novo metagenomics were performed on pig cecal contents. Pigs were selected in pairs with low and high feed conversion ratio. The microorganisms of individuals with different FE were clustered according to diversity. The genus Prevotella was the most enriched in both groups, and the abundance of species Prevotella sp. CAG:604 was significantly increased in low efficiency individuals compared to that in animals showing high efficiency. In contrast, other differential species, including lactic acid bacteria, were all enriched in the group with good feeding characteristics. Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes databases demonstrated that differential genes for the metabolism of carbohydrates were most abundant in both groups, but pathways of pyruvate-related metabolism were more intense in pigs with higher FE. All these data indicated that the microbial environment was closely related to the growth traits of pigs, and regulating microbial composition could aid developing strategies to improve FE for pigs.