Contribution of Early-Postmortem Proteome and Metabolome to Ultimate pH and Pork Quality

This study's objectives were to identify how subtle differences in ultimate pH relate to differences in pork quality and to understand how early-postmortem glycolysis contributes to variation in ultimate pH. The hypothesis was that elements in early-postmortem longissimus thoracis et lumborum proteome and metabolome could be used to predict quality defects associated with pH decline. Temperature and pH of the longissimus thoracis et lumborum were measured at 45 min, 24 h, and 14 d postmortem. Quality measurements were made after 14 d of aging. Groups were classified as normal pH (NpH; x̄ = 5 . 59 [5.53–5.67]; NpH, n = 10) and low pH (LpH; x̄ = 5 . 42 [5.38–5.45]; LpH, n = 10) at 14 d postmortem. Metabolites from 45 min postmortem were identified using GC-MS. Relative differences between proteins were quantified with two-dimensional difference in gel electrophoreses, and spots were identified with MALDI-MS. Western blot analyses were used to measure phosphofructokinase, peroxiredoxin-2, and reduced and non-reduced adenosine monophosphate deaminase-2 at 45 min and 14 d postmortem. Ultimate pH classification did not affect 45-min-postmortem pH (P = 0.64); 14-d pH was different between groups (P < 0.01). NpH had less purge loss (P < 0.01), was darker (P < 0.01), had lower star probe (P < 0.01), and had less intact day-7 desmin (P = 0.02). More pyruvate (P = 0.01) and less lactate (P = 0.09) was observed in NpH, along with more soluble lactate dehydrogenase (P = 0.03) and pyruvate kinase (P < 0.10). These observations indicate that differences in enzyme abundance or solubility may produce more pyruvate and less lactate. Fructose 6-phosphate was more abundant (P = 0.08) in the LpH group, indicating that phosphofructokinase may be involved in glycolytic differences. Furthermore, greater abundance of heat shock proteins, peroxiredoxin-2 (P = 0.02), and malate (P = 0.01) early postmortem all suggest differences in mitochondrial function and oxidative stability that contribute to quality differences. These results show that even subtle changes in ultimate pH can influence pork quality. The proteome and metabolome at 45 min postmortem are associated with variation in the extent of pH decline.

Differentially expressed mRNAs, proteins and miRNAs associated to energy metabolism in skeletal muscle of beef cattle identified for low and high residual feed intake

Background

Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information regarding differences in proteins involved in the energy metabolism of the skeletal muscle in beef cattle divergently identified for feed efficiency is scarce. In this study, we aimed to investigate energy metabolism of skeletal muscle of Nellore beef cattle, identified for low and high residual feed intake using a proteomics approach. We further assessed the expression of candidate microRNAs as a one of the possible mechanisms controlling the biosynthesis of the proteins involved in energy metabolism that were differentially abundant between high and low residual feed intake animals.

Results

A greater abundance of 14–3-3 protein epsilon (P = 0.01) was observed in skeletal muscle of residual feed intake (RFI) high animals (RFI-High). Conversely, a greater abundance of Heat Shock Protein Beta 1 (P < 0.01) was observed in the skeletal muscle of RFI-Low cattle. A greater mRNA expression of YWHAE, which encodes the 14–3-3 protein epsilon, was also observed in the skeletal muscle of RFI-High animals (P = 0.01). A lower mRNA expression of HSPB1, which encodes the Heat Shock Protein Beta 1, was observed in the skeletal muscle of RFI-High animals (P = 0.01). The miR-665 was identified as a potential regulator of the 14–3-3 protein epsilon, and its expression was greater in RFI-Low animals (P < .001). A greater expression of miR-34a (P = 0.01) and miR-2899 (P < .001) was observed in the skeletal muscle of RFI-High animals, as both miRNAs were identified as potential regulators of HSPB1 expression.

Conclusion

Our results show that Nellore cattle divergently identified for feed efficiency by RFI present changes in the abundance of proteins involved in energy expenditure in skeletal muscle. Moreover, our data point towards that miR-665, miR34a and miR-2899 are likely involved in controlling both 14-3-3 epsilon and HSPB1 proteins identified as differentially abundant in the skeletal muscle of RFI-High and RFI-Low Nellore cattle.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5890-z) contains supplementary material, which is available to authorized users.

A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency

BACKGROUND

The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle of pigs divergent for feed efficiency, thus improving our understanding of the molecular mechanisms influencing feed efficiency and enabling the identification of candidate biomarkers. Residual feed intake (RFI) was calculated for two populations of pigs from two different farms of origin/genotype. The 6 most efficient (LRFI) and 6 least efficient (HRFI) animals from each population were selected for further analysis of Longissimus Dorsi muscle (n = 22) and liver (n = 23). Transcriptomic data were generated from liver and muscle collected post-slaughter.

RESULTS

The transcriptomic data segregated based on the RFI value of the pig rather than genotype/farm of origin. A total of 6463 genes were identified as being differentially expressed (DE) in muscle, while 964 genes were identified as being DE in liver. Genes that were commonly DE between muscle and liver (n = 526) were used for the multi-tissue analysis. These 526 genes were associated with protein targeting to membrane, extracellular matrix organisation and immune function. In the muscle-only analysis, genes associated with RNA processing, protein synthesis and energy metabolism were down regulated in the LRFI animals while in the liver-only analysis, genes associated with cell signalling and lipid homeostasis were up regulated in the LRFI animals.

CONCLUSIONS

Differences in the transcriptome segregated on pig RFI value rather than the genotype/farm of origin. Multi-tissue analysis identified that genes associated with GO terms protein targeting to membrane, extracellular matrix organisation and a range of terms relating to immune function were over represented in the differentially expressed genes of both liver and muscle.

Enhanced expression of proteins involved in energy production and transfer in breast muscle of pedigree male broilers exhibiting high feed efficiency

In cells with fluctuating energy demand (e.g., skeletal muscle), a transfer system of proteins across the inner and outer mitochondrial membranes links mitochondrial oxidative phosphorylation to cytosolic phosphorylated creatine (PCr) that serves as a phosphate reservoir for rapid repletion of cytosolic adenosine triphosphate (ATP). Crucial proteins of this energy transfer system include several creatine kinase (CK) isoforms found in the cytosol and mitochondria. In a recent proteomic study (Kong et al., 2016), several components of this system were up-regulated in high feed efficiency (FE) compared to low FE breast muscle; notably adenine nucleotide translocase (ANT), voltage dependent activated channel (VDAC), the brain isoform of creatine kinase (CK-B), and several proteins of the electron transport chain. Reexamination of the original proteomic dataset revealed that the expression of two mitochondrial CK isoforms (CKMT1A and CKMT2) had been detected but were not recognized by the bioinformatics program used by Kong et al. (2016a). The CKMT1A isoform was up-regulated (7.8-fold, P = 0.05) in the high FE phenotype but there was no difference in CKMT2 expression (1.1-fold, P = 0.59). From these findings, we hypothesize that enhanced expression of the energy production and transfer system in breast muscle of the high FE pedigree broiler male could be fundamentally important in the phenotypic expression of feed efficiency.

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.

Improving efficiency in meat production

Selective breeding and improved nutritional management over the past 20–30 years has resulted in dramatic improvements in growth efficiency for pigs and poultry, particularly lean tissue growth. However, this has been achieved using high-quality feed ingredients, such as wheat and soya that are also used for human consumption and more recently biofuels production. Ruminants on the other hand are less efficient, but are normally fed poorer quality ingredients that cannot be digested by human subjects, such as grass or silage. The challenges therefore are to: (i) maintain the current efficiency of growth of pigs and poultry, but using more ingredients not needed to feed the increasing human population or for the production of biofuels; (ii) improve the efficiency of growth in ruminants; (iii) at the same time produce animal products (meat, milk and eggs) of equal or improved quality. This review will describe the use of: (a) enzyme additives for animal feeds, to improve feed digestibility; (b) known growth promoting agents, such as growth hormone, β-agonists and anabolic steroids, currently banned in the European Union but used in other parts of the world; (c) recent transcriptomic studies into molecular mechanisms for improved growth efficiency via low residual feed intake. In doing so, the use of genetic manipulation in animals will also be discussed.

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.

Whole Blood Transcriptomics Is Relevant to Identify Molecular Changes in Response to Genetic Selection for Feed Efficiency and Nutritional Status in the Pig

The molecular mechanisms underlying feed efficiency need to be better understood to improve animal efficiency, a research priority to support a competitive and sustainable livestock production. This study was undertaken to determine whether pig blood transcriptome was affected by differences in feed efficiency and by ingested nutrients. Growing pigs from two lines divergently selected for residual feed intake (RFI) and fed isoproteic and isocaloric diets contrasted in energy source and nutrients were considered. Between 74 and 132 days of age, pigs (n = 12 by diet and by line) received a regular diet rich in cereals and low in fat (LF) or a diet where cereals where partially substituted by lipids and fibers (HF). At the end of the feeding trial, the total number of white blood cells was not affected by the line or by the diet, whereas the red blood cell number was higher (P<0.001) in low RFI than in high RFI pigs. Analysis of the whole blood transcriptome using a porcine microarray reveals a higher number of probes differentially expressed (DE) between RFI lines than between diets (2,154 versus 92 probes DE, P<0.01). This corresponds to 528 overexpressed genes and 477 underexpressed genes in low RFI pigs compared with high RFI pigs, respectively. Overexpressed genes were predominantly associated with translational elongation. Underexpressed genes were mainly involved in the immune response, regulation of inflammatory response, anti-apoptosis process, and cell organization. These findings suggest that selection for RFI has affected the immune status and defense mechanisms of pigs. Genes DE between diets were mainly related to the immune system and lipid metabolism. Altogether, this study demonstrates the usefulness of the blood transcriptome to identify the main biological processes affected by genetic selection and feeding strategies.