Invited Review : Measurable biomarkers linked to meat quality from different pig production systems

Biological processes underlie all livestock traits, including post-mortem meat quality traits. Biomarkers are molecular components of the biological processes showing differential expression associated with the phenotype of the trait. The phenotypes of the meat quality traits are determined by the animal's genotype interacting with the environment affecting the expression of the genome. The omics technologies enable measuring the expression of the genome at all levels: Transcriptome, proteome, and metabolome. Associations between the phenotype of the traits and expressions measured with the omics techniques are a first step in developing biomarkers. Biomarkers enable the monitoring, diagnosis, and prediction of changes in meat quality related to external (environmental, e.g. feed and animal management conditions) stimuli and interactions with the genotype. In this paper we review the development of biomarkers for meat quality of pigs in diverse pig breeds, environments, and pork production chains.</p

Omega-3 alpha-linolenic fatty acid affects the level of telomere binding protein trf1 in porcine skeletal muscle

Omega-3 fatty acids are health-promoting nutrients that contribute to the amelioration of age-related diseases. Recent studies have reported the role of these fatty acids in the aging process, explicitly impacting telomere biology. The shelterin protein complex, located at the extremities of chromosomes, ensures telomere protection and length regulation. Here, we analyzed the impact of dietary omega-3 alpha-linolenic fatty acid from linseed oil on skeletal muscle telomere biology using an animal model of female pigs. Fifteen animals were supplemented with linseed oil for nine weeks and an equal number of individuals were fed with a control diet. Linseed-oil-supplemented animals showed an increased level of alpha-linolenic acid in skeletal muscles compared to control animals. There was no difference between groups in the telomere length measured in leukocytes and muscles. However, muscles of the linseed-oil-supplemented pigs showed lower levels of the shelterin TRF1 protein compared to the control group. Our results suggest that omega-3 linolenic acid counteracts the elevation of TRF1 levels, which increase with age and due to the presence of reactive oxygen species in muscle. The observed effect may be due to attenuation of oxidative stress.</p

Adaptation of livestock to new diets using feed components without competition with human edible protein sources—a review of the possibilities and recommendations

Livestock feed encompasses both human edible and human inedible components. Human edible feed components may become less available for livestock. Especially for proteins, this calls for action. This review focuses on using alternative protein sources in feed and protein efficiency, the expected problems, and how these problems could be solved. Breeding for higher protein efficiency leading to less use of the protein sources may be one strategy. Replacing (part of) the human edible feed components with human inedible components may be another strategy, which could be combined with breeding for livestock that can efficiently digest novel protein feed sources. The potential use of novel protein sources is discussed. We discuss the present knowledge on novel protein sources, including the consequences for animal performance and production costs, and make recommendations for the use and optimization of novel protein sources (1) to improve our knowledge on the inclusion of human inedible protein into the diet of livestock, (2) because cooperation between animal breeders and nutritionists is needed to share knowledge and combine expertise, and (3) to investigate the effect of animal-specific digestibility of protein sources for selective breeding for each protein source and for precision feeding. Nutrigenetics and nutrigenomics will be im-portant tools

Breeding goal traits accounting for feed intake capacity and roughage or concentrate intake separately

Current breeding tools aiming to improve feed efficiency use definitions based on total dry matter intake (DMI); for example, residual feed intake or feed saved. This research aimed to define alternative traits using existing data that differentiate between feed intake capacity and roughage or concentrate intake, and to investigate the phenotypic and genetic relationships among these traits. The data set contained 39,017 weekly milk yield, live weight, and DMI records of 3,164 cows. The 4 defined traits were as follows: (1) Feed intake capacity (FIC), defined as the difference between how much a cow ate and how much she was expected to eat based on diet satiety value and status of the cow (parity and lactation stage); (2) feed saved (FS), defined as the difference between the measured and the predicted DMI, based on the regression of DMI on milk components within experiment; (3) residual roughage intake (RRI), defined as the difference between the measured and the predicted roughage intake, based on the regression of roughage intake on milk components and concentrate intake within experiment; and (4) residual concentrate intake (RCI), defined as the difference between the measured and the predicted concentrate intake, based on the regression of concentrate intake on milk components and roughage intake within experiment. The phenotypic correlations were −0.72 between FIC and FS, −0.84 between FS and RRI, and −0.53 between FS and RCI. Heritability of FIC, FS, RRI, and RCI were estimated to be 0.21, 0.12, 0.15, and 0.03, respectively. The genetic correlations were −0.81 between FS and FIC, −0.96 between FS and RRI, and −0.25 between FS and RCI. Concentrate intake and RCI had low heritability. Genetic correlation between DMI and FIC was 0.98. Although the defined traits had moderate phenotypic correlations, the genetic correlations between DMI, FS, FIC, and RRI were above 0.79 (in absolute terms), suggesting that these traits are genetically similar. Therefore, selecting for FIC is expected to simply increase DMI and RRI, and there seems to be little advantage in separating concentrate and roughage intake in the genetic evaluation, because measured concentrate intake was determined by the feeding system in our data and not by the genetics of the cow

Sanitary Conditions on the Farm Alters Fecal Metabolite Profile in Growing Pigs

The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrasting sanitary conditions and the associated subclinical health status of pigs. We analyzed fecal metabolite profiles by nuclear magnetic resonance (1 H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions differed in fecal metabolites related to the degradation of dietary starch, metabolism of the gut microbiome, and degradation of components of animal (host) origin. The metabolites that differed significantly (FDR < 0.1) were from metabolic processes involved in either maintaining nutrient digestive capacity, including purine metabolism, energy metabolism, bile acid breakdown and recycling, or immune system metabolism. The results show that the fecal metabolite profiles reflect the sanitary conditions under which the pigs are kept. The fecal metabolite profiles closely resembled the profiles of metabolites found in the colon of pigs. Fecal valerate and kynurenic acid could potentially be used as “non-invasive” biomarkers of immune or inflammatory status that could form the basis for monitoring subclinical health status in pigs

Sanitary Conditions Affect the Colonic Microbiome and the Colonic and Systemic Metabolome of Female Pigs

Differences in sanitary conditions, as model to induce differences in subclinical immune stimulation, affect the growth performance and nutrient metabolism in pigs. The objective of the present study was to evaluate the colonic microbiota and the colonic and systemic metabolome of female pigs differing in health status induced by sanitary conditions. We analyzed blood and colon digesta metabolite profiles using Nuclear Magnetic Resonance (1H NMR) and Triple quadrupole mass spectrometry, as well as colonic microbiota profiles. 1H NMR is a quantitative metabolomics technique applicable to biological samples. Weaned piglets of 4 weeks of age were kept under high or low sanitary conditions for the first 9 weeks of life. The microbiota diversity in colon digesta was higher in pigs subjected to low sanitary conditions (n = 18 per treatment group). The abundance of 34 bacterial genera was higher in colon digesta of low sanitary condition pigs, while colon digesta of high sanitary status pigs showed a higher abundance for four bacterial groups including the Megasphaera genus (p < 0.003) involved in lactate fermentation. Metabolite profiles (n = 18 per treatment group) in blood were different between both groups of pigs. These different profiles suggested changes in general nutrient metabolism, and more specifically in amino acid metabolism. Moreover, differences in compounds related to the immune system and responses to stress were observed. Microbiome-specific metabolites in blood were also affected by sanitary status of the pigs. We conclude that the microbiome composition in colon and the systemic metabolite profiles are affected by sanitary conditions and related to suboptimal health. These data are useful for exploring further relationships between health, metabolic status and performance and for the identification of biomarkers related to health (indices) and performance

Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels

Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance

Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response

Heat stress (HS) negatively affects chicken performance. Agricultural expansion will happen in regions that experience high ambient temperatures, where fast-growing commercial chickens are vulnerable. Indigenous chickens of such regions, due to generations of exposure to environmental challenges, might have higher thermal tolerance. In this study, two indigenous chicken ecotypes, from the hot and humid Mombasa (lowland) and the colder Naivasha (highland) regions, were used to investigate the effects of acute (5 h, 35°C) and chronic (3 days of 35°C for 8 h/day) HS on the cardiac and skeletal muscle, through RNA sequencing. The rectal temperature gain and the number of differentially expressed genes (DEGs) [False Discovery Rate (FDR) < 0.05] were two times higher in the acute stage than in the chronic stage in both ecotypes, suggesting that cyclic exposure to HS can lead to adaptation. A tissue- and stage-specific difference in response to HS was observed, with peroxisome proliferator-activated-receptor (PPAR) signaling and mitogen-activate protein kinase (MAPK) signaling pathways, enriched in heart and skeletal muscle, respectively, and the p53 pathway enriched only in the acute stage in both tissues. The acute and chronic stage DEGs were integrated by a region-specific gene coexpression network (GCN), and genes with the highest number of connections (hub genes) were identified. The hub genes in the lowland network were CCNB2, Crb2, CHST9, SESN1, and NR4A3, while COMMD4, TTC32, H1F0, ACYP1, and RPS28 were the hub genes in the highland network. Pathway analysis of genes in the GCN showed that p53 and PPAR signaling pathways were enriched in both low and highland networks, while MAPK signaling and protein processing in endoplasmic reticulum were enriched only in the gene network of highland chickens. This shows that to dissipate the accumulated heat, to reduce heat induced apoptosis, and to promote DNA damage repair, the ecotypes activated or suppressed different genes, indicating the differences in thermal tolerance and HS response mechanisms between the ecotypes. This study provides information on the HS response of chickens, adapted to two different agro climatic environments, extending our understanding of the mechanisms of HS response and the effect of adaptation in counteracting HS.</p