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While some research has looked into the host genetic response in pigs challenged with specific viruses or bacteria, few studies have explored the expression changes of transcripts in the peripheral blood of sick pigs that may be infected with multiple pathogens on farms. In this study, the architecture of the peripheral blood transcriptome of 64 Duroc sired commercial pigs, including 18 healthy animals at entry to a growing facility (set as a control) and 23 pairs of samples from healthy and sick pen mates, was generated using RNA-Seq technology. In total, 246 differentially expressed genes were identified to be specific to the sick animals. Functional enrichment analysis for those genes revealed that the over-represented gene ontology terms for the biological processes category were exclusively immune activity related. The cytokine-cytokine receptor interaction pathway was significantly enriched. Nine functional genes from this pathway encoding members (as well as their receptors) of the interleukins, chemokines, tumor necrosis factors, colony stimulating factors, activins, and interferons exhibited significant transcriptional alteration in sick animals. Our results suggest a subset of novel marker genes that may be useful candidate genes in the evaluation and prediction of health status in pigs under commercial production conditions. Key words: RNA-Seq, transcriptome, porcine, peripheral blood, cytokine. Résumé : Bien que certains travaux de recherche se soient intéressés aux réponses génétiques chez les porcs confrontés à des virus ou des bactéries spécifiques, peu d'études ont exploré les changements transcriptomiques dans le sang périphérique de porcs malades qui sont potentiellement porteurs de pathogènes multiples dans des conditions d'élevage. Dans ce travail, l'architecture transcriptomique du sang périphérique a été examinée chez 64 porcs Duroc en élevage commercial, incluant 18 animaux sains à leur entrée dans le parc d'engraissement (témoin) et 23 paires d'animaux sains et malades occupant le même enclos, par une approche RNA-Seq. Au total, 246 gènes différentiellement exprimés ont été identifiés comme étant spécifiques aux animaux malades. Une analyse d'enrichissement fonctionnel pour ces gènes a révelé que les termes ontologiques les plus surreprésentés au sein de la catégorie des processus biologiques appartenaient tous au processus immunitaire. Le sentier d'interaction cytokine-récepteur de cytokine était significativement enrichi. Neuf gènes fonctionnels appartenant à ce sentier codant pour des membres (ainsi que leurs récepteurs) des interleukines, des chimiokines, des facteurs nécrosant des tumeurs, des facteurs stimulant les colonies, des activines et des interférons présentaient une altération transcriptionnelle significative chez les animaux malades. Ces résultats suggèrent que certains de ces gènes peuvent constituer de nouveaux marqueurs pouvant servir de gènes candidats pour évaluer et prédire le statut sanitaire des porcs en conditions commerciales d'élevage. [Traduit par la Rédaction] Mots-clés : RNA-Seq, transcriptome, porcin, sang périphérique, cytokine., Introduction Pig (Sus scrofa) is one of the most important domestic animals due to the popularity of pork products in many markets, especially Europe, North America, and China. Infectious disease [...]

In commercial livestock populations, QTL detection methods often use existing half-sib family structures and ignore additional relationships within and between families. We reanalyzed the data from a large QTL confirmation experiment with 10 pig lines and 10 chromosome regions using identity-by-descent (IBD) scores and variance component analyses. The IBD scores were obtained using a Monte Carlo Markov Chain method, as implemented in the LOKI software, and were used to model a putative QTL in a mixed animal model. The analyses revealed 61 QTL at a nominal 5% level (out of 650 tests). Twenty-seven QTL mapped to areas where QTL have been reported, and eight of these exceeded the threshold to claim confirmed linkage (P < 0.01). Forty-two of the putative QTL were detected previously using half-sib analyses, whereas 46 QTL previously identified by half-sib analyses could not be confirmed using the variance component approach. Some of the differences could be traced back to the underlying assumptions between the two methods. Using a deterministic approach to estimate IBD scores on a subset of the data gave very similar results to LOKI. We have demonstrated the feasibility of applying variance component QTL analysis to a large amount of data, equivalent to a genome scan. In many situations, the deterministic IBD approach offers a fast alternative to LOKI. Key Words: Best Linear Unbiased Prediction, Genomes, Least Squares, Pigs, Quantitative Trait Loci, Variance Components

Metabolites in plasma of healthy nursery pigs were quantified using nuclear magnetic resonance. Heritabilities of metabolite concentration were estimated along with their phenotypic and genetic correlations with performance, resilience, and carcass traits in growing pigs exposed to a natural polymicrobial disease challenge. Variance components were estimated by GBLUP. Heritability estimates were low to moderate (0.11 ± 0.08 to 0.19 ± 0.08) for 14 metabolites, moderate to high (0.22 ± 0.09 to 0.39 ± 0.08) for 17 metabolites, and highest for l-glutamic acid (0.41 ± 0.09) and hypoxanthine (0.42 ± 0.08). Phenotypic correlation estimates of plasma metabolites with performance and carcass traits were generally very low. Significant genetic correlation estimates with performance and carcass traits were found for several measures of growth and feed intake. Interestingly the plasma concentration of oxoglutarate was genetically negatively correlated with treatments received across the challenge nursery and finisher (− 0.49 ± 0.28; P < 0.05) and creatinine was positively correlated with mortality in the challenge nursery (0.85 ± 0.76; P < 0.05). These results suggest that some plasma metabolite phenotypes collected from healthy nursery pigs are moderately heritable and genetic correlations with measures of performance and resilience after disease challenge suggest they may be potential genetic indicators of disease resilience. [ABSTRACT FROM AUTHOR]