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Génétique et Génomique de la capacité immunitaire chez le porc : approches eQTL et étude de biomarqueurs sanguins

Abstract : A better understanding of the mechanisms for resistance to pathogens along with the characterization of the immune capacity has become a priority for research in breeding. The overall objective of this PhD project was to use phenotyping, genetic and genomic information to study the genetic architecture of the immune capacity in the pig and to contribute to the identification of genetic markers and blood biomarkers that predict variations of immune parameter levels. The study was focused on three complementary axes and the results obtained were based on the use of data collected as part of the IMMOPIG and SUS_FLORA projects financed by the ANR, for which 450 and 560 piglet cohorts were sampled at 60 days of age, three weeks after vaccination against Mycoplasma hyopneumoniae.We analyzed the genetic determinism of gene expression in the blood using an eGWAS (60K SNP genotyping and blood transcriptome for 242 animals) confirmed in part by an allele specific expression (ASE) of transcripts (RNA-Seq on 38 animals). The eGWAS results showed multiple local (n=2839) and distant associations between the SNP polymorphisms and transcription variations, spread over all the chromosomes. The ASE analyses confirmed the cis genetic control of gene expression, with allele regulation being found for 763 genes. The biological functions associated were notably associated with RNA processing and immunity. The region of the major histocompatibility complex was found particularly rich in eQTL signals and genes with ASE in the blood.We studied the co-variations between immune parameters and blood transcriptomes for 243 individuals. The immune parameters included the blood count, cell subpopulation characterization by flow cytometry, serum assays (reactive C protein, haptoglobin, antibodies specific for Mycoplasma hyopneumoniae), immune response after in vitro stimulation of peripheral blood (phagocytosis, IL1b, IL2, IL6, IL8, IL10, TNFa, INFg cytokines). We confirmed the heritability of numerous immune parameters and identified covariations with gene profiles, providing hypotheses on biomarker candidates.We also led a functional analysis on four animals at 70 days-of-age in order to characterize and compare the transcriptome profiles of peripheral blood and three gut-associated lymphoid tissues (mesenteric lymph nodes, jejunal and ileal Payer’s patches). The RNA-Seq data showed differential expression between tissues; this number was more limited between the two types of Peyer’s patches. Interestingly, among the biological functions enriched by the differentially expressed genes between the Peyer’s patches, we identified the Th1 and Th2 lymphocyte differentiation pathways, which was in agreement with an over-abundance of B lymphocytes in the ileal Peyer’s patches.Together these results provide new information on the understanding of the genetic determinism of immune parameter variations in the pig, the search for causal polymorphisms of these variations and the identification of relevant blood biomarkers for phenotyping immune competence.
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Tatiana Maroilley. Génétique et Génomique de la capacité immunitaire chez le porc : approches eQTL et étude de biomarqueurs sanguins. Biologie animale. Université Paris-Saclay, 2017. Français. ⟨NNT : 2017SACLV097⟩. ⟨tel-01734367⟩

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