Insights into the genetic architecture of the porcine immune system based on SNP chip and whole genome sequencing data

Animal health and welfare are key challenges facing pig breeding and production. In this regard, the immune system and immune reaction are important determinants to focus on. Among the multitude of parameters that can be investigated to study these trait complexes, hematological parameters and cytokines are promising phenotypes. Moderate to high heritability of several immune relevant traits was demonstrated in various breeds and developmental stages. However, the genetic architecture of these traits needs extensive clarification to identify genomic regions with a biological relevance for the immunocompetence in piglets and growing pigs. <br> The overall aim of this thesis was to gain insights into the genetic background of immune relevant traits in the maternal pig lines Landrace (LR) and Large White (LW) using single nucleotide polymorphism (SNP) chip data and whole genome sequencing (WGS) data. The results point out a way to properly include immune relevant traits into balanced pig breeding. The phenotypes investigated include the complete and differential blood count, eight cytokines and the acute phase protein haptoglobin recorded under non-challenging conditions in herds kept under high hygienic standards. <br> The first study was based on SNP chip data from 535 LR and 461 LW piglets. Genome-wide association studies were conducted to identify genomic regions associated with immune relevant traits. A total of 477 significant SNPs were identified, which are partly overlapping with previously identified immune-related or other economically important quantitative trait loci. The results uncovered breed differences as well as putative pleiotropic effects. Annotation revealed a few SNPs to have a putative impact on the protein. According to their role in functional pathways or indications in other species, the genes TMBIM1, RBMS3, ROMO1, FGF6, AKAP3 and CTC1 were highlighted as putative candidate genes. <br> In order to benefit from advanced technologies in animal genetics, a subset of 57 animals was selected for WGS and imputation. The second study demonstrates the selection process, combining haplotype- and pedigree methods. The effectiveness of the combined approach (C) for animal selection was measured by the imputation accuracy. This highlighted the benefits of C in the LR and LW populations, compared to alternative strategies, and became particularly apparent in low-frequency markers. <br> The third study brings together SNP chip data, WGS data and imputation in the context of the porcine immunocompetence. The WGS data set was used as reference panel for within-breed imputation. Previous results based on SNP chip data were clustered in 33 (LR) and 34 (LW) windows, which were tested for associations based on imputed WGS (iWGS) data. Using iWGS data, the reliability of genomic regions was mostly verified and detailed insights into the genetic basis were achieved. In this context, evidence for 27 windows in each breed was strengthened. Additionally, the set of putative immune-related candidate genes was expanded and variants with a notable impact on the protein function were identified. <br> In conclusion, genomic data of SNP chip and WGS type in combination with immune relevant phenotypes play a central role in uncovering the genetic foundation of the porcine immunocompetence. The identified genomic regions within this thesis make an important contribution and show potential for breeding-based improvement of the porcine immune system in maternal pig lines.