Identifying genes and mutations related to health and disease resistance in Norwegian pigs

The aim of this project is to identify genes and mutations that make pigs healthier and more resistant to diseases. Breeding for disease resistance is difficult because it is hard to measure how healthy a pig is, and we do not know much about the genes that affect this. Increased knowledge on genes and mutations affecting resistance to disease will be an alternative to phenotyping because genotyping the pigs would give an answer to how susceptible they are to diseases. Our approach is to combine gene expression data with genotyping data and functional testing to identify mutations related to health and disease resistance. The gene expression data will first be used in differential expression analysis to identify new genes and confirm mutations from literature. The gene expression data will thereafter be integrated with genotype data from the same animals to identify regulatory mutations, i.e. mutations that affect the expression of genes. Putative regulatory mutations that are identified will be tested using an expression assay in pig cells to find the mutations with a functional effect on regulatory activity. The combination of differential expression analyses and identification of regulatory mutations will allow us to find new variation in the genome that can be implemented in selection for healthier animals.

The aim of this project is to identify genes and mutations which are associated with health and disease resistance in pigs and to include these on our custom genotyping chip to enable selection of the best animals as parents for the next generation. This will allow us to breed for better health, lower greenhouse gas emissions and contribute to food safety by less use of antibiotics. The pig production industry is aiming for sustainable production and good food safety through focus on welfare and disease resistance. Breeding for traits related to disease resistance is, however, difficult because high-quality phenotypes are difficult to measure and knowledge of the genes and mutations underlying these traits to a large degree is unknown. Having information of mutations influencing traits such as disease resistance/tolerance is an alternative to phenotyping as genotyping the pigs would be enough to indicate their susceptibility to disease. By collecting new data and testing new technologies and pipelines we want to i) identify differentially expressed genes where we use genotypes as intermediate phenotypes to bridge the gap between disease and underlying mutation for diseases where we do not have phenotypes , ii) identify mutations affecting gene expression for health related traits where we have phenotypes available, and ii) verify genes and mutations that can be used in breeding for better disease resistance and health.