Genome-wide identification of genetic defects in innate disease resistance genes of swine

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Infectious diseases and their associated impact on growth performance and production are a significant economic concern in Canadian swine production. It is a multifactorial problem, with various genetic and environmental influences. Currently, there are few genetic markers to assist selection for better disease resistance and growth performance. Within a herd, poor performing pigs may carry genetic defects in one or more essential liver proteins involved in innate disease resistance, and these could contribute negatively to complex polygenic production traits. We are taking a functional genomics approach to discover gene defects that interfere with innate immune factors that could limit health and production. Previously we have found disease-associated single-nucleotide polymorphisms (SNPs) that impair structure, function and/or expression of innate immune proteins produced in the liver. The current project would use a genome-wide expression microarray approach to identify and compare levels of hepatic expression of genes involved in innate immunity in pigs. The promoter region of genes of interest will be sequenced and examined for the presence of SNPs associated with altered expression. The impact of identified gene defects (SNPs) on innate disease resistance to common infectious diseases and altered growth performance will be investigated using new and archived DNA samples from pigs for which ancillary diagnostic and/or performance information is available. This will allow the creation of a SNP panel which will be run on large numbers of pigs with detailed health and production data to determine the effect of selection for increased innate disease resistance on overall production. Ultimately any SNPs of proven value would be included in genetic selection strategies that will improve overall production, improve swine welfare, increase growth performance and decrease the use of antibiotics in swine production which will have societal and production benefits.