Genetic analysis of High Immune Response technology and relationships with disease resilience in pigs

Disease resilience is a viable target for genetic improvement programs in pigs to improve productivity and animal welfare and reduce the use of antibiotics. However, disease resilience is difficult to select for in nucleus breeding programs. Indicator traits that can be measured on (young) pigs without exposure to disease offer possible solutions. The High Immune Response (HIR) technology has been shown to provide such indicator traits in dairy cattle. HIR involves evaluation of antibody-mediated (AMIR) and cell-mediated (CMIR) immune responses. The objectives of this study were to implement HIR technology for young and clinically healthy pigs, to evaluate genetic parameters of, and genomic regions associated with AMIR and CMIR, and estimate genetic correlations of AMIR and CMIR with disease resilience. For the latter, data from a polymicrobial natural disease challenge that pigs were exposed to after HIR evaluation were used. In total, HIR data were collected on 2,295 Yorkshire × Landrace barrows, as well as disease resilience data on these and another 1,800 barrows from the same populations. All pigs had genotypes for 451,389 single-nucleotide polymorphisms (SNPs) across the genome. Both AMIR and CMIR were moderately heritable (0.25 ± 0.06 and 0.20 ± 0.05), with limited evidence of a genetic correlation between them (0.23 ± 0.17). Higher AMIR tended to be genetically correlated with higher growth and health under disease, but the opposite was apparent for CMIR, possibly as a result of the nature of the disease challenge and the clinical disease data that was collected, which tended to emphasize bacterial rather than viral infections. Genetic correlations of AMIR and CMIR with disease resilience traits were also not consistent between two sets of batches of pigs separated in time but this appeared to be the result of genetic differences in disease resilience, possibly because of different disease dynamics, rather than in HIR traits, as the estimate of the genetic correlation between the two sets of batches was low for growth under challenge (0.44 ± 0.38) but high for AMIR (0.86 ± 0.35) and CMIR (0.91 ± 0.48). The major histocompatibility complex was found to explain over 32% of the genetic variation for AMIR, with SNP AX-116767878 explaining the majority of this variation, and was also associated with disease resilience. Three other genomic regions were identified for AMIR, together explaining 12% of genetic variance, while only two regions were identified for CMIR, each explaining less than 2% of genetic variance. All identified regions included genes associated with the immune response. Results suggest that HIR traits, in particular AMIR, are strong candidates as indicator traits that can be measured on young healthy pigs to select for resilience across multiple pathogens.