Plasma protein levels of young healthy pigs as indicators of disease resilience

Lay Summary A challenge of selection for disease resilience is that it is difficult to directly select pigs that have greater resilience to multiple diseases in the healthy nucleus herd environment which is essential for breeding programs. A possible alternative is to select an indicator trait or marker that can be measured in a healthy setting, is heritable, and is associated with the genetics of disease resilience. In this study, we investigated plasma protein levels measured on young healthy pigs as indicator traits to select for disease resilience. For this purpose, we used plasma proteome data collected prior to the natural exposure of nursery pigs to multiple diseases, performed phenotypic and genetic quantitative analyses, and investigated their relationships with disease resilience. Our results suggest that plasma protein levels of young healthy pigs have the potential as biomarkers to select for disease resistance. Selection for disease resilience, which refers to the ability of an animal to maintain performance when exposed to disease, can reduce the impact of infectious diseases. However, direct selection for disease resilience is challenging because nucleus herds must maintain a high health status. A possible solution is indirect selection of indicators of disease resilience. To search for such indicators, we conducted phenotypic and genetic quantitative analyses of the abundances of 377 proteins in plasma samples from 912 young and visually healthy pigs and their relationships with performance and subsequent disease resilience after natural exposure to a polymicrobial disease challenge. Abundances of 100 proteins were significantly heritable (false discovery rate (FDR) <0.10). The abundance of some proteins was or tended to be genetically correlated (r(g)) with disease resilience, including complement system proteins (r(g) = -0.24, FDR = 0.001) and IgG heavy chain proteins (r(g) = -0.68, FDR = 0.22). Gene set enrichment analyses (FDR < 0.2) based on phenotypic and genetic associations of protein abundances with subsequent disease resilience revealed many pathways related to the immune system that were unfavorably associated with subsequent disease resilience, especially the innate immune system. It was not possible to determine whether the observed levels of these proteins reflected baseline levels in these young and visually healthy pigs or were the result of a response to environmental disturbances that the pigs were exposed to before sample collection. Nevertheless, results show that, under these conditions, the abundance of proteins in some immune-related pathways can be used as phenotypic and genetic predictors of disease resilience and have the potential for use in pig breeding and management. Plasma protein levels of young healthy pigs are promising as biomarkers to select for disease resilience.