Abstract
Selection for improved host response to infectious disease offers a desirable alternative to chemical treatment but has proven difficult in practice, due to low heritability estimates of disease traits. Disease data from field studies is often binary, indicating whether an individual has become infected or not following exposure to an infectious disease. Numerous studies have shown that from this data one can infer genetic variation in individuals’ underlying susceptibility. In a previous study, we showed that with an indirect genetic effect (IGE) model it is possible to capture some genetic variation in infectivity, if present, as well as in susceptibility. Infectivity is the propensity of transmitting infection upon contact with a susceptible individual. It is an important factor determining the severity of an epidemic. However, there are severe shortcomings with the Standard IGE models as they do not accommodate the dynamic nature of disease data. Here we adjust the Standard IGE model to (1) make expression of infectivity dependent on the individuals’ disease status (Case Model) and (2) to include timing of infection (Case-ordered Model). The models are evaluated by comparing impact of selection, bias, and accuracy of each model using simulated binary disease data. These were generated for populations with known variation in susceptibility and infectivity thus allowing comparisons between estimated and true breeding values. Overall the Case Model provided better estimates for host genetic susceptibility and infectivity compared to the Standard Model in terms of bias, impact, and accuracy. Furthermore, these estimates were strongly influenced by epidemiological characteristics. However, surprisingly, the Case-Ordered model performed considerably worse than the Standard and the Case Models, pointing toward limitations in incorporating disease dynamics into conventional variance component estimation methodology and software used in animal breeding.
Highlights
Infectious diseases in livestock constitute a major threat to the sustainability of livestock production
We have previously shown (Lipschutz-Powell et al, 2012a) that indirect genetic effect (IGE) models developed for production traits provide a promising tool for estimating genetic variation underlying binary disease data
The hypothesis of this study was that extending an IGE model to allow for disease dynamics ought to improve its ability to estimate genetic variation in susceptibility www.frontiersin.org
Summary
Infectious diseases in livestock constitute a major threat to the sustainability of livestock production. A major barrier to closing the genotype– phenotype gap is uncovering the genetic variance underlying disease phenotypes. Genetic analyses require large sample sizes and disease phenotypes often need to be obtained from field data. Bishop and Woolliams (2010) have demonstrated that shortcomings of current estimation methods for field data which fail to take epidemiological considerations into account cause seemingly low heritability estimates for disease traits in domestic livestock. In a previous study (Lipschutz-Powell et al, 2012a), it was demonstrated that conventional statistical models used for variance component estimation cannot capture genetic variation in host infectivity, when present in disease data, as they consider exposure as an environmental factor
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