Uses and implications of field disease data for livestock genomic and genetics studies

Abstract

This paper identifies issues associated with field disease data and their implications on the interpretation of estimated genetic parameters and experimental designs. The main focus is on concepts relating to the impacts of diagnostic test properties and exposure to infection, and how exposure to infection is intricately related to within-herd epidemic dynamics. The following are raised challenges: (i) to more fully understand and describe the dynamic impacts of disease epidemics on genetic interpretations; (ii) to develop statistical methods to jointly estimate epidemiological and genetic parameters from complex epidemiological data; (iii) to develop and explore optimal experimental designs for case-control studies, exploiting field disease data. Solving these problems would add insight to both disease genetic and epidemiological studies, as well as enabling us to better select animals for increased disease resistance.

Keywords: animal; epidemiology; field data; genome wide association analysis; heritability.

Figure 1

Infection probability as a function of dosage level for three hypothetical major-gene genotypes, illustrating how the inferred mode of resistance will change as dosage level changes.

Figure 2

Numbers of infectious animals during the course of an hypothetical epidemic, for three modes of transmission of infection, (i) SI model in which infected animals remain infectious, (ii) SIR model in which infected animals recover so that they are no longer infectious and remain immune to the infection, (iii) SIRS model in which recovered animals lose their immunity and become immunologically susceptible again. Non-zero parameter values are identical for each model. Population size is 1000 animals.