Using genomic prediction for footrot resistance in sheep based on case-control industry data

Footrot is a highly contagious hoof disease of sheep and other ungulates that has substantial welfare and economic impacts. The extent to which animals are affected by footrot is heritable. However, there are some significant operational limitations to applying traditional pedigree-based selection methods for increasing resistance to footrot. The New Zealand Merino sheep industry have investigated genomic tools in order to use unpedigreed industry animals with footrot phenotypes to predict genomic breeding values. It is imperative to evaluate the accuracy of such genomic predictions. Using cross-validation techniques and a range of reference data sets, we demonstrated a wide range in the average accuracy of prediction for genomic breeding values (GBVs). These were highest with large reference data sets (which included contrasts within flock) and were reduced with lower reference data set size and when predictions were made for flocks outside the reference set. Further analyses will be performed when industry genotypic data are finalised, including validation for sires in ram breeding flocks. However, this preliminary study suggests that there will be some merit for genomic selection against footrot based on industry data.