Multiple trait linkage across flocks

To estimate contrasts between groups of animals or herds or flocks, or to compare groups of animals or herds or flocks, there has to be genetic linkage between those groups. A common problem for all extensively farmed livestock is the absence of such linkage. The main objective of assessing linkage is to determine the accuracy of comparisons between EBVs estimated in different herds or flocks. Several methods have been proposed to evaluate connectedness. However if the main objective of a linkage statistic is to identify flocks where EBVs are poorly contrasted in comparison to EBVs from other flocks, then a method which assesses the accuracy of such comparisons is most appropriate. This paper describes and gives an example from a multiple trait linkage analysis tool for data extracted from the Sheep Genetics Australia database.