A mating method accounting for inbreeding and multi-trait selection in dairy cattle populations

Selection in dairy cattle populations usually takes into account both the breed profiles for many traits and their overall estimated breeding values (EBV). This can result in effective contributions of breeding animals departing substantially from contributions optimised for saving future genetic variability. In this work, we propose a mating method that considers not only inbreeding but also the detailed EBV of progeny or the EBV of sires in reference to acceptance thresholds. Penalties were defined for inbreeding and for inadequate EBV profiles. Relative reductions of penalties yielded by any mating design were expressed on a scale ranging from 0 to 1. A value of 0 represented the average performance of random matings and a value of 1 represented the maximal reduction allowed by a specialized, single-penalty, mating design. The core of the method was an adaptative simulated annealing, where the maximized function was the average of both ratios, under the constraints that both relative penalty reductions should be equal and that the within-herd concentration criterion should be equal to a predefined reasonable value. The method was tested on two French dairy cattle populations originating from the same AI organization. The optimised mating design allowed substantial reductions of penalty: 70% and 64% for the Holstein and the Normandy populations, respectively. Thus, this mating method decreased inbreeding and met various demands from breeders.