An algorithm for efficient constrained mate selection

Background: Mate selection can be used as a framework to balance key technical, cost and logistical issues while implementing a breeding program at a tactical level. The resulting mating lists accommodate optimal contributions of parents to future generations, in conjunction with other factors such as progeny inbreeding, connection between herds, use of reproductive technologies, management of the genetic distribution of nominated traits, and management of allele/genotype frequencies for nominated QTL/markers. Methods: This paper describes a mate selection algorithm that is widely used and presents an extension that makes it possible to apply constraints on certain matings, as dictated through a group mating permission matrix. Results: This full algorithm leads to simpler applications, and to computing speed for the scenario tested, which is several hundred times faster than the previous strategy of penalising solutions that break constraints. Conclusions: The much higher speed of the method presented here extends the use of mate selection and enables implementation in relatively large programs across breeding units.