Management of diversity and inbreeding when importing new stock into an inbred population

This article relates to breeding programs that seek to manage genetic diversity. The method maximizes a multicomponent objective function, applicable across breeding scenarios. However, this paper focuses on breeding decisions following immigration of 10 unrelated individuals into a highly inbred simulated population (F ≈ 0.34). We use Optimal Contribution Selection to maximize retention of genetic diversity. However, some treatments add Coancestry Assortative Mating (CAM). This helps to avoid early dilution of immigrant genetic material, maximizing its ability to contribute to genetic diversity in the longer term. After 20 generations, this resulted in considerably increased genetic diversity, with mean coancestries 59% of what random pairing gave. To manage progeny inbreeding, common practice is to reject matings above an upper limit. As a suboptimal rules-based approach, this resulted in 26% decreased genetic diversity and 8% increased inbreeding in the long term, compared with random pairing. In contrast, including mean progeny inbreeding as a continuous variable in the overall objective function decreased final inbreeding by 37% compared with random pairing. Adding some emphasis on selection for a single trait resulted in a similar pattern of effects on coancestry and inbreeding, with 12% higher trait response under CAM. Results indicate the properties of alternative methods, but we encourage users to do their own investigations of particular scenarios, such as including inbreeding depression. Practical implementation of these methods is discussed: they have been widely adopted in domestic animal breeding and are highly flexible to accommodate a wide range of technical and logistical objectives and constraints.