Strong applied breeding programs rely on carefully balancing the management of genetic diversity with maximising genetic gain. Multiple approaches exist to optimise different decision-making needs within a breeding program, which are often either compelling in theory, but challenging to apply, or are not designed with the specific needs of aquaculture breeding and species-specific reproductive biology in mind.
Based on real-world experience delivering industry-scale aquaculture breeding programs, we highlight the importance of developing efficient and flexible decision support tools to select and direct individual-level crossing of genetically superior broodstock, and to electronically capture data generated during spawning activities. This presentation demonstrates the value of using fast and efficient Optimum Contribution Selection and Simulated Annealing approaches in aquaculture breeding programs. We give particular emphasis on the needs of various aquaculture species and provide examples of the specific biological and practical challenges encountered in Salmo salar, Penaeus vannamei, Penaeus monodon and Pangasianodon hypophthalmus breeding programs during the development of the CSIRO Dating Service software. We also highlight the types of user-controlled parameters that provide practitioners the ability to adapt to the dynamic needs of aquaculture breeding programs when preparing broodstock candidate lists and mate plans. Finally, we demonstrate how accurate and efficient data capture can be used to dynamically adjust subsequent mating plans, to ensure the overall genetic gain and diversity levels remain balanced to achieve a program’s strategic goals.