Genetic selection programmes must maintain a balance between selecting for performance under realistic production conditions and protecting the integrity of the breeding population. Salmonid breeding programmes often maintain nucleus candidates in biosecure freshwater facilities to minimise the risk of a catastrophic loss of genetics that may occur following mass mortality caused by pathogen outbreaks or environmental stresses. Selection for commercial traits can be applied by testing full-siblings of the selection candidates in sea cages, but this design results in reduced breeding value accuracy in the selection candidates causing reduced potential for genetic gain. Whilst genomic selection can, to a large extent, address this shortfall, such approaches are not always feasible in species with limited genomic resources, or in integrated programmes that supply relatively small production volumes, where the cost of high-density genotyping can be prohibitive.
Maintaining some, or all, of the selection candidates in production-like conditions is a viable strategy for maintaining strong rates of genetic progress but comes with substantial biosecurity risks and operational complexity. Deciding on an appropriate breeding programme design requires a detailed understanding of the likely impacts of these choices.
Genetic simulations provide a valuable decision-making framework to test the potential outcomes from contrasting breeding programme designs. We present results from a simulation study examining factors affecting the commercial return when varying proportions of candidates are grown in the production environment and compare these to conventional pedigree-based selection and genomic selection methods. Our results demonstrate that the use of candidates can provide high rates of genetic gain compared to traditional approaches, but optimal design is dependent on the production volume supported.
We illustrate these results with an example from a chinook salmon breeding programme where all candidate are grown in salt-water and spawned directly from sea-cages using a combination of phenotypic pre-selection and genetically informed mating plans. Under this management, this programme has achieved a consistent reduction in time to harvest weight, demonstrating the potential effectiveness of this approach.