Achieving sustained genetic progress in aquaculture breeding programs is now commonly requiring the evaluation and implementation of genotyping tools. Selecting a tool with the optimal or minimum viable number of markers required for the successful long-term implementation of the chosen breeding strategy is key to the success of the breeding program. This presentation outlines and examines through two case studies the role that the number of traits, genome size, linkage disequilibrium (LD) breakdown, recombination rate, genotype by environment interactions (GxE), and the need for sustained precise selection over multiple generations has on the required number of markers.
The number of traits under consideration plays a pivotal role in marker density determination. A multi-trait breeding program demands a higher marker density to capture the genetic variation associated with each trait accurately. Different traits, such as improving growth rate, disease resistance, quality, and reproductive performance, all influence the required density and selection of markers to ensure all gains can be made across traits aligned with the program’s breeding objectives.
Genome size affects the overall genomic landscape, necessitating adjustments in required marker density to adequately cover the entire genome. Linkage disequilibrium breakdown and recombination rate are crucial factors influencing marker spread and effectiveness. Understanding the dynamics of LD breakdown and recombination allows for the strategic placement of markers to ensure coverage of critical regions linked to the target traits. Balancing marker density to accommodate LD decay and recombination events is essential for maintaining breeding program efficacy over generations.
In conclusion, this presentation will underscore the importance of a comprehensive and adaptive approach to marker density planning and genotyping tool choice in aquaculture breeding programs. By considering the number of traits, breeding objectives, GxE interactions, genome size, LD breakdown, recombination rate, and the impact of selection over multiple generations, breeders can develop resilient strategies for sustained genetic improvement in aquaculture species through the appropriate choice of genotyping tools.