Achieving sustained genetic progress in aquaculture breeding depends on selecting genotyping tools with the optimal number of markers for a given breeding strategy. This presentation explores key factors influencing marker density requirements, including the number of traits, genome size, linkage disequilibrium (LD) breakdown, recombination rate, genotype-by-environment interactions (GxE), and the need for precise selection over multiple generations.
Multi-trait breeding programs require higher marker densities to capture genetic variation across traits such as growth, disease resistance, quality, and reproduction. Genome size also impacts marker density needs, influencing genome-wide coverage. LD breakdown and recombination rates affect marker effectiveness, requiring strategic placement to ensure critical trait regions are adequately covered. Balancing marker density with LD decay and recombination events is essential for long-term breeding program success.
This presentation highlights the importance of an adaptive approach to marker density planning, ensuring genotyping tools align with breeding program goals. By optimizing marker selection, aquaculture breeding programs can enhance genetic improvement efficiency, maximize selection accuracy, and sustain progress over generations.