Aquaculture breeding programs continue to evolve as genetic tools become more accessible and integrated into routine practice. Greater availability of reliable genotyping tools has been crucial for enabling genetic progress in breeding programs.
This talk explores how genotyping candidate broodstock early in life within a genomic selection framework can improve breeding outcomes. This approach is widely used in terrestrial livestock breeding programs, such as cattle and swine, but is less commonly applied in aquaculture programs. Using insights from early-life genotyping provides a powerful framework for making earlier and more informed breeding decisions. This approach is particularly valuable in species with longer production cycles, where the cost of raising animals to maturity is high. In this framework, only a small number of high-value candidate broodstock need to be raised to maturity, resulting in greatly reduced costs for feed, facilities, and personnel.
Early-life genotyping enables breeders to assess genetic merit as soon as individuals are large enough to individually tag, improving selection accuracy and intensity while reducing infrastructure requirements and costs. Early genotyping also helps maintain genetic diversity by enabling balanced representation across families, avoiding the unintended loss of valuable genetic variation that can occur with traditional phenotype-based culling strategies. Selective reductions over the course of the life cycle allow for phenotypes to be assessed at multiple time points, decoupling early-life phenotypes from late-life phenotypes, and can result in genetic improvements to production traits that would not be possible from late-growth alone. Importantly, even when unfavourable genetic correlations exist between key traits, the added precision provided by the data allows breeders to make more balanced and informed decisions.
Case examples from commercial breeding programs demonstrate how integrating early-life genotyping into selection strategies can improve key production traits. This strategy not only improves the efficiency and speed of genetic gain but also changes how selection decisions are made across the breeding cycle for more cost-effective aquaculture breeding programs.