Gene editing in breeding

Integrating Genome Editing into Aquaculture Breeding Programs: Achieving Commercial Scale

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Abstract

Selective breeding has driven genetic improvement in aquaculture, delivering gains in growth, efficiency, and robustness across many cultured species. High fecundity and short generation intervals enable rapid response to selection, yet progress is limited by the availability of naturally segregating variation and unfavourable genetic correlations among key traits. Genomic selection has increased selection accuracy and reduced generation intervals but remains dependent on existing genetic diversity. Genome editing (GE) offers a complementary avenue by enabling targeted modification of loci with known or inferred causal effects. Despite increased technical maturity, commercial use of GE requires evaluation of how edited alleles can be introduced, propagated, and fixed within breeding programs without compromising long-term genetic gain or population integrity.This study evaluates GE integration into a commercial aquaculture breeding context by combining empirical biological data with simulation-based assessment. Empirical genome-editing outcomes were generated in Nile tilapia using validated gene targets linked to growth, feed efficiency, and fillet yield. Editing was performed at the embryonic stage using high-throughput microinjection, with editing efficiency and germline transmission assessed using a custom genotyping panel. Edited founders were integrated into existing family-based breeding structures and evaluated alongside non-edited relatives under production-relevant conditions. These empirical results provided biological inputs for simulation analyses.Simulation analyses used a structured breeding framework representative of operational aquaculture programs. Genomes were simulated with a polygenic trait architecture augmented by a major quantitative trait locus representing the genome edit. Scenarios varied in founder population size, number of edited founders, timing of additional editing events, and mating strategy. Outcomes included edited allele frequency trajectories, breeding value responses across generations, and changes in population structure assessed by principal component analysis.Empirical results showed substantial and repeatable improvements in key traits, with growth rate gains exceeding 30% for specific edits and consistent improvements in feed efficiency and fillet yield. Simulation results indicated that beneficial edited alleles could be rapidly propagated and approach fixation within a few generations under realistic selection intensities. Broad, family-wide introduction of edits enabled rapid fixation while maintaining genetic diversity and avoiding detectable population stratification, whereas restricted deployment increased the risk of narrowed genetic contribution. Across all scenarios, large-effect edited alleles were incorporated alongside ongoing polygenic improvement, provided effective population size was maintained.These findings demonstrate that genome editing can be integrated into structured aquaculture breeding programs without undermining long-term genetic gain or established quantitative genetic principles. When combined with genomic selection and family-based deployment, GE provides a practical, scalable tool to accelerate genetic improvement. Where sterility is required for biological containment, genome editing also offers a direct means of producing sterile lines alongside performance-enhancing edits, supporting its inclusion in modern aquaculture breeding programs.

Keywords: 2026

How to Cite:

Verbyla, K., Kriaridou, C., Gutierrez, A., Josephson, M., Pudasaini, A., Jin, Y., Samu, S., Tsai, B. & Buchanan, J., (2026) “Integrating Genome Editing into Aquaculture Breeding Programs: Achieving Commercial Scale”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286158. doi: https://doi.org/10.31274/wcgalp.23864

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