Selecting for Success

In the rapidly evolving aquaculture industry, where seafood demand continues to rise, efficiency and sustainability are more critical than ever. Improved genetic improvement strategies and breeding program management have been a driving force behind global aquaculture growth. Thanks to selective breeding, aquaculture species can now grow faster, with greater disease resistance, require fewer resources, and, in some cases, offer improved nutritional value compared to their wild counterparts.

One of the most significant advantages of selective breeding is its economic impact—allowing farms to boost production yields and long-term profitability. Yet, despite its proven benefits, on-farm breeding programs remain underutilized across many species and farms.

A well-designed breeding program is one of the most powerful tools in an aquaculture breeder and producer’s toolbox. In this article, we explore the importance of selective breeding, the different types of breeding programs, key tools to help make informed, strategic decisions, and what the future holds for incorporating the latest genetic innovation, genome editing, into selective breeding programs.

Why Selective Breeding Matters

Technically speaking, selective breeding is the process of improving one or more desirable traits of a cultured species through the selection of superior parents. A breeding program is how this idea is put into action, using specific tools and methods. It should be designed to maximize the economic return for a commercial producer. Therefore, selective breeding isn’t just a buzzword; it’s a practical strategy that helps aquaculture achieve critical goals:

1. Enhanced Productivity: Productivity is the lifeblood of aquaculture. Selective breeding allows us to create strains of fish, crustaceans, or shellfish that grow faster and more efficiently through improved disease resistance and survival, leading to increased yields and reduced production costs.
2. Improved Quality: One of the primary motivations behind selective breeding is to enhance the quality of farmed aquatic species. By selectively breeding for desirable traits like color, fat or nutrient content, and fillet size and quality, we can produce fish and other aquatic organisms that meet consumer preferences and market demands.
3. Sustainability: Sustainable aquaculture practices are essential for safeguarding our aquatic ecosystems. By selectively breeding for traits that minimize environmental impact, such as reduced waste production and efficient feed utilization, we can create a more sustainable future for the industry.

Building the Foundation for Success

To successfully implement selective breeding programs, aquaculture companies must first establish clear breeding objectives and develop a strong foundation of critical capabilities. This begins with defining the desired physical characteristics of future generations or the economic targets. Once the objectives are clear the next step is to design the optimal strategy to achieve these targets and outcomes. This step requires technical expertise in genetics and breeding alongside operational know-how to design the optimal strategic breeding program plan for implementation. For any breeding program, efficient data collection processes and additional tools are vital for measuring traits and tracking pedigree information accurately. For more complex breeding strategies, such as those utilizing genomic selection, access to cutting-edge genomic technologies is also essential for precision.

Selecting the right genotyping tools

Selecting the right genotyping tool(s) is crucial to enable the genetic progress of a breeding program. The optimal number of genetic markers for your population depends on various factors, including the number of selected traits, the species’ genome size, the linkage disequilibrium (LD) breakdown, the recombination rate, and any genotype-by-environment (GxE) interactions.

Genome characteristics strongly influence marker needs. Genome size will impact marker density due to the common need for genome-wide coverage. LD breakdown and recombination rates affect marker effectiveness when using markers to capture the underlining genes controlling selected traits. This requires strategic placement to cover critical trait regions adequately. Balancing marker density with LD decay and recombination events is essential for long-term effectiveness of a chosen genotyping tool to support breeding program success.

The chosen breeding strategy and program will influence the choice of genotyping tools. A multi-trait genomic selection breeding program, for example, will require high marker densities to ensure the capture of maximal genetic variation across all the traits being selected. In contrast, a simpler breeding programs may require only a low-density set of markers sufficient to establish genetic relatedness and facilitate family assignments. Ultimately, an optimal genotyping solution can normally be designed to support any chosen breeding strategy and to meet specific needs of the ongoing management of the program.

When existing genotyping panels are unavailable, customized solutions can be designed and developed for new and emerging species, allowing clients to gain valuable insights into their populations while also building essential genomic resources for their species and tools to support their breeding programs.

Klara Verbyla, Vice President of Genetic Improvement at the Center for Aquaculture Technologies (CAT) outlines, “At CAT we firmly believe in a tailored approach to marker density planning and genotyping tool choice. By working with our clients we ensure long-term breeding success and genetic gains by creating a customized genotyping solution matched to their requirements.”

She adds, “If a client is running a family-based breeding program that requires mating design and inbreeding management, we would recommend a low-density marker panel to determine parentage and the relatedness between individuals to design the optimal matings to maximize genetic gain and to maintain diversity. Or if a client was interested in utilizing Genomic Selection to accelerate genetic gain, we would recommend high-density marker panels that provide genome-wide coverage and will deliver the most accurate breeding information to be used for decision making.”

Choosing the Right Breeding Program for Your Needs

Breeding program choice is dependent on the breeding objectives, specific needs, and resources available. Multiple options are available, each with its own strengths and are suited to different contexts and situations.

The more complex breeding program strategies, like genomic selection, allow the selection of the best individuals which will significantly increase the accuracy of selection and the rate of genetic gain. These types of programs also require more resources to implement. For this reason, the choice of breeding program should factor in an analysis of the return on investment. Other options, include Family-Based selection where the best families, rather than the best individuals, are identified and are used to create the next generation whilst requiring less resources than Genomics Selection. Mass Selection is the final option and is used to select the individuals based purely on their own performance and visual traits. It requires the least resources but will typically deliver the lowest gains due to the proportion of the observed phenotype that is controlled by genetics. It is only the genetics of an individual that is passed on to its offspring.

Ultimately the key is to make an informed decision that aligns with the breeding objectives, operational feasibility, resources and long-term vision.

Alejandro Gutierrez, Genetic Services Project Lead at CAT shares, “Many clients approach us with an interest in genomic selection, considering it the industry’s go-to solution. In some cases, it is indeed the best approach but not always. We work closely with each client to thoroughly evaluate their production methods, breeding objectives, economic goals, and available resources. This allows us to identify the optimal breeding program strategy and then customize it to meet their specific needs.”

Adding “Navigating breeding strategies and genetic analysis can feel overwhelming, but no one has to go it alone. When faced with challenges in demonstrating the return on investment for genetic improvement or how it aligns with broader production strategies, partnering with experts, like CAT’s team, can help overcome these barriers. By providing clear guidance and tailored solutions we ensure that genetic improvement integrates seamlessly with existing operations. With the right support in genetic analysis, breeding programs, and genomic technologies, our clients are empowered to make confident decisions, optimize their breeding strategies, and achieve long-term sustainable genetic progress.”

The Future of Genetic Improvement

With CAT’s recent collaboration with Brazilian Fish announced to introduce the first commercial-scale genome-edited tilapia in Brazil, the integration of genome editing into breeding programs is even closer.

In the same way as selective breeding which delivers improved genetic progress over time, genome editing precisely targets and delivers genetic changes that could naturally occur. However, instead of taking many years of careful selective breeding, this beneficial variation can now be introduced in a single generation. Using molecular tools like CRISPR-Cas9, scientists can directly create genetic variants in precise locations in the genome to deliver major improvements in performance, without introducing new DNA.

Explaining how genome editing will work within established breeding programs, Alejandro explains “Genome editing will not replace selective breeding, instead it will be incorporated into breeding programs to enhance genetic improvement more precisely and efficiently. By combining both approaches, we can rapidly accelerate progress for specific traits while maintaining the benefits of traditional selective breeding for others. Selective breeding can continue to generate improvements in edited fish. Genome editing therefore complements selective breeding, rather than replacing it.”

Simply put – “Selective breeding establishes the genetic foundation of aquaculture species, while genome editing further refines the improvement of specific traits faster and with greater precision. Together, these approaches can drive sustainable industry growth and improved production outcomes,” notes Verbyla.

Genome-edited fish have the potential to transform multiple aspects of the supply chain, benefiting both producers and consumers. For breeders, this technology means faster-growing stock, improved disease resistance, and better feed efficiency—ultimately reducing costs and increasing profitability. Meanwhile, consumers gain access to high-quality, nutritious protein, contributing to a more sustainable and resilient food system.

By leveraging the latest advancements in genetics, aquaculture producers can unlock even greater potential for efficiency, resilience, and profitability. As selective breeding continues to evolve, the integration of cutting-edge innovations like genome editing offers exciting opportunities to enhance performance and sustainability further. Utilizing the right breeding strategies and tools will be key to staying competitive in this rapidly advancing industry.