Aquaculture breeding programs have traditionally relied on family-based selective breeding to improve traits such as growth rates in species like Litopenaeus vannamei (Pacific white shrimp). However, these programs often encounter challenges due to genotype by environment interactions (G × E), where genetic performance varies across different environments, leading to reduced genetic gains. This issue is particularly pronounced in biosecurity-based breeding schemes (BS), which, while minimizing disease risks, may not fully capture the environmental diversity of commercial farming settings.

A recent study by Kang et al. (2025) explored the potential of genomic selection (GS) to mitigate the adverse effects of G × E in aquaculture breeding programs. Through stochastic simulations focusing on the body weight trait of L. vannamei, the researchers evaluated various strategies, including selective genotyping of test groups (TG) in commercial environments and varying the number of selection group (SG) individuals genotyped at nucleus breeding centers. The study also considered different levels of G × E to assess their impact on genetic gain.

Key Findings:

Impact of G × E on Genetic Gain: 

    The study revealed that BS experienced a loss of genetic gain ranging from 9.4% to 38.9% when using pedigree-based selection, with more substantial losses corresponding to stronger G × E interactions.

Efficacy of Genomic Selection: 
    Implementing GS, particularly with selective genotyping of TG individuals exhibiting extreme performance, effectively compensated for the genetic gain losses associated with G × E.

Optimal Genotyping Strategies: 
        For scenarios with a genetic correlation of 0.8 between nucleus and commercial environments, genotyping 20 SG individuals per family achieved 93.2% of the genetic gain observed in non-biosecurity-based schemes. However, with genetic correlations below 0.5, increasing the number of genotyped SG individuals to 50 or more was necessary to maintain genetic gain.

Long-Term Considerations: 

Over 30 generations, the genetic correlation between nucleus and commercial environments decreased by an average of 0.13, indicating the need for ongoing monitoring and adaptation in breeding strategies.

Implications for Aquaculture Breeding:

The findings underscore the potential of genomic selection to enhance genetic gains in aquaculture breeding programs, even in the presence of significant G × E interactions. By tailoring genotyping strategies—such as selectively genotyping individuals with extreme performances and adjusting the number of genotyped individuals based on the strength of G × E—breeders can optimize outcomes. Regular assessment of G × E levels and strategic genotyping are crucial to sustaining genetic progress in biosecure breeding environments.

Incorporating genomic selection into aquaculture breeding programs offers a promising avenue to overcome the challenges posed by genotype by environment interactions, thereby ensuring sustainable genetic improvements and the long-term viability of aquaculture industries.


References:

Kang, Z., Kong, J., Li, Q., Sui, J., Dai, P., Luo, K., Meng, X., Chen, B., Cao, J., Tan, J. and Fu, Q., 2025. Genomic selection strategies to overcome genotype by environment interactions in biosecurity-based aquaculture breeding programs. Genetics Selection Evolution, 57(1), p.2.