Global breeding programs

Optimizing Shrimp Breeding Programs Using Simulation-Based Strategies for Enhanced Genetic Gain

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Abstract

Shrimp aquaculture is one of the fastest-growing sectors in global food production, yet genetic improvement programs face persistent challenges. Compared to terrestrial species, shrimp are far more susceptible to environmental fluctuations and disease outbreaks, making genotype-by-environment interactions (Gà—E) particularly critical. Nucleus populations in biosecure facilities like Hawaii are biologically and geographically distant from commercial farms in regions such as Indonesia, complicating the translation of genetic gains into field performance. These mismatches can lead to severe consequences for farmers, including early harvests or even complete crop failures, resulting in substantial financial losses. Although generation intervals are short and shrimp produce large numbers of offspring, costly pedigree reconstruction and inconsistent reproductive success hamper selection intensity. Designing efficient breeding programs is therefore essential to improve both productivity and sustainability. The objective of this study was to evaluate alternative breeding strategies for Litopenaeus vannamei using a digital twin approach in MoBPS (Modular Breeding Program Simulator) under real-world challenges such as disease outbreaks and genotype-by-environment interactions. A breeding program was modeled to reflect real-world challenges such as disease outbreaks and environmental variability. Key traits included body weight and survival under disease challenges like Early Mortality Syndrome (EMS) and Enterocytozoon hepatopenaei (EHP), which show low to moderate heritability and variable correlations with growth. Strategies explored how to integrate sentinel data (performance records from related animals tested in commercial environments and linked to nucleus stock through genotyping), alongside variations in selection intensity, family structure, and genotyping approaches. Performance indicators included genetic gain for growth and disease traits, EBV accuracy, and inbreeding rate. Scenarios focused on: (1) Number and structure of genotyped animals (2) Mating strategy and parentage assignments for nucleus population in relation to genomic selection strategy, (3) Genotyping strategies and pedigree structure (e.g., sibs vs. cousins) for disease challenge trials and sentinel programs. Preliminary results show genetic response for disease traits measured in disease challenges (days to death) were highly influenced by genotyping strategy. Using full or half sibs in sentinel programs improved predictive accuracy at the nucleus level by up to 30%, and increased genetic gain by ~20% compared to cousin-based designs. These findings highlight the importance of integrating geographically diverse sentinel data to strengthen links between biosecure nucleus populations and real-world field performance. Simulation-driven strategies enable sustainable genetic improvement in shrimp breeding by reducing uncertainty and optimizing performance across diverse environments, while future models will further integrate disease resistance and complex Gà—E interactions to ensure robustness under commercial production challenges.

Keywords: 2026

How to Cite:

de Klerk, B., Facchini, E., Perez, B., Jamieson, D., Bink, M. & Duijvesteijn, N., (2026) “Optimizing Shrimp Breeding Programs Using Simulation-Based Strategies for Enhanced Genetic Gain”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286348. doi: https://doi.org/10.31274/wcgalp.23945

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