Sequencing & Pangenomes

Integrating DNA Pooling into Aquaculture Breeding Programs: A Practical and Cost-Efficient Approach

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Abstract

Genotyping costs remain a significant barrier to implementing effective breeding programs in aquaculture, whether using low-density SNP panels for parentage assignment or high-density SNP chips for genomic selection. There is a pressing need for cost-efficient genotyping strategies tailored to the unique demands of aquaculture species. To date, no published study has systematically evaluated the use of DNA pooling in either pedigree-based selective breeding or genomic selection. In this study, we present a comprehensive and practical framework for integrating DNA pooling into classical breeding, pedigree-based selection, and genomic selection programs in aquaculture. As a proof of concept, we simulated pooled genotypes across varying pool sizes using a limited number of SNPs and compared the accuracy of estimated breeding values (EBVs) derived from pooled versus individual genotypes. We further conducted in silico simulations using a 60K SNP chip to assess genomic selection, estimating SNP effects and genetic parameters from both pooled and individual data. These approaches were validated using empirical data from two aquatic species genotyped with low- and high-density SNP chips. Our findings demonstrate that DNA pooling can be effectively implemented in aquaculture breeding programs, offering substantial reductions in genotyping costs while maintaining high accuracy. For example, with a pool size of 20, representing just 5% of the genotyping cost, genomic estimated breeding value (GEBV) accuracy reached approximately 0.8 compared to individual genotyping. DNA pooling also proves valuable for evaluating genotype-by-environment interactions (Gà—E), bridging the performance gap between breeding stations and commercial multipliers, and conducting challenge tests. Finally, we discuss practical challenges in adopting DNA pooling and propose solutions to support its broader application in aquaculture breeding.

Keywords: 2026

How to Cite:

Mekkawy, W., Carvalheiro, R., Luke, T., Evans, B., Khaw, H., Van, T., Nguyen, C., Foote, A., Coman, G., Lind, C. & Kijas, J., (2026) “Integrating DNA Pooling into Aquaculture Breeding Programs: A Practical and Cost-Efficient Approach”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283795. doi: https://doi.org/10.31274/wcgalp.23512

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