WWW.WAS.ORG • WORLD AQUACULTURE • MARCH 2026 67 FIGURE 3. Genomic prediction accuracies for key traits (DHA, EPA, ALA, total n-3, and EPA+DHA) demonstrate the strong potential of GS to enhance fillet nutritional value. (CONTINUED ON PAGE 68) Sixteen traits were evaluated, including saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), alpha-linolenic acid (ALA), EPA, DHA, arachidonic acid (ARA), total omega-3 and omega-6 levels, as well as key indices such as the omega-6/omega-3 ratio and PUFA/SFA ratio. Considerable phenotypic variation was observed across all traits, and the distributions demonstrated substantial scope for genetic improvement. Although genome-wide association studies (GWAS) did not identify major QTLs — reflecting the polygenic nature of fatty acid metabolism (Horn et al., 2018; Blay et al., 2021) — genomic selection using a GBLUP model produced promising accuracies ranging from 0.29 to 0.48. DHA and EPA achieved the highest prediction accuracies (Figure 3), which aligns with similar genomic studies in salmon and trout (Horn et al., 2020; Blay et al., 2021). The strong performance of genomic prediction models confirms that fatty acid traits can be reliably selected even when phenotyping is expensive, labor-intensive or influenced by environmental factors. Applying Genomic Selection Across Different Aquaculture Regions Although the study was conducted in Singapore, the genomic principles and results have direct relevance to aquaculture sectors globally. In tropical and subtropical regions, where fish are increasingly fed plant-based diets, maintaining high DHA and EPA is a significant challenge. Genomic selection offers a practical solution by allowing breeders to identify individuals with naturally superior omega-3 biosynthesis or retention capacity, regardless of feed composition. This approach extends particularly well to Australia, where red snapper, barramundi and other premium finfish are cultured across diverse environments. In northern Australia and Queensland, producers can apply genomic selection to select fish that maintain valuable omega-3 levels in warm marine waters where feed types and environmental stressors vary seasonally. Western Australia’s expanding marine cage systems could implement GS to identify fish that perform consistently under fluctuating salinity and temperature conditions while retaining high nutritional value. In temperate southern regions, including South Australia and Tasmania, genomic selection frameworks developed from snapper can be adapted to species such as kingfish and mulloway, enhancing lipid quality without compromising growth performance. Nutritional genomics thus provides a unifying platform capable of improving product quality and sustainability across Australia’s entire aquaculture landscape. Industry Significance and Future Directions The integration of genomic selection into breeding programs represents a pivotal advancement in aquaculture nutrition and sustainability. By enabling early-life prediction of fatty acid composition, GS reduces reliance on costly chemical assays and allows hatcheries to retain only the highest-performing broodstock. As fish oil prices remain volatile and environmental regulations tighten, the ability to produce omega-3-rich fish on sustainable feeds will become a defining competitive advantage. The development of Singapore’s first national genomic selection platform for red snapper — stemming directly from this study — illustrates the scalability of the approach and its potential application across the wider Asia-Pacific region. As genomic resources expand and training populations grow, prediction accuracies will likely improve further, enabling more precise control over nutritional traits alongside growth, disease resistance and environmental resilience. Applying Genomic Selection Across Different Aquaculture Regions of Australia The genomic framework developed in this study is highly adaptable to Australia’s diverse aquaculture environments. Each region presents unique environmental conditions, species portfolios and production challenges, making genomic selection an ideal tool for nutritional improvement (Figure 4). In Northern Australia, which includes northern Queensland and the Northern Territory, tropical marine finfish such as barramundi (Lates calcarifer), red snapper and mixed reef-dwelling species are cultured in warm waters with pronounced seasonal variability. These environments are influenced by monsoonal rainfall, fluctuating salinity and high summer temperatures, all of which impact lipid FIGURE 4. Genomic selection applications across Australia’s major aquaculture regions, highlighting species-specific improvements in omega-3 traits: Barramundi and Red Snapper (North), Red Emperor and Pink Snapper (West), Kingfish and Mulloway (South), and Atlantic salmon (Tasmania).
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