Investigating genomic prediction accuracies for muscle fatty acids composition in Malabar red snapper (Lutjanus malabaricus)

This study evaluated the genomic prediction accuracy of fatty acid composition in fillets of Malabar red snapper ( Lutjanus malabaricus ) reared in a sea-based farm and sampled at 18 months of age, with an average body weight of 454 ± 102 g. In addition to body weight, phenotypic (534 individuals) and genotypic (39,780 SNPs) data were available for 16 fatty acid traits, grouped into four categories: polyunsaturated Omega-3 fatty acids, Omega-6 fatty acids, saturated and monounsaturated fatty acids, and various fatty acid ratios and indices. Genomic predictive abilities varied across traits, yielding low to moderate accuracies (0.29–0.48). These accuracies were comparable to, or slightly higher than, theoretical expectations based on heritability and training population size. Notably, moderate to high prediction accuracies were observed for DHA (0.47 ± 0.16), EPA (0.43 ± 0.15), and total Omega-3 (0.47 ± 0.19), highlighting the potential of genomic selection to enhance the nutritional quality of farmed red snapper. The absence of significant SNPs supports the polygenic nature of these traits and underscores the appropriateness of genomic selection. These findings demonstrate the feasibility of incorporating genomic selection into breeding programs to improve fatty acid composition in Malabar red snapper. • Sixteen muscle fatty acids analyzed in 534 red snappers using 39,780 SNP markers. • Moderate to high prediction accuracy for DHA, EPA and total Omega-3. • Traits like DHA/ALA ratio offer insights into Omega-3 biosynthesis efficiency. • GS and GWAS show potential to breed red snapper with higher EPA and DHA.