Hidden Genomic Diversity in Aquaculture Fishes: Pangenome Structural Variation with Elusive Links to Adaptation and Resistance

Recent fish pangenome and structural variant (SV) studies reveal abundant hidden genomic variation beyond single-reference SNP (single-nucleotide polymorphism) maps. For example, Atlantic salmon (Salmo salar) genomes harbor ~15,483 SVs and European seabass (Dicentrarchus labrax) ~21,428 SVs. However, links between these SV/PAVs (presence-absence variants) and climate- or disease-related traits remain unclear. In this study, we review the fish pangenome literature (2020–2026) to evaluate the extent of SV/PAV discovery and any reported associations with adaptive aquaculture phenotypes. We performed a structured literature search of PubMed, Web of Science, and Google Scholar for 2020–2026 using terms like “fish pangenome”, “structural variants fish”, and related keywords. We included original whole-genome sequencing studies of aquaculture or wild fishes reporting SV/PAV, and extracted species, methods, and any reported trait associations. SV and PAV discoveries are reported for only a few aquaculture species. Atlantic salmon studies identified ~15,483 high-confidence SVs in 492 genomes, including ~14,000 deletions, 1,244 duplications, and hundreds of inversions. In European seabass, ~21,428 SVs were found in farmed populations. These SVs captured population differentiation and domestication signals (e.g., allele-frequency shifts in brain/behavior genes). However, none of the reviewed studies report validated associations between SV/PAV and thermal tolerance, salinity tolerance, hypoxia tolerance, or disease resistance. Known examples of SV-driven adaptation (e.g. inversions affecting salmonid migration timing) come from separate SNP-based analyses; no direct SV-phenotype link in fish aquaculture is documented. Pangenome analyses reveal abundant hidden SV/PAV diversity in fish beyond single-reference SNPs, offering a more complete view of genomic variation. This rich SV landscape could potentially inform adaptive breeding, but, currently, no direct SV–trait links (for climate or disease resilience) have been demonstrated. Our review highlights this knowledge gap and recommends the integration of pangenomic variation with genome-wide association studies (GWASs) and functional assays to uncover any adaptive roles of SVs/PAVs.