biostudies-literatureLi QNational Natural Science Foundation of China (National Science Foundation of China)1579https://www.ebi.ac.uk/biostudies/studies/S-EPMC12480761biostudies-literatureUnknown12(1)This data descriptor presents a multi-omics resource for Crassostrea gigas and Crassostrea angulata, comprising genomic variants and transcriptomic profiles relevant to fatty acid metabolism traits. A 458-individual F₂ hybrid population genotyped with a 100 K SNP array identified 344 SNPs and 742 candidate genes linked to C18:3ω3, EPA, and DHA variation. KEGG analysis highlighted 24 key genes, with 23 validated via GS-assisted GWAS, dominant genotype screening, and wild population resequencing. Differential expression analysis revealed 458 DEGs (266 between high/low EPA + DHA groups; 192 between species), overlapping with 152 genes from GWAS and selective sweeps. This integrated dataset provides foundational genetic references for studying ω-3 fatty acid dynamics, enabling futurScientific dataGenetic Resources for Research on the Regulatory Mechanism of ω-3 Fatty Acids in Oysters.PMC124807612022YFD2400304Zhang GCong RWang CQi HLi QWang WLi LfalseGenetic Resources for Research on the Regulatory Mechanism of ω-3 Fatty Acids in Oysters.This data descriptor presents a multi-omics resource for Crassostrea gigas and Crassostrea angulata, comprising genomic variants and transcriptomic profiles relevant to fatty acid metabolism traits. A 458-individual F₂ hybrid population genotyped with a 100 K SNP array identified 344 SNPs and 742 candidate genes linked to C18:3ω3, EPA, and DHA variation. KEGG analysis highlighted 24 key genes, with 23 validated via GS-assisted GWAS, dominant genotype screening, and wild population resequencing. Differential expression analysis revealed 458 DEGs (266 between high/low EPA + DHA groups; 192 between species), overlapping with 152 genes from GWAS and selective sweeps. This integrated dataset provides foundational genetic references for studying ω-3 fatty acid dynamics, enabling futur2025-01-01T00:00:00Z2025 Sep2026-06-04T00:07:06.346Z2026-05-03T03:12:26.605ZS-EPMC124807614102288710.1038/s41597-025-05822-y