Genome wide association study and transcriptome analysis identify the SNPs and genes related to muscular polyunsaturated fatty acid content in common carp (Cyprinus carpio)

Fatty acids (FAs) play central roles in growth and development through their involvement in membrane lipids, which are crucial for the health of both humans and fish. Particularly, the biosynthesis of polyunsaturated fatty acids (PUFAs)is essential for improvingfor human and fish health, and is also key character for evaluating the nutrient quality of fish fillets. The endogenous biosynthesis of FAs and PUFAs in fish involves complex mechanisms including fatty acid uptake, synthesis, hydrolysis, and deposition. To identify putative SNPs and underlying genes regulating FA and PUFA biosynthesis in common carp (Cyprinus carpio), we combined genome resequencing and RNA sequencing to detect genetic variants associated with different fatty acid contents. Genome resequencing was performed and yield 2,757,424 high-quality SNPs in 280 individual common carp. Among these, 1,410 SNPs and their surrounding 1,391 genes were significantly related to 16 types of FA contentswith the suggestive thresthold of P-value 3.63×10-5. These genes were enriched in gene regulation of biological process, oxidization of molecular function, and PUFA deposition. Using an optimal genomic selection program with all significantly associated SNPs for FA traits, we evaluated high and positive correlations ranging from 0.65 to 0.92 between phenotypes and estimated breeding values. For TPUFAs, subsequent RNA-seq analysis of liver tissues from groups with higher and lower TPUFA content revealed 715 differentially expressed genes (DEGs). combined These DEGs were primarily enriched in hormone-mediated signaling pathways. Combined genome-wide association and differential gene expression (DGE) analysis revealed that the ubiquitination and β-oxidation pathways are novel contributors to muscular PUFA content. We suggest that higher levels of ubiquitination and lower levels of β-oxidation may contribute to increased TPUFA deposition. These findings provide novel candidate genes for studying the molecular mechanisms governing PUFA metabolism. The identified SNPs and the optimal genomic selection program will be valuable tools for future selective breeding programs aimed at enhancing PUFA content in common carp.