Genome-wide association study and transcriptome analysis provide the SNPs and molecular insights into the visceral nodular disease tolerance in half-smooth tongue sole (Cynoglossus semilaevis)

Half-smooth tongue sole (Cynoglossus semilaevis) is an economic flatfish in seawater factory farming along the coastal areas of China. However, the farming of C. semilaevis is plagued by visceral nodular disease (VND) infections caused by Mycobacterium marinum, resulting in substantial economic losses for the industry. Therefore, it is crucial to understand the molecular mechanisms of VND tolerance in C. semilaevis. To achieve this, we employed a combination of genome-wide association studies (GWAS) and RNA sequencing (RNA-seq) to identify single nucleotide polymorphisms (SNPs) and to elucidate their roles in regulating tolerance to VND in C. semilaevis. Initially, we genotyped 300 individual C. semilaevis using whole genome resequencing (WGS), identifying 4,773,887 high-quality SNPs. Seven significantly associated SNPs were found on chromosomes 1 and 12. Subsequent RNA-seq analysis of liver tissues from both disease sensitive (DS) and disease tolerance (DT) groups during M. marinum infection revealed a total of 2576 differentially expressed genes (DEGs). Potential candidate genes identified from GWAS and DEGs were further integrated. From that, genes involved in transcription factor activity, innate immune response and protein kinase activity, such as rela, jun, ccl36.1, nfkbiab, pik3r3b and map2k1, were found to be important for VND tolerance in C. semilaevis. In addition, the expression pattern of candidate genes and genotypes of SNPs associated with disease tolerance traits were validated. These findings provide novel insights into the molecular mechanisms governing disease tolerance and lay the groundwork for genomic selection and molecular breeding strategies enhance VND tolerance in fish. •Reveal the genetic basis and potential regulatory mechanisms of visceral nodular disease in half-smooth tongue sole.•Three significant associated and four suggestive associated SNPs were observed on chromosomes 1 and 12.•Potential candidate genes involved in transcription factor activity, innate immune response and protein kinase activity