Genomic features of common carp that are relevant for resistance against Aeromonas hydrophila infection

Abstract

The common carp is an important aquaculture fish species which farmed worldwide. Intensive rearing in aquaculture causes increasing susceptibility to various pathogens. One of the most common and frequently encountered pathogens is Aeromonas hydrophila, which causes severe losses of the carp industry. The genetic mechanism underlying host resistance to pathogens have attracted increasing attention, however, genome-wide scale studies on genetic architecture of common carp against A. hydrophila infection have been rarely applied. In the present study, we conducted whole genome resequencing of susceptible and resistant fish samples, generated high-throughput genotyping data, and conducted genome-wide association analysis. A total of 8 significantly and 51 suggestively associated SNPs were identified. Within the 8 significant SNPs, 6 SNPs were located within 6 immune-related genes, respectively, and these genes were rab26, dcc, trim71, ptpn21, muc5b and trim25. Further examining detailed position of the 6 SNPs within the gene sequences region showed that there was one SNP located at the CDS region of gene trim25, which could cause a mutation of turning an isoleucine into a threonine. In addition, genes within and surrounding the 59 SNPs were searched and a total of 659 genes were captured, of which, 76 were immune- or defense- related genes. GO enrichment and gene pathway analysis were performed, indicating more evidence for the association of candidate genes with A. hydrophila resistance. Our study advanced the knowledge to better understand the molecular process of immune response against bacterial infection in common carp, and provided fundamental information for future selection of resistant strains of common carp.