Genome-wide association analysis on host resistance against the rotten body disease in a naturally infected population of large yellow croaker Larimichthys crocea

Large yellow croaker (Larimichthys crocea) is one of the most important marine fish in China, representing the highest yield of fish species in marine net cage aquaculture. In recent years, the rotten body disease caused by scuticociliate was the main perniciousness for the fish fry, and led considerable economic losses. To date, no treatments had proven to be effective to the disease, so it was urgent to carry out the researches on disease-resistance breeding of this fish. Based on genome resequence for a natural population, a genome-wide association study (GWAS) to identify those loci associated with the rotten body disease resistance was performed in this work. A total of 3000 fish from 6 sub-populations were collected, and 270 phenotypic extremes were selected for genotyping. Two analysis models were employed to verify the accuracy and reliability of GWAS results. 2,019,067 SNPs were remained, and 14 SNPs were finally identified to be correlated with disease resistance, explaining phenotypic variance ranging from 5.4% to 9.2%. Within these regions, 5 candidate genes, NF-kappa B1, UBXN1, PTX3, DAB2IP and CYR61, which were involved in NF-kappa B signaling pathway, suggested the importance of NF-kappa B signaling pathway in the disease resistance. These results showed the complex polygenic architecture in large yellow croaker resistance against parasite scuticociliate. It also provided valuable foundation for future marker-assisted selection breeding of large yellow croaker against scuticociliate.