Genome-wide association study toward efficient selection breeding of resistance to Vibrio alginolyticus in Pacific oyster, Crassostrea gigas

The oysters are facing with risk of pathogen infection due to complex and variable intertidal habitats, which frequently causes serious disease problem to oyster industry globally. Genetic improvement of disease resistance can be an effective solution to resolve this problem, while dissection of genetic basis underlying disease resistance is critical toward efficient selection breeding. In this work, we performed a genome wide association study (GWAS) in the Pacific oyster (Crassostrea gigas) to identify genetic loci underlying resistance to bacterial Vibrios, a major group of pathogens in the ocean. We performed artificial infection of 1402 oysters collected from 52 families using the previously isolated pathogenic Vibrio alginolyticus. Selective genotyping of 295 resistant and susceptible individuals were conducted using ddRAD sequencing approach. A total of 48,099 high quality SNPs were detected across whole genome of C. gigas. Linkage disequilibrium analysis revealed a rapid decay of linkage across the genome. GWAS revealed polygenic architecture of resistance traits, and identified a total of 18 SNP loci and three QTL underlying the trait of resistance to Vibrio, allowing for identification of 178 genes involved in various processes of immune response, including pathogen recognition, immune signaling, and immune defense. This work provides insights into genetic basis of resistance to V. alginolyticus, and valuable genetic resources toward genomic selection breeding of strains resistant to Vibrio in the C. gigas. •Genome wide association analysis revealed polygenic architecture of resistance to Vibrio alginolyticus in C. gigas.•A total of 18 loci and three QTL associated with Vibrio resistance were detected and annotated.•Vibrio resistance lies in a series of immune process, including pathogen recognition, signal transduction, and defense response, in C. gigas.