Genomic selection for parasitic ciliate Cryptocaryon irritans resistance in large yellow croaker

Abstract

Large yellow croaker is an important marine aquaculture species in the southeast coast of China. It suffers serious diseases caused by Cryptocaryon irritans, a parasitic cilliate which causes huge economic losses to the aquaculture industry of large yellow croaker. This study aims to apply genomic selection (GS) technology to the selection breeding of large yellow croaker with resistance to C. irritans. The resistant phenotype was measured as a binary trait, survival or death, in challenge experiments using reference population. Double-digest restriction-associated DNA (ddRAD) sequencing approach was used to generate genome-wide single nucleotide polymorphism (SNP) genotypes for reference population and selection candidates. A database of 811 individuals and 16,515 SNPs was constructed and used for GS analysis. The GS model containing the top 600 SNP markers with the smallest P value possessed highest predictability and was used to calculate genetic estimated breeding value (GEBV) in selection candidates. The individuals with high GEBV in selection candidates was selected as broodstocks for the breeding of resistant strain (RS), and the remaining individuals for the control strain (CS). Significant resistance difference between RS and CS was detected in a C. irritans challenge test. After 96-h, the survival rate of RS and CS were 59.2% and 9.9%, respectively. Moreover, 120-h survival rate of RS declined to 40.8%, while CS had no surviving individuals. The results confirmed that GS was effective genetic breeding techniques in resistant breeding against C. irritans in large yellow croaker.