Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella

Grass carp (Ctenopharyngodon idella) is an important economic species in freshwater aquaculture and its industry has been confined due to variety degeneration and frequent diseases. Marker-assisted selection is a feasible method for selective breeding of new varieties. Transcriptome data have greatly facilitated high-throughput single nucleotide polymorphism (SNP) marker discovery and phenotype association study. In this study, we gained a total of 25,981 and 5,775 high quality SNPs in two transcriptomes from individuals and cell lines, respectively. Comparative transcriptome analysis identified 413 and 832 grass carp reovirus (GCRV)-resistant-association SNPs as well as 1,381 and 1,606 GCRV-susceptible-association SNPs in individuals and cell lines, respectively. Integrated analysis indicated 22 genes with single SNP share common resistant/susceptible traits in two transcriptomes. Furthermore, we infected grass carp with GCRV, genotyping and association analyses were performed, and 9 in 22 SNPs were confirmed by PCR-RFLP. Meanwhile, mRNA expression profiles of 6 genes containing confirmed SNPs were examined by qRT-PCR. The results demonstrated that mRNA expressions were significant differences in resistant/susceptible individuals and cell lines. The present study develops an important strategy for high throughput screening of phenotype association genetic markers and the results will serve in grass carp breeding for GCRV resistance.