Genomic sequence comparison, promoter activity, SNP detection of RIG-I gene and association with resistance/susceptibility to grass carp reovirus in grass carp (Ctenopharyngodon idella)

As an intracellular pattern recognition receptor (PRR), retinoic acid-inducible gene-I (RIG-I) is responsible for detection of nucleic acids from pathogens in infected cells and activation of type I interferon (IFN). In the present study, the 5′-flanking region, introns and single nucleotide polymorphisms (SNPs) of CiRIG-I (Ctenopharyngodon idella RIG-I) were identified and characterized. The genomic CiRIG-I was 12810 bp in length, consisted of an 1864 bp 5′-flank region whose promoter activity was confirmed, 15 exons and 14 introns. By pooled DNA sequencing, two SNPs were detected in the 5′-flanking region; 10 SNPs were discovered in introns; and one SNP was found in exons. After a challenge experiment, these SNPs were selected to analyze their association with the resistance/susceptibility of C. idella to grass carp reovirus (GCRV), using case-control study. Chi-square test was employed to assess the association. The result showed that −780 C/T, 4731 C/T, 4945 A/G, 8461 C/T, and haplotype 3428A–3432G were significantly associated with the phenotype (P < 0.05). To confirm the correlation, another independent challenge experiment was performed, in which the cumulative mortality of −780 genotype CC, 4731 genotype CC and 4945 genotype AA were significantly lower than that of −780 genotype TT, 4731 genotype TT and 4945 genotype GG, respectively (P < 0.05). In addition, the SNP–SNP interaction analysis revealed that there was no significant interaction among those SNPs (P > 0.05). These significant SNPs and the haplotype might be potential genetic markers for the molecular selection of C. idella strains that are resistant to GCRV.

► Complete genomic sequence of RIG-I from grass carp was identified. ► The promoter activity of the 5′-flanking region was estimated. ► Four SNPs in grass carp RIG-I may be significantly related to GCRV resistance. ► Linkage disequilibrium and haplotype were assayed. ► The SNP–SNP interaction among SNPs in RIG-I and LGP2 of grass carp was examined.