title: 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).
abstract: 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.
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
authors.forename: Quanyuan
authors.initials: Q
authors.lastname: Wan
authors.forename: Jianguo
authors.initials: J
authors.lastname: Su
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Chen
authors.forename: Chunrong
authors.initials: C
authors.lastname: Yang
authors.forename: Lijun
authors.initials: L
authors.lastname: Chen
authors.forename: Nana
authors.initials: N
authors.lastname: Yan
authors.forename: Yixuan
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D015415:Biomarkers; D002347:Carps / Q000235:genetics* / Q000276:immunology / Q000821:virology; D016022:Case-Control Studies; D002478:Cells, Cultured; D004198:Disease Susceptibility; D005393:Fish Diseases / Q000276:immunology* / Q000821:virology; D020022:Genetic Predisposition to Disease; D005838:Genotype; D007370:Interferon Type I / Q000276:immunology; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D051192:Receptors, Pattern Recognition / Q000235:genetics* / Q000276:immunology; D018168:Receptors, Retinoic Acid / Q000235:genetics / Q000378:metabolism*; D012087:Reoviridae / Q000276:immunology; D012088:Reoviridae Infections / Q000276:immunology / Q000662:veterinary* / Q000821:virology; D017422:Sequence Analysis, DNA / Q000662:veterinary
chemical_list: D015415:Biomarkers; D007370:Interferon Type I; D051192:Receptors, Pattern Recognition; D018168:Receptors, Retinoic Acid