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)
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- 作者：Quanyuan Wan ; Jianguo Su ; su.jianguo@gmail.com ; Xiaohui Chen ; Chunrong Yang ; Lijun Chen ; Nana Yan ; Yixuan Zhang
- 关键词：Grass carp (Ctenopharyngodon idella) ; RIG-I ; Genomic structure ; Promoter activity ; Single nucleotide polymorphism ; Grass carp reovirus
- 刊名：Developmental and Comparative Immunology
- 出版年：2013
- 出版时间：April, 2013
- 年：2013
- 卷：39
- 期：4
- 页码：333-342
- 全文大小：774 K
文摘
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¡ä-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¡ä-flank region whose promoter activity was confirmed, 15 exons and 14 introns. By pooled DNA sequencing, two SNPs were detected in the 5¡ä-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.