哈萨克羊DRB1基因外显子3多态性及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2018.03.021

摘要/Abstract

摘要：

试验旨在研究白细胞表面抗原DRB1基因外显子3多态性与哈萨克羊布鲁氏菌病易感性的相关性。运用混合DNA池结合PCR产物直接测序方法，对哈萨克羊DRB1基因外显子3进行多态性分析，经卡方检验分析每个SNP位点的等位基因频率、基因型频率及其多态性与布鲁氏菌病易感性的相关性，利用生物信息学分析软件对PCR扩增所获序列进行RNA二级结构及蛋白质的二级结构和抗原表位分析。结果表明，在282 bp的外显子3序列中共检测到7个SNPs，分别为：T10C、C119T（Trp→Arg）、G215C（Gln→Glu）、A238G、T245G（Ser→Ala）、G256A、C259T，这些位点在病例组和对照组之间的等位基因频率及各基因型间不存在显著性差异（P > 0.05）；进一步分析发现，各突变位点均引起RNA二级结构和最小自由能的改变，各错义突变位点均未引起蛋白质二级结构和抗原表位的改变。由此得出，DRB1基因外显子3的7个SNPs位点（T10C、C119T、G215C、A238G、T245G、G256A和C259T）与哈萨克羊布鲁氏菌病易感性无相关性。

关键词: DRB1基因; DNA池; 布鲁氏菌病; 易感性; 生物信息学

Abstract:

This study was aimed to investigate the association between the polymorphism of lymphocyte antigen DRB1 gene exon 3 and the brucellosis susceptibility to Kazakh sheep.The polymorphism of DRB1 gene exon 3 in Kazakh sheep was analyzed using direct sequencing method of mixed DNA pooling combined with PCR products.The differences in gene frequency and genotype frequency of each SNP site were analyzed by chi-square test.Bioinformatics software was used to analyze the secondary structure of RNA,the secondary structure of protein and antigen epitope of the PCR amplification sequence.The sequencing result showed that 7 SNPs sites were detected in 282 bp DNA sequence,including T10C,C119T(Trp→Arg),G215C(Gln→Glu),A238G,T245G(Ser→Ala),G256A and C259T,there was no significant difference in gene frequency and genetype frequency between brucellosis case and control groups (P > 0.05).The further analysis showed that the mutation site all caused the change of the secondary structure of RNA and minimum free energy,each missense mutation did not cause the change of protein secondary structure and antigen epitope.The results showed that the 7 SNPs sites (T10C,C119T,G215C,A238G,T245G,G256A and C259T) of DRB1 gene exon 3 had no correlation with brucellosis susceptibility in Kazakh sheep.

Key words: DRB1 gene; DNA pooling; brucellosis; susceptibility; bioinformatics

中图分类号:

S813.3

王元元, 严国, 罗成, 齐江姣, 周光普, 谭君, 高剑峰. 哈萨克羊DRB1基因外显子3多态性及生物信息学分析[J]. 《中国畜牧兽医》, 2018, 45(3): 721-729.

WANG Yuanyuan, YAN Guo, LUO Cheng, QI Jiangjiao, ZHOU Guangpu, TAN Jun, GAO Jianfeng. Polymorphism and Bioinformatics Analysis of DRB1 Gene Exon 3 in Kazakh Sheep[J]. , 2018, 45(3): 721-729.

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