Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis
Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis
复制标题
利用 GWAS 和转录组微阵列分析筛选猪链球菌血清型 2 耐药基因
DOI：
10.1186/s12864-018-5339-9
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发表时间：
2018-12-12
期刊：
影响因子：
4.4
通讯作者：
Fan, Hongjie
中科院分区：
文献类型：
--
作者：
Ma, Zhe;Zhu, Haodan;Fan, Hongjie
背景猪链球菌病给养猪业造成了巨大的经济损失，其主要病原是猪链球菌2型（Streptococcus Suis serotype 2，SS 2）。抗病育种是解决这一问题的根本途径。随着GWAS和转录组芯片技术的发展，我们现在有了强大的研究工具来鉴定SS 2耐药基因。通过这两个小鼠品系的F-2代和GWAS分析，我们鉴定了与SS 2抗性性状相关的286个显著小鼠基因组SNP位点。利用基因芯片技术分析了SS 2感染压力下C57 BL/6和A/J的基因表达谱。在SS 2感染过程中，这两种小鼠品系之间总共鉴定出251个差异表达基因。在结合GWAS和基因表达谱数据后，我们定位了两个与SS 2抗性显著相关的基因，它们是含有1个乌巴结构域的基因（Ubac 1）和Epn 1基因（Epn 1）。GO分类和过度表达分析显示9个与免疫功能相关的基因表达上调，可能与C57 BL/6猪的SS 2抗性有关。结论本研究首次将SNP芯片和基因表达谱芯片用于小鼠SS 2抗性基因的鉴定，为猪SS 2抗性育种提供了依据。
BackgroundSwine streptococcosis has caused great economic loss in the swine industry, and the major pathogen responsible for this disease is Streptococcus Suis serotype 2 (SS2). Disease resistance breeding is a fundamental way of resolving this problem. With the development of GWAS and transcriptomic microarray technology, we now have powerful research tools to identify SS2 resistance genes.ResultsIn this research, we generated an F-2 generation of SS2 resistant C57BL/6 and SS2 susceptive A/J mice. With the F-2 generation of these two mice strains and GWAS analysis, we identified 286 significant mouse genome SNPs sites associated with the SS2 resistance trait. Gene expression profiles for C57BL/6 and A/J were analyzed under SS2 infection pressure by microarray. In total, 251 differentially expressed genes were identified between these two mouse strains during SS2 infection. After combining the GWAS and gene expression profile data, we located two genes that were significantly associated with SS2 resistance, which were the UBA domain containing 1 gene (Ubac1) and Epsin 1 gene (Epn 1). GO classification and over-representation analysis revealed nine up-regulated related to immune function, which could potentially be involved in the C57BL/6 SS2 resistance trait.ConclusionThis is the first study to use both SNP chip and gene express profile chip for SS2 resistance gene identification in mouse, and these results will contribute to swine SS2 resistance breeding.