高低产群香猪X染色体的结构变异比较分析

发布时间：2019-02-18 22:38

【摘要】：为了明确香猪(Sus scrofa)基因组的结构变化与繁殖调节机制之间的联系,采用二代测序技术对6头香猪进行了基因组重测序。结合数种生物信息学分析方法,从香猪高产组(XH)与低产组(XL)X染色体中检测到丰富的结构变异(structural variations,SV)。在香猪X染色体(chr X)上检测到3 246个SVs,进一步比较发现有311个SVs是XH组特有的,138个SVs只存在于XL组,合计449个SVs;XH组chr X染色体上61~109 Mb发现一个SV热点区域,XH组的热点区中有138个SVs,其中65个为缺失类型。449个SVs中,80个SVs位于基因内,影响了47个蛋白编码基因,31个基因位于繁殖相关的数量性状位点(quantitative trait locus,QTL)区域内,其中包括NLGN4X、GPR143、ZDHHC15、ATRX、NXF2、AMOT、GRIA3、THOC2等。对47个基因进行基因本体论(Gene Ontology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)通路分析表明这些基因涉及繁殖、免疫及脂代谢相关的生物功能和通路,如肾上腺发育(adrenal gland development)、胞内类固醇激素受体信号调控通路(regulation of intracellular steroid hormone receptor signaling pathway)、RIG-I受体信号通路(RIG-I-like receptor signaling pathway)和脂蛋白代谢过程(lipoprotein metabolic process)。利用PCR方法对10/47个SVs进行群体验证,得出SV_GPR143在高低产群中存在差异(P0.05),基因型DD的产仔数低于基因型NN的产仔数(n=1.96,P0.05),与产仔数有一定的相关性(ρ=0.217)。本研究深入细致的SV分析表明XH组存在更为丰富的SVs,可为解析香猪产仔数变化的遗传机制提供理论依据。
[Abstract]:In order to clarify the relationship between the structural changes of (Sus scrofa) genome and the mechanism of reproduction regulation, six Xiang pig genomes were resequenced by the second generation sequencing technique. Combined with several bioinformatics analysis methods, abundant structural variations (structural variations,SV) were detected from (XL) X chromosomes of high yield and low yield groups of Xiang pigs. A further comparison of 3 246 SVs, detected on X chromosome (chr X) of Xiang pig showed that 311 SVs were unique to XH group, 138 SVs only existed in XL group, with a total of 449 SVs;. A SV hot spot region was found on chr X chromosome 61n109 Mb in XH group, and 138 SVs, were found in XH group. Of 449 SVs, 80 SVs were located in the gene, which affected 47 protein coding genes. 31 genes, including NLGN4X,GPR143,ZDHHC15,ATRX,NXF2,AMOT,GRIA3,THOC2, are located in the (quantitative trait locus,QTL region of reproductive related quantitative trait loci. Genetic ontology (Gene Ontology,GO) and (Kyoto Encyclopedia of Genes and Genomes,KEGG pathway analysis of 47 genes showed that these genes were involved in biological functions and pathways related to reproduction, immunity and lipid metabolism. Intracellular steroid hormone receptor signaling regulatory pathway for adrenal development (adrenal gland development), (regulation of intracellular steroid hormone receptor signaling pathway), RIG-I receptor signaling pathway (RIG-I-like receptor signaling pathway) and lipoprotein metabolism (lipoprotein metabolic process).) PCR method was used to validate 10 / 47 SVs populations. The results showed that there were differences in SV_GPR143 between high and low yield groups (P0.05). The number of offspring of genotype DD was lower than that of genotype NN (nng1.96% P0.05). There was a certain correlation between litter size and litter size (蟻 = 0.217). In this study, detailed SV analysis showed that the existence of more abundant SVs, in XH group could provide theoretical basis for the analysis of genetic mechanism of piglet litter size change.
【作者单位】：贵州大学生命科学学院/农业生物工程研究院;贵州大学动物科学学院;
【基金】：国家高技术研究发展计划(863)项目(No.2013AA102503) 贵州省“百”层次创新型人才项目(黔科合人才2016-4012号) 贵州省农业攻关项目(黔科合NY[2013]3073号) 国家自然科学基金项目(No.31672390)
【分类号】：S828

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