利用犬170 K高密度SNP芯片检测16个中国地方犬种全基因组拷贝数变异

发布时间：2018-05-07 08:51

本文选题：犬 + SNP芯片　；参考：《畜牧兽医学报》2017年06期

【摘要】：旨在解析中国地方犬全基因组拷贝数变异(CNV)分布情况,为分析CNV对犬表型变异的影响提供前期基础。本研究采集了16个来自中国不同地方犬品种和9头罗威纳犬共计185头犬的血液样品,使用血液DNA提取试剂盒提取DNA,利用犬170KSNP芯片和PennCNV软件对中国地方犬进行全基因组范围内的CNV分析。参照Illumina芯片标准操作流程进行芯片扫描和基因分型。将质控后的SNP参考PennCNV软件使用说明书,设定分析参数进行CNV检测分析。从分析结果中随机挑选8个CNV区间(CNVRs)使用实时定量PCR进行验证。利用BioMart以及DAVID软件进行基因和功能注释分析。结果表明,在185个个体中共发现了477个CNV,这些CNV随机分布在38条常染色体上,合并后可以得到220个CNVR,总长度约占犬整个基因组序列的1.25%,平均长度为142.24kb。在220个CNVR中,115个为缺失,74个为重复,31个为缺失/重复CNVR。此外,笔者发现53个CNVR为潜在的中国地方犬品种特异性CNVR。在基因和功能注释中,本研究共发现162个基因位于所检测到的CNVR内,这些基因主要富集的功能类别是嗅觉受体活动,嗅觉的感知,对化学刺激物的感知,感官知觉和神经系统过程。这些结果解析了中国地方犬基因组结构变异分布情况,将有助于进一步研究CNV与犬表型变异的关联性。
[Abstract]:The aim of this study was to analyze the distribution of complete copy number variation (CNVs) in Chinese local dogs, and to provide a preliminary basis for the analysis of the effect of CNV on the phenotypic variation of dogs. In this study, blood samples were collected from a total of 185 dogs from 16 different breeds of dogs from different parts of China and 9 Rovina dogs. The blood DNA extraction kit was used to extract the DNA, and the genomic CNV was analyzed by using the canine 170KSNP chip and PennCNV software. According to the standard operating procedure of Illumina chip, the chip scanning and genotyping were carried out. SNP after quality control refer to the PennCNV software instructions, set the analysis parameters for CNV detection and analysis. Eight CNV intervals were randomly selected from the analysis results to be verified by real time quantitative PCR. BioMart and DAVID software were used to analyze gene and function annotation. The results showed that 477 CNVs were found in 185 individuals. These CNV were randomly distributed on 38 autosomes, and 220 CNVRs were obtained after merging. The total length of CNVs was about 1.25 kb of the total genome sequence in dogs, with an average length of 142.24 kb. Of 220 CNVR, 115 were deletions, 74 were duplicates, and 31 were deletions / repeats. In addition, 53 CNVR were found to be potential Chinese local breeds specific CNVRs. In gene and functional annotations, 162 genes were found to be located in the detected CNVR. The major functional types of these genes are olfactory receptor activity, olfactory perception, and perception of chemical stimuli. Sensory perception and nervous system processes. These results are helpful to further study the relationship between CNV and phenotypic variation in dogs.
【作者单位】：江西农业大学省部共建猪遗传改良与养殖技术国家重点实验室;公安部南昌警犬基地;
【基金】：国家高技术研究发展计划(863计划)(2013AA102502)
【分类号】：S829.2

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