利用犬170K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

doi:10.11843/j.issn.0366-6964.2017.06.006

摘要/Abstract

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170 K SNP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142.24 kb。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。

关键词: 犬, SNP 芯片, 拷贝数变异, 基因组, 拷贝数变异基因

Abstract:

The main purpose of this study was to decipher the genomic copy number variation (CNV) of Chinese indigenous dog breeds and provide the basic information for elucidating the effect of CNV on canine phenotypic variation. In this study, we collected the blood samples of 176 dogs from 16 different Chinese indigenous breeds and 9 Rottweiler dogs. DNA was extracted by blood DNA extraction kit. All experimental dogs were genotyped using Illumina CanineHD 170 K SNP chip according to the manufacturer's instructions. The CNV detection covering genome-wide was conducted after quality control according to the protocol of PennCNV software. We randomly selected 8 CNVRs for validation by real-time quantitative PCR. And the genes and their functional annotations were performed with BioMart and DAVID. We totally found 477 CNVs in 185 individuals. These CNVs were randomly distributed on 38 autosomes. We identified 220 CNVRs by merging the 477 CNVs. These CNVRs occupied about 1.25% of dog whole-genome sequence, their average length was 142.24 kb. Among the 220 CNVRs, 115 were deletion, 74 were duplication and 31 were deletion/duplication. Furthermore, 53 CNVRs observed were specifically identified in Chinese indigenous breeds. We found that 162 genes were located within the CNVRs detected in this study. These CNV-genes were enriched in function terms of olfactory receptor activity, sensory perception of smell, sensory perception of chemical stimulus, sensory perception and neurological system process.The present study illustrate the distribution of CNVs in the genome of Chinese indigenous dogs, and will benefit for further research on the relationship between CNV and canine phenotypic variation.

Key words: dog, SNP chip, copy number variation, genome, copy number variation genes

中图分类号:

S829.2

刘晨龙, 杨前勇, 陈浩, 黄晓畅, 陈从英. 利用犬170K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[J]. 畜牧兽医学报, 2017, 48(6): 1017-1027.

LIU Chen-long, YANG Qian-yong, CHEN Hao, HUANG Xiao-chang, CHEN Cong-ying. Uncovering Genome-wide Copy Number Variations in 16 Chinese Indigenous Dog Breeds Using Canine 170 K High-Density SNP Chips[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(6): 1017-1027.

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