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

Abstract

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.

CLC Number:

S829.2

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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Uncovering Genome-wide Copy Number Variations in 16 Chinese Indigenous Dog Breeds Using Canine 170 K High-Density SNP Chips

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