Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600\u2009K SNP array

Qing Ma,Xiaohong He,Qianjun Zhao,Yabin Pu,Xuexue Liu,Yuehui Ma,Yingkang Li,Jianfei Pan,Lin Jiang,Lina Ma

doi:10.1038/s41598-017-00847-9

Abstract

Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs. Subsequently, ten novel CNVRs were randomly chosen for further quantitative real-time PCR (qPCR) confirmation, and eight were successfully validated. Gene functional enrichment revealed that these CNVRs cluster into Gene Ontology (GO) categories of homeobox and embryonic skeletal system morphogenesis. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. We constructed a Chinese indigenous sheep genomic CNV map based on the Illumina Ovine SNP 600 K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep.

Highlights

Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array
The pea-comb phenotype is caused by a Copy number variants (CNVs) in intron 1 of the SOX5 gene[4], and the late feathering locus comprises a partial duplication of the PRLR and SPEF2 genes[5]
We found that approximately 48.5% of the CNVs range from 10 kb to 50 kb, 21.7% of CNVs range from 50 kb to 100 kb in size, with 12.2% being small fragment CNVs (

Summary

Introduction

Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array. Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. We used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. One CNVR overlapping with the homeobox transcription factor DLX3 and previously shown to be associated with curly hair in sheep was identified as the candidate CNV for the special curly fleece phenotype in Tan sheep. K BeadChip array, providing an important addition to published sheep CNVs, which will be helpful for future investigations of the genomic structural variations underlying traits of interest in sheep. More efforts are needed to identify CNVs, one of the most important types of genomic variation, in the sheep genome

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Conclusion