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

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.

Figure 1

Length distribution of CNVs (a) and CNVRs (b) in Tan sheep.

Figure 2

Genome-wide distribution of autosomal CNVRs in Tan sheep. (a) A map of CNVRs in the sheep genome; blue, green and red represent gain, loss and both (gain and loss), respectively. (b) Correlation between CNVR counts and chromosome length.

Figure 3

A summary of CNVRs identified in the previous study and in the current study. (a) Number of known and novel CNVRs identified in the present study; gray and black boxes indicate known and novel CNVRs, respectively. (b) PCA plot of different studies. (c) qPCR validation of eight selected CNVRs.

Figure 4

CNVR-harboring genes. (a) Number of CNVRs located within the genic and intergenic regions; black and gray indicate the genic and intergenic CNVRs, respectively. (b) Number of genes located in different QTL categories. (c) Venn diagram of CNVR numbers in four different Chinese indigenous sheep breeds.