Abstract
BackgroundIn recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity.ResultsAnalyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies.ConclusionsIn this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.
Highlights
In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes
SNP genotyping The genomic DNA of 329 individual samples from three sheep breeds (German Mutton sheep, Dorper and Sunite sheep) were genotyped using Illumina OvineSNP50 Genotyping BeadChip according to the manufacturer’s protocol, and the PennCNV software was used to identify the copy number variations (CNVs) in the sheep genome (Table 1)
In a comparison of the results from the PennCNV and CNVpartition programs, we found 47 CNV regions (CNVRs) identified by the PennCNV program (19.7%) that overlapped with the CNVpartition data, and the ‘losses’ and ‘gains’ of 47 CNVRs were consistent with the CNVpartition data
Summary
Genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. Genome-wide association studies (GWAS) have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex diseases or traits [1]. With the development of high density SNP arrays, higher resolution of genomic regions can be achieved [29] Due to their low cost and high-density, commercial SNP arrays have been widely used for CNV detection in domestic animals, and CNV mapping and functional studies have made important progress. There are no reports on CNV detection of sheep based on SNP array data
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