Abstract
Recent studies of mammalian genomes have uncovered the vast extent of copy number variations (CNVs) that contribute to phenotypic diversity. Compared to SNP, a CNV can cover a wider chromosome region, which may potentially incur substantial sequence changes and induce more significant effects on phenotypes. CNV has been becoming an alternative promising genetic marker in the field of genetic analyses. Here we firstly report an account of CNV regions in the cattle genome in Chinese Holstein population. The Illumina Bovine SNP50K Beadchips were used for screening 2047 Holstein individuals. Three different programes (PennCNV, cnvPartition and GADA) were implemented to detect potential CNVs. After a strict CNV calling pipeline, a total of 99 CNV regions were identified in cattle genome. These CNV regions cover 23.24 Mb in total with an average size of 151.69 Kb. 52 out of these CNV regions have frequencies of above 1%. 51 out of these CNV regions completely or partially overlap with 138 cattle genes, which are significantly enriched for specific biological functions, such as signaling pathway, sensory perception response and cellular processes. The results provide valuable information for constructing a more comprehensive CNV map in the cattle genome and offer an important resource for investigation of genome structure and genomic variation underlying traits of interest in cattle.
Highlights
With the rapid progress of genome sequencing, the abundance of single nucleotide polymorphisms (SNPs) as a major source of genetic variation has been widely recognized
The numbers of copy number variations (CNVs) called by PennCNV, GADA and cnvPartition were 219, 169 and 140, respectively (Fig. 1)
The total length of all CNV regions (CNVRs) is 23.24 Mb and covers 0.91% of the whole bovine genome. These CNVRs are located on all chromosomes except BTAs 22, 25, 29 and X
Summary
With the rapid progress of genome sequencing, the abundance of single nucleotide polymorphisms (SNPs) as a major source of genetic variation has been widely recognized. Great efforts were made to develop high-throughput SNP genotyping platforms, and genome-wide high density SNP chips have been designed for many species including human and major farm animal species, such as cattle, swine, sheep, and chicken. Using these SNP chips, a large number of genome-wide association studies (GWAS) have been carried out in milking and meat production as well as diseases in cattle [1,2,3]. It has been found that many CNVs contribute to phenotypic variation in animals [32,33,34] as well as in humans [35,36,37,38,39]
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