Abstract
Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
Highlights
The availability of several forms of DNA variants, such as single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), has played an important role in phenotypic variation studies
The average number of CNVs involved in CNV regions (CNVR) was 14.58 per individual, with an average length and median size of 324.27 kb and 172.58 kb, respectively
This is partially due to the fact that the BeadChip SNP50K assay was originally developed for high-throughput SNP genotyping in association studies
Summary
The availability of several forms of DNA variants, such as single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), has played an important role in phenotypic variation studies. GWAS between CNVs and milk traits in sheep have been shown to be associated with complex traits in several species, including chimpanzees [7], rats [8], and mice [9], and in livestock species such as cattle [10,11,12,13,14], goats [15], and pigs [16, 17]. CNVs have recently been used as markers of phenotypic variation, environmental adaptability, and for economically important traits or disease susceptibility in livestock species [18,19,20]. To the best of our knowledge, no GWAS between CNVs detected using the OvineSNP50K BeadChip array and economically important traits (milk, meat, etc) in sheep breeds have been published
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