Abstract
BackgroundRecently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain CNV region has been found to be associated with the onset of diseases. Therefore, CNV is now known as an important genomic variation in biological mechanisms. However, most CNV studies have only involved the human genome. The study of CNV involving other animals, including cattle, is severely lacking.ResultsIn our study of cattle, we used Illumina BovineSNP50 BeadChip (54,001 markers) to obtain each marker's signal intensity (Log R ratio) and allelic intensity (B allele frequency), which led to our discovery of 855 bovine CNVs from 265 cows. For these animals, the average number of CNVs was 3.2, average size was 149.8 kb, and median size was 171.5 kb. Taking into consideration some overlapping regions among the identified bovine CNVs, 368 unique CNV regions were detected. Among them, there were 76 common CNVRs with > 1% CNV frequency. Together, these CNVRs contained 538 genes. Heritability errors of 156 bovine pedigrees and comparative pairwise analyses were analyzed to detect 448 common deletion polymorphisms. Identified variations in this study were successfully validated using visual examination of the genoplot image, Mendelian inconsistency, another CNV identification program, and quantitative PCR.ConclusionsIn this study, we describe a map of bovine CNVs and provide important resources for future bovine genome research. This result will contribute to animal breeding and protection from diseases with the aid of genomic information.
Highlights
The discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed
After all CNVs were aggregated for the CNV region (CNVR), 368 CNV regions (CNVRs) were identified (Additional file 2; table s2)
76 CNVRs with > 1% frequency, 22 CNVRs with > 2.5% frequency, and 6 CNVRs with > 5% frequency were inferred from this study
Summary
The discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Structural variations that include CNV affect gene expression and are related to the onset of many diseases [7,8,9,10]. These studies usually focused only on the human genome, while studies of other animals such as cows have been minimal. A recent study found 25 CNVs in three Holsteins by array comparative genomic hybridization (aCGH) [11], an analysis that uses many bovine samples to find a way to utilize the cow’s genomic character economically is yet to be conducted. In order to investigate the association between various economically beneficial phenotypes and CNVs, more bovine CNVs would need to be discovered
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