Detection of Genome-Wide Copy Number Variation in Bovine Using the Axiom® Genotyping Solution from Affymetrix

Background: In Bovine, copy number variations (CNVs) have been implicated in both disease phenotypes and phenotypic variation associated with quantitative traits. The Axiom® Genome-Wide BOS 1 Bovine Array, along with the available software tools from Affymetrix and BioDiscovery, offer a valuable resource for evaluation of the impact of CNVs with respect to variation in bovine health and production traits. The Axiom® CNV Summary Tools Software uses intensity and genotypes to calculate log2 ratios and B allele frequencies (BAF) from genotyping data. The files generated are compatible for use with BioDiscovery Nexus Copy Number^TMSoftware package for further detailed analysis and visualization. Log2 ratios and BAFs are provided as input to the software, where the SNP-FASST2 segmentation algorithm, with customizable thresholds, can be used.

Results: Examples of copy number gains and losses across and within breeds have been identified. Analysis of a large set of animals belonging to several different breeds shows multiple CNV events of 30 Kb or larger per sample. A roughly 1Mb gain was found on chromosome 12 in a majority of the Hereford samples corresponding to the CD164 gene. This gain was also reproduced in five replicates of the same animal. A 50Kb loss was observed on chromosome 3 across animals of multiple breeds: Nelore, Gir, Brahman, and Hereford.