Identification of Copy Number Variants in the Nellore and Angus Founders of a Mapping Population

Copy Number Variation (CNV) is a distinct class of structural variation that includes insertions and deletions in the genome ranging for 1 kb to 5 Mb. Illumina paired end 100 bp reads for 7 Nellore bulls and 6 Angus cows (33 to 88x coverage), which were the founders of a multigenerational mapping population, were aligned with BWA to the UMD3.1 bovine assembly.  One Angus cow was the reference individual for all pairwise comparisons with cnv-seq, which identifies CNV based on differences in read depths after normalization for depth of coverage across the genome.  We used strict threshold values for CNV detection (P = 0.001 and log₂ threshold = 0.7) and compared results from analyses with overlapping windows of 3kb, 4kb, or 5 kb, and used 10 consecutive windows for annotation. We detected putative CNV regions (CNVR) on all 29 autosomes and the X chromosome. Counts per individual ranged from 271 to 3,795 for 10 x 3 kb windows and 141 to 1914 for 10 x 5kb windows. Some CNVR were common to both breeds, and there were more CNVR detected between the breeds than within breed.  Of the CNVR detected in at least 80% of the animals per breed, 56.56% and 57.14% overlapped Ensembl genes in Nellore and Angus, respectively.