Single Nucleotide Variants and Indels Identified from Whole-Genome Re-Sequencing of Gyr, Girolando and Holstein Cattle Breeds

Whole-genome re-sequencing, alignment and annotation analyses were undertaken for ten sires representing Gyr, Girolando and Holstein cattle breeds to detect and make publicly available genome-wide single nucleotide variations (SNVs) and insertions/deletions (InDels). A total of approximately 3.5 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. Sequencing reads were mapped to the UMD 3.1 bovine genome assembly using the Burrows-Wheeler Aligner tool (v. 0.7.10-r789) with default parameters. Picard tools (v. 1.54) were used to eliminate PCR duplicates and the variant calling was conducted with Freebayes. The resulting variant list obtained for each animal were filtered by vcffilter in order to remove variants with quality scores lower than 30 or coverage lower than 7. A total of 23,743,970 SNVs and 3,171,711 InDels were detected in the samples, of which approximately 2,224,013 SNVs and 798,8910 InDels were novel. The high number of genetic variants identified for each animal within the same breed shows the importance of re-sequencing to identify novel variants for monitoring genetic diversity in the cattle breeds and for developing strategies to prevent some eventual loss of genetic variability. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed by David (v. 6.8) tool and revealed that variants in the olfactory transduction pathway was over represented in all three cattle breeds, while the ECM-receptor interaction pathway was over represented only in Girolando breed, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. Therefore, the genetic variants discovered in this study provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, and Holstein breeding programs.