Performance of Illumina and Affymetrix Bovine High Density Genotyping Platforms in Holsteins and Jerseys

The performance of the Illumina High–Density Bovine BeadChip Array (777,962 SNP) and the Affymetrix Axiom Genome–Wide BOS 1 Array (648,874 SNP) was evaluated using DNA samples derived from 10 Holstein and 6 Jersey cattle. An independent set of DNA samples taken from 46 Jerseys and 18 Holsteins was used to ascertain the amount of SNP variation accounted by the 16 experimental samples. Data were edited to remove SNP having a call rate less than 90%, and those in linkage disequilibrium (r² ≥ 0.9). Maximum, average and median gaps were calculated for each analysis based on the SNP position on the bovine UMD3.1 genome assembly. All samples were successfully genotyped (≥98% SNP genotyped) with both platforms. Based on genomic position, 107,896 SNP were shared between the two platforms. Both Affymetrix BOS 1 and Illumina BovineHD genotyping platforms are well designed and provide high quality genotypes and similar coverage of informative SNP. Despite fewer total SNP on BOS 1, 19% more SNP remained after LD pruning, resulting in a smaller gap size (5.2kb vs 6.9kb) relative to BovineHD. Genome-wide CNV analyses were performed using intensity files from both platforms. The BovineHD platform provided an advantage on the CNV data compared to the BOS 1 because of the larger number of SNP, higher intensity signals and lower background effects. The combined use of both platforms significantly improved coverage over either platform alone and reduced the gap size between SNP, providing a valuable tool for fine mapping QTL and multibreed animal evaluation.