Comparison of Two Genotyping Platforms in Canadian Beef Cattle

Two high-density single nucleotide polymorphism genotyping platforms were recently produced, the Affymetrix Axiom Genome-Wide BOS1 Array (648,874 SNP) and the Illumina High-Density Bovine Bead Chip Array (777,962 SNP). This study compares the performance of the two genotyping platforms in a multi-breed Canadian beef cattle population. DNA samples were collected from 96 beef cattle, Angus (n=42), Piedmontese (n=18), Charolais (n=9), Limousin (n=5), Salers (n=2), Gelbvieh (n=1), Blonde d’Aquitaine (n=1) and crossbreds (n=17) consisting of the reported breeds as well as Simmental. All samples were successfully genotyped with both arrays and non-autosomal SNP genotypes were removed. The average number of remaining SNP in the BovineHD and BOS1 platform were 735,293 and 630,974, respectively. SNP not in HWE (p=0.000001) or having excess of heterozgosity > 0.15, low MAF (<0.05) and call rate (<0.9) were excluded. Remaining SNP in the BovineHD platform dropped to 598,682 and 386,779 for the BOS1 platform with average gap of 4.1kbp and 6.4kbp, respectively. After LD pruning to remove linked SNP (r² ≥ 0.9) BOS1 had more SNP (240,087 vs 211,478) with smaller average gap (11.01kbp vs 11.62kbp) in comparison to BovineHD. Combining informative SNP from both platforms (1,261,128 SNP) had better coverage and performance than either platform with less average gap between SNP.