Ascertainment Bias in Cattle SNP Arrays and Implications for Multibreed Genomic Predictions

Ascertainment bias of SNP for genotyping arrays, where markers are discovered largely in one breed then used to genotype other breeds, can affect scaling and dispersion of genomic breeding values in multibreed genomic evaluations. Detecting and addressing this bias is crucial for robust genetic analyses. Using whole genome sequence data, we demonstrate the extent of ascertainment bias in the most commonly used bovine high density SNP marker array. Results show that arrays such as the Bovine high density (HD) array severely underrepresents diversity in Bos taurus indicus relative to Bos taurus taurus (particularly Herefords). This will have consequences for dispersion of genomic breeding values and how well these genomic breeding values capture genetic merit within and across breeds. Genomic evaluations that include both subspecies should account for ascertainment bias.