Relationship between call rate per individual and genotyping accuracy of bovine single-nucleotide polymorphism array using deoxyribonucleic acid of various qualities

Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding. However, the relationship among sample genotyping efficiency (call rate per individual), accuracy of SNP genotypes, and DNA quality (integrity, concentration, and mixture of DNA, i.e., chimerism) remains unknown. We determined the effect of DNA quality on call rate per individual and accuracy of SNP genotypes using artificial DNA samples of various qualities. Integrity and concentration of DNA were less sensitive to call rate per individual and accuracy of genotyping in the SNP array. Chimerism strongly affected call rate per individual and accuracy of SNP genotypes. Artificial chimerism experiments showed that relative to unmixed DNA, the genotypic matching error (%) of mixed DNAs linearly increased with mix ratio, whereas the call rate per individual in some samples at 50% mix ratio was >0.95. However, individuals with higher chimerism were readily identified based on standard deviation of B-allele frequency (BAF) and BAF distribution across the genome from SNP array data. Thus, we effectively managed the balance by maximizing genotyping accuracy and minimizing the number of samples for re-genotyping by using quality control for combining call rate per individual with BAF.