Detection of hemizygous deletions in the genome of Fleckvieh cattle using SNP chip data and the concept of Mendelian mismatches in parent–offspring pairs

Abstract Single nucleotide polymorphisms (SNPs) can serve as genetic markers to identify genetic differences between individuals. The primary objective of this study was to use SNP chip data and the concept of Mendelian mismatches to locate genomic regions that contain deletions. The dataset comprises 298 850 Fleckvieh cattle, primarily from Austria and Germany. Animal genotyping was conducted using the Illumina 50K Bead Chip and data from 40 144 autosomal SNPs were utilized. Among the 298 850 animals, sire genotypes were available for 267 393, and dam genotypes were available for 56 546 individuals. Data analysis was performed using plink and SAS. A large number (567 996) of Mendelian mismatches caused by deletions were detected, and the inheritance of the deletions could be traced back to a few ancestors. This study has shown that the detection of hemizygous deletions based on Mendelian mismatches in parent–offspring pairs is a promising approach due to the low cost and wide availability of SNP chip data for cattle. The exact positions and sizes of the deletions may be explored with whole‐genome sequence data of animals carrying these deletions.