Acta Univ. Agric. Silvic. Mendelianae Brun. 2019, 67, 1447-1452
Published online 2019-12-22

Detection of Autosomal Hemizygous Regions in the Fleckvieh Population Based on SNP-chip Data and Parent Offspring Pairs

Judith Himmelbauer, Gábor Mészáros, Johann Sölkner

Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Straße 33, AT-1180 Wien, Austria

Received August 9, 2019
Accepted November 11, 2019

A Copy Number Variation (CNV) is a loss or a gain in the DNA sequence, ranging from 50 basepairs to a few megabasepairs. Most studies use whole genome sequencing data to detect deletions. Due to the fact that SNP-chip data is more commonly used in livestock, especially in cattle, the detection of deletions based on SNP-chip data is of interest. In the present study an approach based on SNP chip data and the analysis of Mendelian mismatches in parent-offspring-pairs was developed. Use was made of the fact that deletions appear as homozygous after SNP Chip genotyping. For some SNPs with high number of mismatches, the inheritance of the mismatches could be traced back to one or a few bulls and thereby regions of possible deletions were defined. The study has shown that an approach based on Mendelian mismatches and SNP-chip data is a promising way of detecting deletions.


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