Detection of runs of homozygosity in Norwegian Red: Density, criteria and genotyping quality control

Abstract

© 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group. Runs of homozygosity (ROH) are long, homozygote segments of an individual’s genome, traceable to the parents and might be identical by descent. Due to the lack of standards for quality control of genotyping and criteria to define ROH, Norwegian Red was used to find the effects of SNP density, genotyping quality control and ROH criteria on the detection of ROH. A total of 384 bulls were genotyped with the Illumina HD-chip containing 777,962 SNP markers. A total of 22 data subsets were derived to examine the effects of SNP density, quality control of genotyping and ROH criteria. ROH was detected by PLINK. High SNP density led to increased resolution, fewer false-positive ROH segment, and made it possible to detect shorter ROH. Considering the ROH criteria, we demonstrated that allowing for heterozygote SNP could generate false positives. Furthermore, genotyping quality control should be tuned towards keeping as many SNP as possible, also low minor allele frequency SNP, as otherwise many ROH segments will be lost.