Runs of Homozygosity Reveal Genome- wide Autozygosity in the Austrian Fleckvieh Cattle

Abstract

Summary Runs of homozygosity (ROH) are recognized as potential inbreeding measure in studies on humans. Inbreeding coeffi cients derived from ROH (F ROH ) measure proportion of the genome arranged in long homozygous segments and highly correlate with those derived from pedigree (F ped ). From that we assumed that ROH represent an alternative to pedigree inbreeding levels in studies on animals too, because pedigree can be incorrect, incomplete and can not fully explain what happened in meiosis. To confi rm our premise we used pedigree and genotype data from 500 Austrian dual purpose Simmental bulls to determine correlation between F ROH and F ped . ROH were obtained using Fortran 90 soft ware created by the authors. Proportions of genome in ROH were calculated for lengths of ROH of >1, >2, >4, >8 and >16 Mb. Pedigree data were analyzed and inbreeding coeffi cients for complete pedigree (FpedT) and fi ve generations (F ped5 ) were calculated using ENDOG soft ware. We found low F pedT and F ped5 (means of 1.5% and 0.9%) while FROH for segments >1Mb suggested much higher values (9.0%) indicating old inbreeding that can not be traced using pedigree. Th e highest correlations were found between FROH calculated from ROH of length >4Mb and F pedT (0.68) that is consistent with studies on humans. We conclude that inbreeding coeffi cients derived from ROH are useful for measuring levels of inbreeding in cattle, because ROH are not subject to mistakes as pedigrees and calculations made from those.