Runs of homozygosity and levels of inbreeding in cattle breeds.

Inbreeding results in identity by descent of maternally and paternally inherited alleles. Due to the process of recombination that combines maternal and paternal DNA in very large chunks during meiosis, inbreeding to a recent ancestor results in relatively long homozygous segments of the genome, "runs of homozygosity". High density genotyping renders the search for such homozygous segments relatively easy. Runs of homozygosity that are several megabases (Mb) long are due to inbreeding to a recent ancestor. We have searched for runs of homozygosity that are longer than 2 Mb, 4 Mb, 6 Mb, 8 Mb and 10 Mb, respectively, and expressed these segments as proportions of the total length of the autozygous genome, based on SNP positions available. Very long segments most likely result from recent inbreeding while shorter segments may have been caused by inbreeding to ancestors further in the past. The breeds involved in the study are Fleckvieh (dual purpose Simmental), Brown Swiss, Norwegian Red, 500 animals each, and Tyrol Grey, 213 animals. On long and informative pedigrees, inbreeding coefficients were calculated for the full pedigree available and for subsets including a maximum of 5 generations for each individual. Results indicate a high correlation (>0.80) of individual runs of homozygosity with pedigree inbreeding coefficients of animals when calculating correlations across breeds. Within breeds, correlations were smaller (~0.70) because of differences in inbreeding levels in these breeds. We conclude that the proportion of the genome arranged in long homozygous segments provides a good indication of level of inbreeding of an animal that is more informative than the probability of autozygosity derived from from pedigree data.