Edin did his thesis on inbreeding levels of cattle

Thesis title

Levels of inbreeding derived from runs of homozygosity (ROH): A comparison of Austrian and Norwegian cattle breeds

Summary

Levels of inbreeding for livestock animals are conventionally estimated by using pedigree data. The main aim of this study was to empirically validate runs of homozygosity (ROH), a newly proposed measure derived from high-throughput genomic data, as a quantitative indicator of autozygosity. A run of homozygosity is a continuous segment of DNA sequence without heterozygosity in the diploid state. We calculated levels of homozygosity derived from the proportion of ROH in the genome (FROH) and compared this with pedigree based inbreeding estimates (FPED). In total, 1428 animals were analyzed, and genotype and pedigree data from four cattle breeds (Brown Swiss, Norwegian Red, Tyrol Grey and Fleckvieh – dual purpose Simmental) were compared. Proportions of genome in ROH were calculated for five cut-off lengths (1Mb, 2Mb, 4Mb, 8Mb, 16Mb).

Inbreeding levels from pedigree data were derived using all pedigree information available (complete generation equivalents ranged from 7.30 to 9.02 for the four breeds) and from pedigrees including only the recent 5 generations. Levels of autozygosity from the complete pedigree information were similar to those derived from ROH >8Mb. The strongest correlations with pedigree inbreeding coefficients were obtained between levels of homozygosity derived from ROH for cut-off length of 4Mb (FROH4 ) and inbreeding coefficients for complete pedigrees (FPED) varying from 0.619 for Norwegian Red up to 0.718 for Tyrol Grey. Our conclusion is that the proportion of the genome arranged in long homozygous segments provides a good indication of inbreeding levels and that the choice of cut-off lengths of ROH allows determining autozygosity derived from recent or remote ancestors.