Levels of inbreeding dervied from runs of homozygosity : a comparison of Austrian and Norwegian cattle breeds
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- Master's theses (IHA) 
Conventionally, levels of inbreeding for livestock animals are estimated analyzing pedigree data. The recent availability of high density SNP arrays for the bovine genome has provided the opportunity for investigation of levels of autozygosity based on runs of homozygosity (ROH). A run of homozygosity is a continuous segment of DNA sequence without heterozygosity in the diploid state. Levels of homozygosity derived from ROH are recognized as potential inbreeding measure in livestock animals. Here we compare levels of homozygosity derived from proportion of ROH in genome (FROH) and pedigree inbreeding estimates (Fped). We analyzed genotype and pedigree data from 1687 animals from four cattle breeds (Brown Swiss, Norwegian Red, Tyrol Grey and Fleckvieh – dual purpose Simmental). Distribution of ROH was obtained by PLINK software, while proportions of genome in ROH were calculated for five cut-off lengths (1Mb, 2Mb, 4Mb, 8Mb, 16Mb). Pedigree data was analyzed by PEDIG software and inbreeding coefficients for complete pedigree (average complete generation equivalents ranging from 6.46 to 9.02 for the four breeds) and over 5 generations were calculated. Levels of autozygosity from 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 (FpedT) varying from 0.619 for Norwegian Red up to 0.705 for Tyrol Grey. We conclude that 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.