Analysis of genome regions showing strong inbreeding in Brown Swiss and Fleckvieh cattle

  • H Schwarzenbacher


Two breeds with diverse breeding history were analysed for footprints of recent inbreeding. For this purpose, SNP chip data from 4,049 Brown Swiss and 8,307 Fleckvieh bulls was analysed for long homozygous segments, so called ‘runs of homozygosity’. Presence and length of homozygous blocks in the genome was substantially higher in Brown Swiss when compared to Fleckvieh. Across chromo-somes, BTA 5 and 6 showed the strongest inbreeding, particularly in Brown Swiss. The genome-wide search for regions with extensive homozygosity revealed large runs of homozygosity around 35 and particularly 91 MB on BTA 6. At a single location on BTA 6 a large homozygous block of more than 5 MB was present in 50% of all Brown Swiss bulls.