Interpretive Summary: Runs of homozygosity and analysis of inbreeding depression
By Anne Zinn
Pedigree information has traditionally been used to assess inbreeding, but assessment of autozygosity across chromosomal segments using ROH has emerged as a valuable tool to estimate inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. Therefore, a study recently published in the Journal of Animal Science aimed to develop an approach to determine the minimum length of an autozygous segment to be declared as runs of homozygosity (ROH) and assess the implications of the minimum length threshold on measuring inbreeding depression in a purebred Hereford beef cattle population.
A search algorithm was developed to identify the minimum length of autozygous segments to be declared as ROH; the algorithm approximates the mutation enrichment at the individual level using available phenotypic information. This strategy is valuable in practice because the direct assessment of mutation enrichment using genetic/genomic information is often unavailable for the majority of livestock populations and complex traits.The assessment of the proposed method showed potential benefits regarding the estimates of the genome-wide level of autozygosity as well as the calculation of inbreeding depression. The history of line 1 Hereford cattle population was reasonably revealed by the patterns of ROH length distribution, where the intermediate-size ROH segments were predominant followed by a significant portion of short autozygous segments, reflecting immediate population bottleneck and breeding management of the herd. The results of the present study highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses.
The full study can be found on the Journal of Animal Science webpage.