Runs of homozygosity and population history in cattle
Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that are present in an individual due to parents transmitting identical haplotypes to their offspring. The extent and frequency of ROHs may inform on the ancestry of an individual and its population. Here we use high density (n = 777,962) bi-allelic SNPs in a range of cattle breed samples to correlate ROH with the pedigree-based inbreeding coefficients and to validate subsequent analyses using 54,001 SNP genotypes. This study provides a first testing of the inference drawn from ROH through comparison with estimates of inbreeding from calculations based on the detailed pedigree data available for several breeds.
All animals genotyped on the HD panel displayed at least one ROH that was between 1–5 Mb in length with certain regions of the genome more likely to be involved in a ROH than others. Strong correlations (r = 0.75, p < 0.0001) existed between the pedigree-based inbreeding coefficient and a statistic based on sum of ROH of length > 0.5 KB and suggests that in the absence of an animal’s pedigree data, the extent of a genome under ROH may be used to infer aspects of recent population history even from relatively few samples.
Our findings suggest that ROH are frequent across all breeds but differing patterns of ROH length and burden illustrate variations in breed origins and recent management.
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- Runs of homozygosity and population history in cattle
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
- Online Date
- August 2012
- Online ISSN
- BioMed Central
- Additional Links
- Runs of homozygosity
- Cattle population history
- Author Affiliations
- 1. Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
- 2. Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co, Cork, Ireland