Runs of homozygosity and population history in cattle

TLDR

Runs of homozygosity are contiguous stretches of homozygous genotypes inherited from identical parental haplotypes, and their extent and frequency can reveal an individual’s ancestry and population history. The study correlates ROH with pedigree‑based inbreeding coefficients using 777,962 high‑density SNPs across cattle breeds and validates the approach with 54,001 SNP genotypes. All genotyped animals exhibited at least one 1–5 Mb ROH, and strong correlations (r = 0.75, p < 0.0001) between pedigree‑based inbreeding and the sum of ROH > 0.5 kb demonstrate that ROH extent can infer recent population history, with breed‑specific patterns reflecting origins and management.

Abstract

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.