Type

Journal Article

Authors

Sinead McParland
Donagh P. Berry
Daniel Gerard Mary Bradley
Deirdre C Purfield

Subjects

Veterinary

Topics
cattle animals high density bi allelic snps single nucleotide polymorphism pedigree based inbreeding coefficients history heterozygosity nonhuman pedigree snp genotypes correlation coefficient runs of homozygosity genotype population gene frequency run of homozygosity chromosomal localization homozygosity inbreeding

Runs of homozygosity and population history in cattle (2012)

Abstract Background: 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.Results: 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.Conclusions: 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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Full list of authors on original publication

Sinead McParland, Donagh P. Berry, Daniel Gerard Mary Bradley, Deirdre C Purfield

Experts in our system

1
S McParland
Teagasc
Total Publications: 44
 
2
D P Berry
Teagasc
Total Publications: 243
 
3
Daniel Bradley
Trinity College Dublin
Total Publications: 84
 
4
Deirdre C Purfield
Teagasc
Total Publications: 23