Data from: Application of genomic estimation methods of inbreeding and population structure in an Arabian horse herd

Horse breeders rely heavily on pedigrees for identification of ancestry in
breeding stock. Inaccurate pedigrees may erroneously assign individuals to
false lineages or breed memberships resulting in wrong estimates of
inbreeding and coancestry. Moreover, discrepancies in pedigree records can
lead breeders seeking to limit inbreeding into making misguided breeding
decisions. Genome-wide SNPs provide a quantitative tool to aid in the
resolution of lineage assignments and the calculation of genomic measures
of relatedness. The aim of this project was to pilot a comparison between
pedigree and genomic relatedness and inbreeding measures in a herd of 36
pedigreed Egyptian Arabian horses genotyped using the Equine SNP70
platform (Geneseek, Inc.). Moreover, we sought to estimate the minimum
number of markers sufficient for genomic inbreeding calculations. Pedigree
inbreeding values were moderately correlated with genomic inbreeding
values (r = 0.406), whereas genomic relationships and pedigree
relationships have a high correlation (r = 0.77). Although first degree
relationships were successfully reconstructed, more distant relationships
were difficult to resolve. Multi-dimensional scaling and clustering
analysis agreed with within-herd pedigree information. In comparing the
herd to a reference sample of United States, Polish, and Egyptian Arabian
horses, the herd's historically recorded Egyptian lineage was
successfully recovered. We conclude that genomic estimates of inbreeding
and relationships are superior to their pedigree counterparts. They can be
thus utilized in conservation of valuable lines of livestock, and in
breeds at risk for loss of genomic diversity. We also postulate a minimum
of 2000 markers in linkage equilibrium to be used for inbreeding
estimation.