Data from: Genetic diversity of Persian Arabian horses and their relationship to other native Iranian horse breeds

The principal aims of this study were to explore genetic diversity and
genome-wide selection signatures in Persian Arabian horses and to
determine genetic relationship of Persian Arabians with other Iranian
horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to
47 mares from the mid to late 19th century, using the equine 670k SNP
BeadChip. Mean observed and expected heterozygosity were (0.43) and
(0.45), respectively, average inbreeding measures (FROH and FPED) were
low, indicating high genetic diversity in Persian Arabian horses. Analysis
of population genetic structure using STRUCTURE and Principal Component
Analysis suggested that Persian Arabian horses can be divided into three
groups, however the groups do not match traditional matrilineal strains.
In total, 15 genomic regions were identified by at least two of the three
implemented methods, Tajima’s D, H, and H12, as potentially under
selection in Persian Arabian horses. Most of these peaks were found on
chromosome 9, overlapping with QTLs previously associated with horse
temperament. Biological function analysis of identified candidate genes
highlighted enrichment of GO term “response to lipopolysaccharide” and
KEGG pathway “chemokine-mediated signaling pathway”, which are associated
with immune responses and may have been targets of selection in Persian
Arabian horses. Independent analyses of SNP data from 30 horses of four
other Iranian breeds suggested distinct population structure between
Persian Arabian, and Turkemen and Caspian horse breeds. Overall, the
results of this study suggest a rich genetic diversity in the Persian
Arabian horses and a clear genetic differentiation with Turkemen and
Caspian breeds.