Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses

Abstract

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.

Y Chromosome Haplotypes Enlighten Origin, Influence, and Breeding History of North African Barb Horses

“…Biological samples were collected from 119 males, of Barbs (n = 84) and Arab-Barbs (n = 35) in Morocco, Algeria, Tunisia, and the European subpopulations. To ensure that many patrilines were represented in the dataset, pedigree information (available for 86 horses), provided by breeding authorities and associations, was considered in the sampling strategy as previously described [ 39 ]. Hence, oversampling of relatives was averted from the dataset by keeping six males per foundation sire at maximum.…”

“…We inferred MSY haplotype spectrum of 119 samples according to the previously reported horse Y phylogeny [ 38 , 39 ]. For genotyping, we created a downscaled HT structure based on 65 selected HT-determining variants as markers (61 SNVs, 3 short Indels, and 1 microsatellite, see Supplementary Table S2 ).…”

“…Samples with known allelic state were included as positive controls, while DNA from females and non-template controls were used as negative controls. Information on variants (coordinates on LipY764, alleles, and flanking regions) are published in [ 38 , 39 ].…”

“…The MSY HTs of domestic horses are clearly distinct from those in the extant Przewalski’s horses. The most pronounced MSY signature among domestic horses is the ~2000-year-old “Crown” haplogroup (HG), recounting various breeds from Central and South Europe, East Asia, North and South America [ 38 , 39 ]. It was proposed that the dominance of the Crown HG is a hallmark of the recent breeding influence of stallions of Oriental origin [ 38 , 40 ].…”

“…Only some Asian horses [ 43 , 44 ] and Northern European breeds (e.g., [ 45 ]) seemed to be unaffected by the recent Oriental introgression, and thus kept their autochthonous HTs outside the Crown (“Non Crown”). Within the Crown, three HGs were defined (H, A, and T) and the HT signatures of three English Thoroughbred founders [ 38 ], as well as Arabian patrilines [ 39 ] were recently successfully delineated.…”