Lara Radovic Lara Radovic Viktoria Remer Viktoria Remer Doris Rigler Doris Rigler Elif Bozlak Elif Bozlak Lucy Allen Lucy Allen Gottfried Brem Gottfried Brem Monika Reissman Monika Reissman Gudrun A. Brockmann Gudrun A. Brockmann Katarzyna Ropka-Molik Katarzyna Ropka-Molik Monika Stefaniuk-Szmukier Monika Stefaniuk-Szmukier Liliya Kalinkova Liliya Kalinkova Valery V. Kalashnikov Valery V. Kalashnikov Alexander M. Zaitev Alexander M. Zaitev Terje Raudsepp Terje Raudsepp Caitlin Castaneda Caitlin Castaneda Ines von Butler-Wemken Ines von Butler-Wemken Laura Patterson Rosa Laura Patterson Rosa Samantha A. Brooks Samantha A. Brooks Miguel Novoa-Bravo Miguel Novoa-Bravo Nikos Kostaras Nikos Kostaras Abdugani Abdurasulov Abdugani Abdurasulov Douglas F. Antczak Douglas F. Antczak Donald C. Miller Donald C. Miller Maria Susana Lopes Maria Susana Lopes Artur da Câmara Machado Artur da Câmara Machado Gabriella Lindgren Gabriella Lindgren Rytis Juras Rytis Juras Gus Cothran Gus Cothran Barbara Wallner Barbara Wallner National Academy of Sciences 2024 Since their domestication, horses have accompanied mankind, and humans have constantly shaped horses according to their needs through stallion-centered breeding. Consequently, the male-specific portion of the Y chromosome (MSY) is extremely uniform in modern horse breeds. The majority of stallions worldwide carry MSY haplotypes (HT) attributed to an only ~1,500-y-old, so-called, "Crown" haplogroup. The predominance of the Crown in modern horse breeds is thought to represent a footprint of the vast impact of stallions of "Oriental origin" in the past millennium. Here, we report the results of a fine-scaled MSY haplotyping of large datasets of patrilines comprising 1,517 males of 189 modern horse breeds, covering a broad phenotypic and geographic spectrum. We can disentangle the multilayered influence of Oriental stallions over the last few hundred years, exposing the intense linebreeding and the wide-ranging impact of Arabian, English Thoroughbred, and Coldblood sires. Iberian and New World horse breeds contain a wide range of diversified Crown lineages. Their broad HT spectrum illustrates the spread of horses of Oriental origin via the Iberian Peninsula after the Middle Ages, which is commonly referred to as the "Spanish influence." Our survey also revealed a second major historical dissemination of horses from Western Asia, attributed to the expansion of the Ottoman Empire. Our analysis shows that MSY analysis can uncover the complex history of horse breeds and can be used to establish the paternal ancestry of modern horse breeds. PDFDocument eng 2025-01-31T09:36:30.725171Z 2024 Horses Genetics Animals Y Chromosome Genetics Male Haplotypes Genetics Breeding Domestication Phylogeny 4465893 b application/pdf http://creativecommons.org/licenses/by/4.0/