{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T11:46:48Z","timestamp":1790423208321,"version":"4.1.0"},"reference-count":27,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T00:00:00Z","timestamp":1701129600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Science and Higher Education of the Russian Federation","award":["075-15-2021-1037"],"award-info":[{"award-number":["075-15-2021-1037"]}]},{"name":"Ministry of Science and Higher Education of the Russian Federation","award":["15.BRK.21.0001"],"award-info":[{"award-number":["15.BRK.21.0001"]}]},{"name":"Ministry of Science and Higher Education of the Russian Federation","award":["123013100005-2"],"award-info":[{"award-number":["123013100005-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and Vyatka. Data on the origin of each animal from which the material was collected were taken into account. DNA genotyping was carried out using GGP Equine 70 k \u00ae array chips (Thermo Fisher Scientific, USA). Genetic diversity of horse breeds was estimated using Admixture 1.3. and PLINK 1.9 software. FROH inbreeding was computed via the R detectRUNS package. The minimum length for ROH was set at 1 Mb to reduce the occurrence of false positives. We conducted PCA analysis using PLINK 1.9, and used the ggplot2 library in R for visualizing the results. Indigenous equine breeds, such as Vyatka, Tuva, and Yakut, are very hardy, and well adapted to local environmental and climatic conditions. They are employed as draft power, as well as for milk and meat. Both the Akhal-Teke breed and the Arabian breed have retained a minimum effective population size over many generations. We note significant accumulations of homozygosity in these breeds. In equestrian sports, performance is a top priority. ADMIXTURE and PCA analyses showed similarities between Don equine breeds and Kabardin, as well as some Arabian breed animals. Earlier research indicated the presence of thoroughbred traits in Don stallions. The Orlov Trotter breed stands out as a separate cluster in the structural and PCA analyses. Considering the small population size of this breed, our study found high FROH in all tested animals. The general reduction in the diversity of the horse breed gene pool, due to numerous crosses for breed improvement with thoroughbreds, has lead to a decline in the differences between the top sporting breeds. Our study presents new opportunities for exploring the genetic factors that influence the formation of adaptive traits in indigenous breeds, and for finding ways to preserve genetic diversity for effective population reproduction.<\/jats:p>","DOI":"10.3390\/genes14122148","type":"journal-article","created":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T06:45:35Z","timestamp":1701153935000},"page":"2148","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["The Genetic Diversity of Horse Native Breeds in Russia"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6023-0332","authenticated-orcid":false,"given":"Mikhail","family":"Atroshchenko","sequence":"first","affiliation":[{"name":"All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Dementieva","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Farm Animal Genetics and Breeding\u2014Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri","family":"Shcherbakov","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Farm Animal Genetics and Breeding\u2014Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Nikolaeva","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Farm Animal Genetics and Breeding\u2014Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasiia","family":"Azovtseva","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Farm Animal Genetics and Breeding\u2014Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Ryabova","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Farm Animal Genetics and Breeding\u2014Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Nikitkina","sequence":"additional","affiliation":[{"name":"Russian Research Institute of Farm Animal Genetics and Breeding\u2014Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, 55A, Moskovskoye Sh., Tyarlevo, St. Petersburg, Pushkin 196625, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oksana","family":"Makhmutova","sequence":"additional","affiliation":[{"name":"All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrey","family":"Datsyshin","sequence":"additional","affiliation":[{"name":"All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktor","family":"Zakharov","sequence":"additional","affiliation":[{"name":"All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4260-602X","authenticated-orcid":false,"given":"Alexander","family":"Zaitsev","sequence":"additional","affiliation":[{"name":"All-Russian Research Institute of Horse Breeding (ARRIH), Ryazan Region, Rybnovskij District, Divovo 391105, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,28]]},"reference":[{"key":"ref_1","first-page":"216","article-title":"The Origin and Domestication History of Domestic Horses and the Domestication Characteristics of Breeds","volume":"44","author":"Fu","year":"2022","journal-title":"Yi Chuan"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1099896","DOI":"10.3389\/fgene.2023.1099896","article-title":"Exploring the Italian Equine Gene Pool via High-Throughput Genotyping","volume":"14","author":"Capomaccio","year":"2023","journal-title":"Front. 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