The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable for the past three decades. The conducted monitoring revealed a slight increase in the Wright’s inbreeding coefficient in all age and sex groups of TB horses (stallions, broodmares, and foals) from 0.68% to 0.90%, which was followed by a decrease in the degree of heterozygosity, Ho, from 68.5% to 67.6%. The Spearman’s rank correlation coefficient between the level of inbreeding and the degree of homozygosity was estimated (r = 0.022; p > 0.05). The obtained data on the DNA genotypes of horses of different breeds provide a unique base for the evaluation of genetic variability and the control of genetic variability of horses in selection programs.

The Thoroughbred (TB) horse is the best racehorse breed used in the racing industry. This breed has had a closed studbook for about 300 years. In Russia TB horses have been bred since the second half of the XVIII century. The modern Russian Stud Book register of TB horses is partially presented by stallions and broodmares imported from different countries. The genealogical structure of the breed is represented by 17 lines, among which the Northern Dancer line dominates (30.9 %). The study of features of different lines of TB was carried out on 17 loci of DNA microsatellites (VHL20, HTG4, AHT4, HMS7, HTG6, AHT5, HMS6, ASB23, ASB2, HTG10, HTG7, HMS3, HMS2, ASB17, LEX3, HMS1 and CA425) to assess genetic differentiation of the genealogical structure. The results of the DNA typing of 8091 Thoroughbred horses across microsatellite loci show that the gene pool of the domestic population is represented by 100 alleles typical of the breed. A comparative analysis of the genotypes of horses representing different lines indicates that they differ in the number of alleles (85–99), allele frequencies, the level of polymorphism Ae (2.93–3.48) and the degree of the observed heterozygosity Ho (0.653–0.739). The genetic distances between the lines varied in a wide range from 0.014 (Nasrullah – Northern Dancer) to 0.125 (Massine – Teddy). The correspondence to HWE was maintained in most lines, which is confirmed by the negative values of Fis. Cluster analysis demonstrated the correspondence of the obtained dendrogram of Nei’s genetic distances to its genealogical scheme of lines. Genetic differentiation of lines by index Fst varied in a range 0.005–0.073 at the mean value Fst = 0.024. The data indicate genetic differentiation of lines of TB at the STR markers and confirm the effectiveness of the system of linear breeding for the maintenance of interbreed biodiversity.

The Zabaikalskaya horse is an indigenous breed of horses from Siberia with diverse use. It is characterized by e durance and good adaptability to year-round herd maintenance in the harsh conditions of the Baikal steppes. To determine the genetic characteristics of the maternal lineage of the Zabaikalskaya horse breed based on mitochondrial DNA polymorphisms, we collected hair samples from 31 horses belonging to breeding farms in the Trans-Baikal Territory. Analysis of the 530 bp sequence of the mtDNA D-loop was performed using the maximum composite likelihood (MCL) model in combination with bootstrap analysis. When studying the polymorphism of the hypervariable region of the mtDNA D-loop in Zabaikalskaya horses, we identified 31 haplotypes representing 8 haplogroups: B, C, G, H, L, M, Q and R according to modern classification. The sequenced fragment of the D-loop from nucleotide position 15471 to 16000 contained 17 polymorphic sites, mainly represented by the A→G, G→A and T→C transitions. The haplogroups Q (25.81 %), B (19.35 %), G (16.13 %) and H (12.90 %) were prevailing in the mtDNA structure of this breed. Genetic analysis of the mitochondrial genome of the Zabaikalskaya horse revealed a high level of diversity of haplotypes and haplogroups, which are typical for the horse populations of Eurasia.

Russia has a significant pedigree diversity of horse breeds with unique gene pools that are well adapted to a wide variety of harsh natural and climatic conditions, are characterized by universal performance and high productive qualities, and are of significant interest to the world horse breeding. Genetic studies of population diversity in horse breeding are very relevant, since many domestic horse breeds are under threat of extinction. Biomaterials (hair, blood, semen) from horses of 15 local breeds bred in the Russian Federation and neighboring countries (CIS) were selected for the research. The sample included 2,193 horses, including: Altaiskaya (n = 48), Bashkirskaya (n = 130), Buryat skaya (n = 30), Vyatskaya (n = 220), Zabaikalskaya (n = 34), Kyrgyzskaya (n = 100), Mezenskaya (n = 148), Mugalzhar skaya (n = 109), Novoaltaiskaya (n = 514), Pechorskaya (n = 31), Shetland pony (n = 47), Priobskaya (n = 85), Tuvinskaya (n = 600), Khakasskaya (n = 47) and Yakutskaya (n = 50) breeds. The following indicators were used in the genetic and population analysis: the total number of allele variants (Na) in 17 microsatellite loci, the level of polymorphism (Ae), the average number of alleles per locus (Nv), observed (Ho) and expected (He) heterozygosity, coefficients of genetic similarity and genetic distances, as well as the coefficient of intrapopulation inbreeding (Fis). Modern local horse breeds, even relatively small in number, have a high level of biodiversity and a peculiar genetic structure, often with the presence of private alleles, which persists despite periodic crossing with stud breeds of different specializations. It was found that horses of local breeds possess a number of unique alleles, including ASB2T, HMS7S, HMS6J, HMS6H, HMS2T, HMS1O, HTG7L, HTG6L, HTG6H, VHL20S, ASB17Z, ASB17X, ASB17U, LEX3S, LEX3R and CA425E, which were not detected in representatives of stud breeds in the studied European populations. The majority of the studied breeds were characterized by a negative Fis value and the absence of inbreeding. The coefficients of genetic similarity of local breeds varied in a relatively wide range (0.828–0.973) and testified to the uniqueness of the gene pools of most local horse breeds of the Russian Federation, as well as confirmed the common origin of the Kyrgyzskaya horse with the horse populations of Southern Siberia.

Донская порода лошадей, получившая известность в России уже в середине 18 века, была получена методом длительного скрещивания лошадей кочевников с культурными восточными породами. В связи с сокращением численности поголовья донских маток до 200 племенных кобыл изучение генетических особенностей этой породы приобретает особую актуальность. Целью проведенных исследований было изучение матрилинейной структуры донской породы лошадей на основании филогенетического анализа 530 пар нуклеотидов (п.н.) гипервариабельного участка D-петли митохондриальной ДНК (мтДНК) у 26 кобыл, представляющих основные женские семейства. Анализ последовательности мтДНК проводили с использованием Neighbor-Joining (NJ) метода в сочетании с бутстрэп-анализом в программе MEGA7. В митохондриальных геномах протестированных донских лошадей было выявлено 26 различных гаплотипов, входящих в состав 10 гаплогрупп мтДНК, включая A, B, D, G, L, M, N, O, P и Q, согласно современной классификации. Дополнительно было выявлено еще четыре новых гаплогруппы, ведущих линию от черноморских кобыл и нетипичных для большинства европейских пород. Секвенированный фрагмент D-петли c 15471 по 16000 п.н включал 115 полиморфных сайтов, в основном представленных трансверсиями. В структуре мтДНК донской породы преобладали гаплогруппы G (19.2%), B (15.4%) и L (11.5%). Все проанализированные маточные семейства были четко дифференцированы на уровне гаплогрупп и гаплотипов с высоким показателем бутстрэп-поддержки (58-100%), что свидетельствует о высоком генетическом разнообразии генеалогической матрилинейной структуры донской породы лошадей.

Priobskaya horse belongs to the group of northern forest breed and is located in Khanty-Mansi Autonomous Region along Ob River and its tributaries. Among other local horse breeds of Siberia this breed stands out for its endurance and resistance to mosquitoes and other insects. The aim of our work was to study the features of the population structure of Priobskaya horses by 17 distinctive markers: VHL20, HTG4, AHT4, HMS7, HTG6, AHT5, HMS6, ASB23, ASB2, HTG10, HTG7, HMS3, HMS2, ASB17, LEX3, HMS1 and CA425. The results of biotechnological DNA typing of 25 Priobskaya horses by STR loci show that gene pool of the studied population is represented by 121 alleles, typical of local horse breeds. Horses of this breed had a number of rare alleles, including unique variant HMS1R, which was not found in horses of European origin (Van de Goor et al., 2010). The breed had fairly high rates of genetic diversity, the mean number of alleles per loci (MNA) reached 7.12, the effective number of alleles (A_e) – 4.16. The analysis demonstrated good compliance between the observed (H_o=0.741) and the expected (H_e=0.731) heterozygosity level and the absence of population inbreeding (F_is=-0.017). Analysis of the phylogenetic relations between local horse breeds showed that Priobskaya breed has the highest coefficient of genetic similarity with Tuvinskaya (0.845) and Narymskaya (0.844) horses. Cluster analysis confirmed genetic uniqueness of Priobskaya.