Search Results (12)

This study aims to examine the genetic structure and diversity levels of seven indigenous Greek horse breeds: Andravida, Pindos, Thessaly, Skyros, Penia, Messara and Rodos, using 15 microsatellites. Phenotypic traits were combined with factorial correspondence analyses to create two datasets: one “Baseline” containing typical samples, and one “Unknown” with non-typical or of disputed origin samples. In the Greek “Baseline” horses, 142 alleles were found. The mean observed and effective number of alleles, the polymorphism information content and the allelic richness were 6.75, 4.14, 0.63 and 5.12, respectively. The expected and observed heterozygosity and inbreeding coefficient varied between 0.81 and 0.29 and 0.79 and 0.24. The above dataset was enriched with data from 41 foreign horse breeds and 40 Przewalski samples to perform a breed assignment. The highest percentage of successfully assigned samples was for Skyros, Messara and Rodos, with rates of 93%, 89% and 100%, respectively, suggesting their considerable homogeneity, while Andravida, Pindos, Thessaly and Penia scored 32.5, 34.1, 44.0 and 45.7%, respectively. Structural analysis confirmed the results of FCA and showed the genetic similarities of the above breeds. The results revealed the influence of foreign breeds (mainly Garrano, Turkoman, Irish Draft, Hanoverian and Belgian Draft). There is an urgent need to implement management measures for the pure homogeneous breeds and selection strategies for the remaining breeds which are genetically similar. Full article

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 ^® 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. Full article

The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistological fecal studies of horse diet composition on steppe pasture. The alpha diversity analysis showed horses had a more abundant and diverse gut microbiota in summer. There were significant effects on the beta diversity of microbial families, which were clustered by the warm and cold season in a principal coordinate analysis (PCoA), with 45% of the variation explained by two principal coordinates. This clustering by season was further confirmed by the significant differences observed in the relative abundances of microbial families and genera. The obtained results can serve as an experimental substantiation for further study of the impact of pasture grasses, which have a pharmacological effect, on the diversity of the gut microbiome and horse health. Full article

In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had varying degrees of impact on various horse breeds. However, recent inbreeding events were uncommon, particularly among indigenous horse breeds. Consequently, the ROH-based genomic inbreeding coefficient could aid in monitoring the level of inbreeding. Using the Thoroughbred population as a case study, we discovered 24 ROH islands containing 72 candidate genes associated with artificial selection traits. We found that the candidate genes in Thoroughbreds were involved in neurotransmission (CHRNA6, PRKN, and GRM1), muscle development (ADAMTS15 and QKI), positive regulation of heart rate and heart contraction (HEY2 and TRDN), regulation of insulin secretion (CACNA1S, KCNMB2, and KCNMB3), and spermatogenesis (JAM3, PACRG, and SPATA6L). Our findings provide insight into horse breed characteristics and future breeding strategies. Full article

Farm Animal Genetic Resources (FAnGR) ensures food security and maintains genetic diversity. The efforts to conserve FAnGR are minimal in Bhutan. In the pursuit of increasing livestock productivity, farmers are rearing livestock that narrows the range of genetic diversity. This review attempts to summarize the status of FAnGR and the efforts to conserve them. Some unique livestock breeds in Bhutan are Nublang (cattle breed), Yak, Saphak (pig breed), Yuta (horse breed), Merak-Saktenpa (horse breed), and Belochem (chicken breed). There was a drop in the yak, buffalo, equine, pig, sheep, and goat populations. Both in situ and ex situ conservation measures are in place for some of the breeds and strains (e.g., Nublang and traditional chicken). Conservation efforts are limited to the government, but other individuals, stakeholders and non-government organizations must play an increasing role in preserving genetic diversity. It is pertinent that Bhutan comes up with a policy framework to conserve its indigenous cattle. Full article

The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in a key region of the Silk Road, it was speculated that the origin of the Chakouyi horse might involve the foreign horse breeds found along this ancient commercial artery. In this study, whole-genome resequencing data of 12 horse breeds, including both indigenous and foreign horses, were applied to reveal the genetic relationships between the Chakouyi horse and other breeds, as well as the ancestry of this ancient breed. An analysis of the population structure and admixture showed that there is no close genetic affinity between the Chakouyi horse and the foreign horses while Chinese indigenous horse populations were grouped together in accordance with their geographic locations, and the Chakouyi horse showed a closer relationship with Kazak horses, Mongolian horses, and Tibetan horses. The results from the ancestral composition prediction indicated that the Kazak horse and the Mongolian horse might be two ancestors of the Chakouyi horse. Furthermore, the genome-wide selection signature analysis revealed that the DMRT3 gene was positively selected in the Chakouyi horse and related to the gait trait of the breed. Our results provide insights into the native origin of the Chakouyi horse and indicate that Kazak and Mongolian horses played important roles in the formation of the Chakouyi horse. Genetic communication between the Chakouyi horse and other horse populations could be attributed, at least partially, to population migrations and trade activities along the ancient commercial routes. Full article

The Mezőhegyes Stud was founded in 1784 where three different horse breeds were developed: the Furioso-North Star, the Gidran, and the Nonius. These breeds were based on the same mare population, but each breed had different utilization purposes. Our aim was to analyze the pedigree information of these three indigenous breeds. The genealogical information was traced back from the actual breeding population back to the founder animals, and the final database contained more than 47,000 horses. The reference populations were defined as the registered breeding animals in 2019. The complete generation equivalent was 16.45 for the Gidran breed, 15.18 for Furioso-North Star, and 12.64 for Nonius, respectively. Due to the utilization of English Thoroughbred during the breeding history, the average maximum generations were close to 36 generations for each breed. The average relatedness was approximately 4%. The average Wright’s inbreeding coefficient was the highest for the Nonius breed (5.59%). Kalinowski’s decomposition of inbreeding showed that inbreeding is originated mainly from the past; the current fixation of alleles was higher for the Nonius horse breed. There was a reasonable bottleneck effect for each breed. The estimated effective population sizes suggest that there is no problem with the maintaining of Mezőhegyes horse breeds. Full article

In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in the Jinjiang horse population. By removing repetitive CNV regions between breeds, a total of 239 CNVRs were identified in the Chinese indigenous horse breeds including 102 losses, 133 gains and 4 of both events (losses and gains in the same region), in which 131 CNVRs were novel and only detected in the present study compared with previous studies. The total detected CNVR length was 41.74 Mb, accounting for 1.83% of the total length of equine autosomal chromosomes. The coverage of CNVRs on each chromosome varied from 0.47% to 15.68%, with the highest coverage on ECA 12, but the highest number of CNVRs was detected on ECA1 and ECA24. A total of 229 genes overlapping with CNVRs were detected in the Jinjiang horse population, which is an indigenous horse breed unique to the southeastern coast of China exhibiting adaptability to high temperature and humidity. The functional annotation of these genes showed significant relation to cellular heat acclimation and immunity. The expression levels of the candidate genes were validated by heat shock treatment of various durations on fibroblasts of horses. The results show that the expression levels of HSPA1A were significantly increased among the different heat shock durations. The expression level of NFKBIA and SOCS4 declined from the beginning of heat shock to 2 h after heat shock and then showed a gradual increase until it reached the highest value at 6 h and 10 h of heat shock, respectively. Breed-specific CNVRs of Chinese indigenous horse breeds were revealed in the present study, and the results facilitate mapping CNVs on the whole genome and also provide valuable insights into the molecular mechanisms of adaptation to high temperature and humidity in the Jinjiang horse. Full article

In this work, a new multi-criteria model for the evaluation of traditional and indigenous horse breeds, the HORQUAL model, was developed by applying the DEX (Decision Expert) method. The idea for this study culminated from brainstorming among researchers who had the importance of conserving traditional and indigenous horse breeds in Slovenia and their universal uses (recreative and sport) in mind. The conservation of native domestic animal breeds is one of the important indicators of sustainable agricultural development in particular countries. Here, the assessment process considered the horse breeds in terms of lifestyle, expectations, requirements and experiences. The development process was based on the multi-criteria decision analysis approach, and it was applied to seven traditional and indigenous Slovenian horse breeds. The horse breeds were classified into four groups of breed ratings according to the chosen criteria. The horse breeds were categorised as follows: “does not correspond to the criteria”, “less correspondence with the criteria”, “corresponds to the criteria” and “completely corresponds to the criteria”. The results of the HORQUAL model clearly show that it is easier and more effective to choose the most suitable breeds for specific purposes (i.e., recreative/sport horses with the potential for breeding along with acceptable costs, favourable temperament and suitable price) as they can easily be analysed or compared with each other, according to the criteria chosen in this paper. The rating by group takes the criteria for the multi-attribute evaluation that were identified by an expert group into account and balances between the assessment of recreational and sports needs for riders and the life expectancy for breeders. Additionally, incorporating the Plus-minus-1 analysis proved to be a useful support tool to analyse the assessments and to further improve horse breeding plans. Full article

Fédération Equestre Internationale (FEI) has described equine endurance racing as the second largest discipline in the world, above which is only show jumping. The Žemaitukai is an ancient indigenous Lithuanian horse breed known since the 6th or 7th century. The Arabian horse breed is one of the oldest human-developed horse breeds in the world. Compared with other race horse breeds, the muscle tissue of Arabian horses is characterized by significant differences in structure—a predominance of oxidative fiber type I is observed in Arabians, making them the prevailing breed in endurance racing. The Arabian horses are recognized as the leading breed in endurance competitions. Speed, pace, and total time in the race strategy have been extensively studied in human sports, and in contrast, this strategy appears to have been virtually ignored in equestrian sport, despite the potential for contributing to performance optimization. In relation to speed and total time in the race, there are limited data on postrace physical, biochemical, and blood gas parameters of endurance horses. Thus, this study was carried out to investigate the effects of speed on the blood parameters of the Arabian and Žemaitukai horses during an endurance race. Blood samples were taken before and immediately after the exercise. Biochemical and blood gas indicators were analyzed. The study showed significant increases in mean blood gasometrical indicators, such as partial carbon dioxide pressure (8.09–15.18%, p < 0.001); base excess in the extracellular fluid (14.01%, p < 0.001 in the Arabian horses and 172.01% in the Žemaitukai breed, p = 0.006); decreases of the blood electrolyte ionized calcium (4.38–8.72%, p < 0.001) and the hematocrit and hemoglobin values (20.05–20.12%, p < 0.001 in the Arabian horses and 6.22–6.23% in the Žemaitukai breed, p = 0.003–0.004); and decreases in the base excess in the blood values (29.24–39.38%, p < 0.001) and lactate (13.45–31.97%, p < 0.001) in the blood of both breeds in the post-competition horses. Significant increases after competition were determined for the values of creatinine (21.34–30.82%, p = 0.001–0.004), total bilirubin (50.84–56.24%, PH < 0.001), and albumin (2.63–4.48%, p = 0.048–0.001) for both breeds. For the faster Arabian horse breed, recovering after racing took half the time that the local Žemaitukai breed did. Full article

The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged. Full article

The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse breeds, and we integrated the published genotyped data of 352 individuals from 14 foreign horse breeds to study the relationships between Jinjiang horses and horse breeds from around the world. Principal component analysis (PCA), linkage disequilibrium (LD), runs of homozygosity (ROH) analysis, and ancestry estimating methods were conducted to study the population relationships and the ancestral sources and genetic structure of Jinjiang horses. The results showed that there is no close relationship between foreign horse breeds and Jinjiang horses, and Jinjiang horses shared a similar genetic background with Baise horses. TreeMix analysis revealed that there was gene flow from Chakouyi horses to Jinjiang horses. The ancestry analysis showed that Baise horses and Chakouyi horses are the most closely related ancestors of Jinjiang horses. In conclusion, our results showed that Jinjiang horses have a native origin and that Baise horses and Chakouyi horses were key ancestral sources of Jinjiang horses. The study also suggested that ancient trade activities and the migration of human beings had important effects on indigenous horse breeds in China. Full article