Maternal and paternal genetic variation in Estonian local horse breeds in the context of geographically adjacent and distant Eurasian breeds

CKM intron: an appropriate marker for the determination of the genetic relationships among horse populations and breeds

To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; CKM) variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse sequences. From these, 40 haplotypes were inferred. Haplotype diversity (H) values differed from 0.6424 to 0.7881 and nucleotide diversity (π) values ranged from 0.00150 to 0.00211. The differences between Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations with respect to CKM intron sequences suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and CMH are very closely related and the introgression (interbreeding) between them is serious. Our results suggest that Sanhe and Wushen require prompt and powerful protection. Overall, CKM intron was an appropriate marker for the determination of genetic relationships among horse populations and breeds.

The Genetic Diversity of Horse Native Breeds in Russia

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.

Y-Chromosome Haplotype Report among Eight Italian Horse Breeds

Horse domestication and breed selection processes have profoundly influenced the development and transformation of human society and civilization over time. Therefore, their origin and history have always attracted much attention. In Italy, several local breeds have won prestigious awards thanks to their unique traits and socio-cultural peculiarities. Here, for the first time, we report the genetic variation of three loci of the male-specific region of the Y chromosome (MSY) of four local breeds and another one (Lipizzan, UNESCO) well-represented in the Italian Peninsula. The analysis also includes data from three Sardinian breeds and another forty-eight Eurasian and Mediterranean horse breeds retrieved from GenBank for comparison. Three haplotypes (HT1, HT2, and HT3) were found in Italian stallions, with different spatial distributions between breeds. HT1 (the ancestral haplotype) was frequent, especially in Bardigiano and Monterufolino, HT2 (Neapolitan/Oriental wave) was found in almost all local breeds, and HT3 (Thoroughbred wave) was detected in Maremmano and two Sardinian breeds (Sardinian Anglo-Arab and Sarcidano). This differential distribution is due to three paternal introgressions of imported stallions from foreign countries to improve local herds; however, further genetic analyses are essential to reconstruct the genetic history of native horse breeds, evaluate the impact of selection events, and enable conservation strategies.

Genetic History of the Altai Breed Horses: From Ancient Times to Modernity

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.

Unlocking Horse Y Chromosome Diversity

The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.

Variability analyses of the maternal lineage of horses and donkeys

Equid breeds originating from the Iberian Peninsula and North Africa are believed to have genetically contributed to the formation of breeds and ecotypes from Brazil. The country has numerous breeds and ecotypes of horses and donkeys but there are no extensive studies on maternal genetic diversity and their origins. This study reports the results of the first genetic analysis of all horse and donkey breeds/ecotypes from Brazil based on sequences of the mitochondrial DNA control region (D-loop) whose main objective was to characterize the genetic variation in these animals. These analyses will contribute to the understanding of the current population structure and diversity of breeds/ecotypes of horses and donkeys raised in the Brazil. We analyzed 310 D-loop sequences representing 41 breeds/ecotypes of Equus caballus and Equus asinus, including 14 native horse breeds/ecotypes, 3 native donkey breeds/ecotypes and 24 cosmopolite horse breeds. The results revealed that the breeds are well structured genetically and that they comprise different groups. A total of 80 and 14 haplotypes were identified for horses and donkeys, respectively. Most of the horse mtDNA haplotypes were shared by many breeds, whereas donkey mtDNA haplotypes seemed to be more group-especif. Some groups presented a low intrabreed distance and/or a low haplotype/nucleotide diversity such as Lavradeiro, Crioulo, Piquira and Percheron horses and Brazilian donkey. Thus, specific actions must be designed for each population. The different levels of genetic diversity provided important information for conservation resource management of adapted groups as well as for mating orientation of breed associations. Some autochthonous ecotypes require attention because of their low genetic variability.