Modern Horse Research Articles

Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers.

Extremely low nucleotide diversity of modern horse Y-chromosome has been reported, and only poor phylogenetic resolution could be resulted from limited Y-chromosome markers. In this study, three types of horse Y-chromosome markers, including Single-nucleotide polymorphisms (SNPs), copy number variants (CNVs), and allele-specific CNVs, were developed by screening more than 300 male horses from 23 indigenous Chinese horse populations and 4 imported horse breeds. Fourteen segregating sites including a novel SNP in the AMELY gene were found in approximately 53 kb of male-specific Y-chromosome sequences. CNVs were detected at 11 of 14 sites, while allele-specific CNVs at 6 polymorphic sites in repeated fragments were also determined. The phylogenetic analyses with the SNPs identified in this study and previously published 51 SNPs obtained mainly from European horses showed that indigenous Chinese horses exhibit much deeper divergence than European and Middle Eastern horses, while individuals of Chinese horses with the C allele of the AMELY gene constituted the most ancient group. Via SNPs, CNVs, and allele-specific CNVs, much higher diversity of paternal lines can be detected than those identified with merely SNPs. Our results indicated that there are ancient paternal horse lines preserved in southwestern China, which sheds new light on the domestication and immigration of horses, and suggest that the priorities of the conservation should be given to the ancient and rare paternal lines. These three marker types provided finer phylogenetic resolution of horse patrilineal lines, and the strategies used in the present study also provide valuable reference for the genetic studies of other mammalian patrilineages.

Mitochondrial DNA variation in the Italian Heavy Draught Horse.

BackgroundIn the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook.MethodologyTo provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds.ResultsAmong the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.

Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types.

Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.

POLESYE HORSE: HISTORY OF ORIGIN AND CURRENT SITUATION

POLESYE HORSE: HISTORY OF ORIGIN AND CURRENT SITUATION

Mitochondrial Profiles of the East Bulgarian and the Pleven Horse Breeds

It is well known that horse breeding in Bulgaria is a cultural heritage in Bulgaria, dating from prehistoric and historic times. Until now, molecular data on Bulgarian horses from the plain regions of the country were not available. Therefore, for the first time, we have collected genetic information about some modern horse breeds from the plain regions in Bulgaria. A total of 50 horses originating from different families from two different breeds were investigated: the first one was the Pleven horse (n = 11, breeding in the Danubian Plain), and the second one was the East Bulgarian horse breed (n = 39, Shumen district). These breeds were genotyped according to the mitochondrial D-loop region. The results showed that the Pleven horse particularly carries the European haplogroup L (45.45%), followed by the Middle East haplogroup C (27.27%). In contrast to the Pleven horse, the East Bulgarian horse breed revealed almost equal frequencies of the European specific haplogroup L (33.33%) and the Central Asiatic haplogroup Q (35.90%). Analyses of these two horse breeds revealed a specific genetic profile, but it is obvious that the East Bulgarian horse showed an unusual, mixed profile—a massive admixture with the Asiatic-type haplogroup Q and a high haplogroup diversity. In conclusion, the differences in genetic structure of the two plain horse breeds may be explained with the various horse breeds involved in their formation.

Abundant genetic diversity and maternal origins of modern horses

To clarify the origin and genetic diversity of modern horses, mitochondrial DNA (mtDNA) D-loop sequences were generated for 3965 horses from 12 geographical regions. From these sequences, we observed 439 haplotypes defined by 138 polymorphic nucleotide sites. All horses were genetically diverse (HD = 0.973 ± 0.001, π = 0.0243 ± 0.0005), which showed that maternal lineages of the domestic horse are worldwide highly diverse. In general, all 18 haplogroups were presented in the Asian horse. The majority of modern horse sequences belong to haplogroups L, Q, and A. At the same time, 194 archaeological samples from four geographical regions were obtained. Indeed, haplogroup distributions are overlapping in modern and ancient samples, indicating that most haplogroups were already present in ancient times at least in Europe and Asia. The network showed that breeds of Asian and Europe regions overlapped, suggesting that extensive gene flow had occurred between different horse breeds in Asian and European regions.

Local origin or external input: modern horse origin in East Asia

BackgroundDespite decades of research, the horse domestication scenario in East Asia remains poorly understood.ResultsThe study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial genomes of 317 horse samples. The time to the most recent common ancestor of the 16 haplogroups ranges from [0.8–3.1] thousand years ago (KYA) to [7.9–27.1] KYA. With combined analyses of the mitochondrial control region for 35 extant Przewalski’s horses, 3544 modern and 203 ancient horses across the world, researchers provide evidence for that East Asian prevalent haplogroups Q and R were indigenously domesticated or they were involved in numerous distinct genetic components from wild horses in the southern part of East Asia. These events of haplotypes Q and R occurred during 4.7 to 16.3 KYA and 2.1 to 11.5 KYA, respectively. The diffusion of preponderant European haplogroups L from west to East Asia is consistent with the external gene input. Furthermore, genetic differences were detected between northern East Asia and southern East Asia cohorts by Principal Component Analysis, Analysis of Molecular Variance test, the χ2 test and phylogeographic analyses.ConclusionsAll results suggest a complex picture of horse domestication, as well as geographic pattern in East Asia. Both local origin and external input occurred in East Asia horse populations. And besides, there are at least two different domestication or hybridization centers in East Asia.

Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations.

The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

The Genomic Makeup of Nine Horse Populations Sampled in the Netherlands.

The spectrum of modern horse populations encompasses populations with a long history of development in isolation and relatively recently formed types. To increase our understanding of the evolutionary history and provide information on how to optimally conserve or improve these populations with varying development and background for the future, we analyzed genotype data of 184 horses from 9 Dutch or common horse populations in the Netherlands: The Belgian draft horse, Friesian horse, Shetland pony, Icelandic horse, Gelder horse, Groninger horse, harness horse, KWPN sport horse and the Lipizzaner horse population. Various parameters were estimated (e.g., runs of homozygosity and FST values) to gain insight into genetic diversity and relationships within and among these populations. The identified genomic makeup and quantified relationships did mostly conform to the development of these populations as well as past and current breeding practices. In general, populations that allow gene-flow showed less inbreeding and homozygosity. Also, recent bottlenecks (e.g., related to high selective pressure) caused a larger contribution of long ROHs to inbreeding. Maintaining genetic diversity through tailor-made breeding practices is crucial for a healthy continuation of the investigated, mostly inbred and (effectively) small sized horse populations, of which several already experience inbreeding related issues.

A Primitive Trait in Two Breeds of Equus Caballus Revealed by Comparative Anatomy of the Distal Limb.

Simple SummaryUnderstanding the complexities and evolutionary links between extinct and extant equids has been vital to genetic conservation and preservation of primitive traits. As domestication of the equid expanded, the loss of primitive traits that ensured survival in a wild environment has not been documented. In this study, the presence of functional interosseous muscle II and IV in the distal limb has been reported, and yet its existence could only be confirmed in relatives and two closely bred descendants of the extinct Tarpan. The morphology described was ligamentous in structure displaying clear longitudinal fibres with a skeletal origin and soft tissue insertion into the medial and lateral branches of the interosseous muscle III (suspensory ligament) dorsal to the sesamoids, similar in orientation to the flexor digitorum profundus ligamentum accessorium (inferior check ligament). Hence, providing a functional medial and lateral stability to the metacarpophalangeal joint (fetlock joint), which equates to one of the functions of the medial and lateral digits in the Mesohippus and Merychippus. The comparable anatomic links between species of the same family that experienced geographical isolation yet display structural conformity appears to be in response to a specific environment. Surmising this potential remnant of functional evolution is a primitive trait and not a breed anomaly.The 55-million-year history of equine phylogeny has been well-documented from the skeletal record; however, this is less true for the soft tissue structures that are now vestigial in modern horse. A recent study reported that two ligamentous structures resembling functional interosseous muscle II and IV were evident in Dutch Konik horses. The current study investigates this finding and compares it to members of the genus Equus to identify either a breed anomaly or functional primitive trait. Distal limbs (n = 574) were dissected from four species of Equus; E. caballus, E. asinus, E. przewalskii and E. quagga boehmi. E. caballus is represented by 18 breeds of horse, including the primitive Dutch Konik’. The interosseous muscle II and IV were evident in all four species, but only two breeds of E. caballus expressed this trait-the Dutch Konik and Bosnian Mountain Horse. These two breeds were the only close descendants of the extinct Equus ferus ferus (Tarpan) represented in this study. In conclusion, the interosseous muscle II and IV originated from the distal nodule of metacarpal II and IV, respectively, and inserted into the corresponding branches of interosseous muscle III proximal to the sesamoids. This suggests a functional role in medial and lateral joint stability and a primitive trait in modern equids.

The Role of Grass vs. Exogenous Abrasives in the Paleodietary Patterns of North American Ungulates

The attainment of high crowned teeth (hypsodonty) has often been thought to be associated with grazing because many abrasive opal particles are known in grass that are presumed to wear down mammalian teeth. Equids have often been discussed regarding tooth morphological change due to the evolution of highly hypsodont teeth over time, the hyper-grazing habits of modern horses, and the originally-held view that the acquisition of hypsodonty and the widespread appearance of grasslands were synchronous. Recent studies, however, have reported asynchrony in the origin of hypsodonty and the widespread appearance of grasslands and have considered exposure to exogenous grit as important evolutionary drivers of hypsodonty in ungulates. We tracked changes in crown height (hypsodonty index), relative abrasion (mesowear) and food and grit scar topography on dental enamel (microwear) to examine the relative contributions of grass versus grit as a driving force in ungulate tooth changes during the evolution of North American Equidae compared to four North American ruminant artiodactyl families (Camelidae, Antilocapridae, Dromomerycidae, and Merycoidodontidae). We found that the overall pattern of the timing of the attainment of hypsodonty is inconsistent with grazing as the main impetus for the “Great Transition” within equids nor within the artiodactyl families as highly hypsodont ungulates post-date the spread of widespread grasslands. Mesowear closely mirrored hypsodonty trends in all families. Microwear patterns, particularly high degrees of enamel pitting (particularly large pits) and unusually coarse scratch textures in all five families, are consistent with exposure to exogenous grit as the main driver of hypsodonty acquisition prior to the consumption of significant levels of grass. Equidae exhibited a wider array of dietary behavior than the other families through most of their evolutionary history. Even so, grass was a much more common dietary item for equids than for the other families, and when combined with exogenous grit, which was more accelerated from the early Miocene onward based on more pitting and coarser scratch textures, may explain the more extreme acquisition of hypsodonty in equids compared to the artiodactyl families studied and set the stage for the Equidae alone to become hypergrazers in the Recent.

Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model

BackgroundHorses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exists between breeds, making the horse particularly well suited for genetic studies of athleticism. To identify genomic regions associated with athleticism as it pertains to trotting racing ability in the horse, the current study applies a pooled sequence analysis approach using a unique Nordic horse model.ResultsPooled sequence data from three Nordic horse populations were used for FST analysis. After strict filtering, FST analysis yielded 580 differentiated regions for trotting racing ability. Candidate regions on equine chromosomes 7 and 11 contained the largest number of SNPs (n = 214 and 147, respectively). GO analyses identified multiple genes related to intelligence, energy metabolism, and skeletal development as potential candidate genes. However, only one candidate region for trotting racing ability overlapped a known racing ability QTL.ConclusionsNot unexpected for genomic investigations of complex traits, the current study identified hundreds of candidate regions contributing to trotting racing ability in the horse. Likely resulting from the cumulative effects of many variants across the genome, racing ability continues to demonstrate its polygenic nature with candidate regions implicating genes influencing both musculature and neurological development.

Development of a prototype for referees to monitor whip use in horse racing

There is no standard surveillance system for modern flat horse racing in Sweden, so the surveillance camera placement and image quality varies between tracks. Reported whip misuse and unauthorised whipping often occur outside of the camera’s view and are therefore unrecorded. Thorough investigation of the current monitoring system used in Sweden revealed concerns about whether the stewards have enough time to estimate the number of whip strikes per horse, even when camera quality is sufficient, and has led to the development of an enhanced whip system. The system prototype offers a technical solution for the supervision of whip use in modern horse racing, and it would be useful in countries where there are regulations limiting the number of strikes. Current specifications allow the system to record the attributes and number of strikes and to relay the data contemporaneously to the stewards. The system does not interfere with the operation of the camera monitoring system. Since the number of strikes is reported with total accuracy, stewards are afforded more time to focus on matters of interference and actions that are important to the final result list. The prototype is a whip with a custom-made force sensor placed on both sides of the cushion pad. The sensors measure an area 24mm wide by 275mm long and cover the entire padded part of the approved race whip. The sensor is constructed of polyester that is 0.203mm thick. The force sensor is connected to a microcontroller mounted in the handle of the whip. The microcontroller processes the sensor data and sends the information via radio waves up to 1.7km in outdoor conditions to a second microcontroller located in the steward’s office. The whip strike sensor prototype is able to distinguish between a wave of the arm that leads to no impact and a strike. The software allows the force of each strike impact to be recorded. The intention is to embed the whip strike sensor within the body of whips used in a range of equestrian disciplines in which whip use is permitted. The possibility to register the properties of whip strikes will help to safeguard the welfare of horses used in these disciplines and provide information to the equestrian community that could change the way whips are used in training and racing. Lay person message: The whipping of horses in racing leads to concerns about animal welfare globally. A whip strike sensor prototype has been developed that will facilitate detailed exploration of the effect whips have on horses and allow stewards to accurately assess the number of strikes made and forces used. It is intended to integrate strike sensors into whips used in disciplines where whipping is allowed; this will help to safeguard the welfare of horses used in these disciplines.

The farrier's role

Clive Meers Rainger RSS BII discusses the shoeing needs of the modern horse and the evolving farriery industry

Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives.

The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski’s horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski’s horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500–11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution.

Niche modeling reveals lack of broad-scale habitat partitioning in extinct horses of North America

The classic traits of modern horses (Equidae) – large body size, high-crowned teeth (hypsodonty), and a single toe (monodactyly) – are often considered adaptations to grassland environments. However, extinct horses that varied in these three traits overlapped geographically for millions of years during the Miocene and Pliocene. It has been hypothesized that co-occurring horse species partitioned habitats, with large-bodied, hypsodont, and monodactyl equids dominating open grasslands, while equids with different combinations of traits lived in more wooded areas. We tested for the presence of broad-scale habitat partitioning by compiling a large database of North American horse fossil occurrences with data on trait state (body size, hypsodonty index, and toe number) and paleoenvironment (derived from paleovegetation records). Null modeling of niche overlap in each of the North American Land Mammal Ages of the Miocene and Pliocene revealed that taxonomic and trait-based groups show no differences in habitat occupancy. Cluster dendrograms visualizing niche overlap showed that some ecological guilds shared derived traits, but derived traits were not associated exclusively with grassland habitats. Trait values are not predicted by the proportion of grassland habitats in time bins. Further, the three traits show no co-evolution across the equid tree when corrected for phylogenetic relatedness. Together, these results suggest that the evolution of large body size, hypsodonty, and monodactyly in equids was not due to a shared selective regime in response to expanding grassland habitats; instead, these traits may have evolved separately, likely due to a variety of small-scale selective pressures acting across the variety of habitats present in the Miocene and Pliocene.

Revisiting the origins of modern horses

Ancient Genomes The domestication of horses was very important in the history of humankind. However, the ancestry of modern horses and the location and timing of their emergence remain unclear. Gaunitz et al. generated 42 ancient-horse genomes. Their source samples included the Botai archaeological

The Disappearing Lamellae: Implications of New Findings in the Family Equidae Suggest the Loss of Nuchal Ligament Lamellae on C6 and C7 Occurred After Domestication

Conflicting data predominantly describes the equine nuchal ligament lamellae (NLL) attachments as C2–C6 or C2–C7; however, preliminary evidence suggests C2–C5. This study aimed to identify morphological variations in the attachments of the NLL in four species of the family equidae and determine if the variations were species or breed linked. Cadaveric examination evaluated 98 equids; Equusasinus (n = 2), Equus ferus caballus (n = 93), Equus przewalskii (n = 2), and Equus quagga boehmi (n = 1). Twenty breeds of E. f. caballus were included according to breed type—modern horse (n = 81), ancient type (n = 10), primitive (n = 4). Of the 98 equids, observations were divided into three categories according to the NLL attachments: C2–C5, C2–C6, and C2–C7; in category C2–C7, E. f. caballus (n = 3/93), modern horse 0 of 81, ancient 1 of 8, primitive 2 of 4; in category C2–C6, modern horse 2 of 81; in category C2–C5, modern horse 79 of 81, ancient type 7 of 8, primitive 2 of 4. Equus asinus, E. przewalskii, and E. q. boehmi all expressed category C2–C7. In total, 88 of 98 expressed category C2–C5; 2 of 98 category C2–C6; and 8 of 98 category C2–C7. These findings suggest that category C2–C5 provides sufficient evidence to suggest a normal occurrence. The high incidence of an absent NLL on C6 and C7 may be considered a contributing factor in caudal cervical osteoarthritis. Furthermore, category C2–C7 still exists in an ancient and primitive breed closely related to the tarpan, implying the NLL may have been attached from C2 to C7 in prehistoric horse before domestication. This hypothesis is supported by the findings of E. asinus, E. przewalskii, and E. q. boehmi, displaying attachments from C2 to C7.

Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski's horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.

A Novel Non-Invasive Selection Criterion for the Preservation of Primitive Dutch Konik Horses.

The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed, particularly in height at the wither, colour (mouse to grey dun) and presence of primitive markings. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik (n = 47) and modern domesticated horses (n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed.