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Genetic Aspects of
Domestication, Breeds
and Their Origins
2Genetic A.T.
A.T. Bowling Bowling
Aspects
and 1 and A. Ruvinsky2
ofA.Domestication
Ruvinsky
1Veterinary Genetics Laboratory, School of Veterinary Medicine,
University of California, Davis, CA 95616–8744, USA; 2Animal

Science, SRSNR, University of New England, Armidale, NSW 2351,
Australia
Introduction 25
Origin of the Domestic Horse 26
The wild ancestors of the horse 26
Reasons, pre-condition and the initial steps of horse
domestication 29
History of horse domestication 30
Genetic Studies of Domestic Horses and Przewalski’s Horse 32
Chromosomes 32
Nuclear genes detected by immunogenetic and
biochemical techniques 33
Molecular polymorphisms – mtDNA and microsatellites 34
Worldwide Distribution of the Domestic Horse 35
Stud books define the gene pool of a breed and the rules
for managing it 36
Examples of horse breeds 38
Genetic similarity studies of breeds provide information
to assess genetic relatedness 42
Addressing questions of introgression between domestic
breeds 47
Future Prospects for Domestic Horses 48
Acknowledgements 48
References 48
Introduction
In human history, no other domestic animal has played such a direct role in
accelerating social processes and political developments as the horse; it has
been central to the rise and fall of empires, the conquest of entire continents.
©CAB International 2000. The Genetics of the Horse (eds A.T. Bowling and A. Ruvinsky) 25
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26 A.T. Bowling and A. Ruvinsky
No other domestic species has been used so widely as a means of transport in

war and peace, for communications and agricultural progress; only the dog
has been used more widely in sport and recreation.
The 20th century has seen an end to many practical uses for which horses
have traditionally been important throughout the 6000 years since their domes-
tication. However, the recent trend shows that humans choose to maintain
their association with horses, even in an era of modern cars, tractors and
planes, if for no other reason than appreciation of the horse’s beauty and
romantic traditions. Mutual trust and strong affiliation between humans and
horses is the basis for stories, legends and myths. Research increasingly shows
that the human–animal bond plays an important role in maintaining physical
and mental health in the human half of the partnership.
The highly developed ability of the wild horse to run fast and for a long
distance was possibly the major attraction for domestication. This adaptation
was vitally important for survival of the horse in natural conditions and
possibly reached morphological and physiological limits. It seems unlikely that
this trait improved significantly during domestication of the horse. However,
other traits, which were focuses of artificial selection, changed dramatically
(Fig. 2.1).
Tremendous progress in mammalian genetics during the last decade
did not by-pass the horse. This knowledge is very important for a number of
reasons including a better understanding of the history of horse domestication,
which still is full of gaps and questions. Preservation of existing breeds and
their further development, as well as creation of new horse breeds, is a contin-
uing focus of activity. Hopefully this book will facilitate further investigations
which will enrich our understanding of horse genetics and domestication.
Origin of the Domestic Horse

The wild ancestors of the horse
While horses present a great spectrum of morphological differences, including

size, shape, gait and colours, all breeds of horses are contained within the sin-
gle species Equus caballus (L.). All breeds of horses have the same karyotype;
crosses between breeds produce viable and fertile offspring. The immediate
progenitor species for the domestic horse is not clearly defined but, by most
accounts, the first domestic horses probably derived from wild horses in
Eurasia (Fig. 2.2). At present, the earliest evidence for domestic horses is at
an excavated settlement in southern Ukraine at Dereivka, radiocarbon dated
to 4200–3800 BC (Anthony et al., 1991; The Institute for Ancient Equestrian
Studies, 1997; http://www.hartwick.edu/anthropology/iaes.html). There were
at least two subspecies of wild horse in historic times, a western subspecies
Equus ferus ferus and the eastern Equus ferus przewalskii. Separate domestica-
tion events may have occurred in central Asia and Western Europe, but there is
no direct evidence to substantiate or reject that possibility at present.
26
Genetic Aspects of Domestication 27
Fig. 2.1. (A) Tarpan-like horse, reconstructed in Germany by the Heck brothers, to resemble the
tarpan. Selected mares from Polish Koniks, Icelandic ponies, Swedish Gotlands and Polish primi-
tive horses (from the preserve in Bialowieza) were mated to Przewalski’s horse. Heck assumed
that the wild Przewalski horse would serve as a catalyst to draw out the latent tarpan characteris-
tics dormant in these more modern breeds (http://www.ansi.okstate.edu/breeds/horses/).
(Photograph by ©Sorrel, Germany; permission kindly granted by Ms Gaby Kärcher). (B) Arabian
horse (photograph by Michael Bowling, permission kindly granted).
27
Dogs, sheep, goats, pigs and cattle were domesticated earlier, presumably
to ensure food sources. The horse was likely to have been domesticated
primarily for purposes other than food, namely for transportation or for
draught power, although these uses do not preclude use as a food source
(meat or milk). Still, domestication and selection of the horse differs from that
of other species, in that the chief functions for which the horse was useful to
humans reinforced the trends of natural selection. Cows producing 8000 kg
of milk per lactation would never appear in natural conditions; nor would
sheep producing 7 kg of superfine wool per year. Horses in the wild, however,
would be selected for speed, strength and endurance – the very traits that
would make them useful under domestication.
Equus f. ferus (http://www.ansi.okstate.edu/breeds/horses/tarpan/index.
htm), or tarpan, persisted in the southern regions of Eastern Europe until the
19th century (Fig. 2.2). The last tarpan in the wild was killed in December
1879, 35 km from Askania-Nova in the Herson region, Ukraine. The last tarpan
captured in the same area lived in the Moscow Zoo until the late 1880s. One
stallion, which may not have been a pure tarpan, lived on a farm in the Poltava
region, Ukraine, until 1918 (Bannikov and Flint, 1989).
The Russian naturalist Gmelin in 1769 provided the first good description
of the tarpan in nature (from a site near Voronezsh ~400 km southeast of
Fig. 2.2. Area of horse domestication and likely directions of migration.
28
Moscow). The horses that Gmelin saw were ‘hardly as large as the smallest
Russian’ and had extraordinary thick heads, pointed ears and short upstanding
manes. These horses were mouse-coloured; according to other descriptions,
some animals were ash-grey and even white. The belly was ash-grey and the
points were black. Their hair was very long and thick and like a pelt. The tail
was more or less covered with hair, but always shorter than in domestic
horses. The tarpan ran with ‘the utmost speed, and at least twice as fast as a
good tame horse’ (cited from Zeuner, 1963, pp. 311–313; Groves, 1994). It
seems doubtful that the speed estimation was correct, but it is likely that
the tarpan, in spite of its small size (~130–140 cm), was very fast indeed. It
is nearly universally accepted that the tarpan was the wild ancestor of the
modern horse – unfortunately, direct karyological and molecular comparisons
are not possible due to the extinction of this species.
Equus f. przewalskii, also known by its Mongolian name takh, is the
eastern subspecies of the wild horse (http://www.ansi.okstate.edu/breeds/
horses/przew/index.htm). Its name commemorates the Russian naturalist and
explorer of Asia, Colonel N.M. Przewalski, who first encountered wild horses
in northwest China near the Mongolian border in 1879. A detailed description
of external characters of Przewalski’s horse can be found elsewhere (Groves,
1994; see Chapter 1). This is a robust animal with a thick short neck and a
heavy head. Males are about 138–146 cm at the withers, females generally
5 cm smaller. The body colour is pale grey–yellow or bright yellowish
red–brown. A dark dorsal stripe and dark points are typical, along with a more
or less pale belly and light muzzle. Most authors exclude E. f. przewalskii from
direct ancestry of the domestic horse mainly due to differences in karyotype.
Przewalski’s horse has 66 chromosomes while the domestic horse Equus
caballus has 64 (see Chapter 9 for details). It is not ruled out that the takh
could have been the subject of independent domestication in Mongolia and
northwestern China and later have been replaced by domestic horses of
western origin.
Reasons, pre-condition and the initial steps of horse domestication
High intelligence of the wild progenitors and plasticity of their behaviour were
among key characters essential for successful adaptation to domestication.
Indeed, the animals that successfully underwent the domestication process
have been ‘pre-adapted’ by their previous evolution. Candidates must have
had abilities that would not fully overlap with those of other domestic animals.
The tarpan seems to fit these demands (Budiansky, 1997). It was a large animal
able to run for a long time at high speed. A very specialized caecal digestive
system allowed it to run immediately after eating. This specialized digestive
system enabled horses to survive on a diet that is not sufficient for ruminants
(cattle, sheep and goats) and thus reduced food competition with previously
domesticated mammals.
29
Shifts in genetically determined behaviour may cause changes in the

neuroendocrine system and in levels of hormones. These changes in hierarchi-
cal systems regulating gene expression during development may affect basic
morphogenetic processes (Belyaev, 1979; Trut, 1997), including a shift toward
neoteny. It is obvious that a significant change in behaviour was a pre-
condition for success in managing at least the first several generations of nearly
wild horses. It can be presumed that taming and feeding of young foals may
somewhat lessen the problem when they reached maturity, but strong selec-
tion must have operated for individual horses able to cooperate with people
and demonstrate submissive behaviour. Interestingly a comparison of concen-
tration of α-tocopherol in plasma showed that in Przewalski’s horse this
parameter was substantially higher than in the domestic horse (Dierenfeld
et al., 1997).
We do not know much about different types of behaviour in the tarpan
population, but experience with Przewalski’s horses living for a number of
generations close to humans (e.g. in zoos) shows that while some Przewalski’s
horses can be petted and brushed, they resist restraint and generally cannot be
haltered and led. For the most part, they must be substantially restrained even
to obtain a blood sample. Unlike feral horses, they cannot be easily ‘tamed’.
There are pictures of Przewalski’s horses saddled and with riders on them, but
this does not necessarily mean that these horses were useful riding horses.
Attempts to tame zebras, another representative of wild equids, have been
numerous and unsuccessful. Budiansky (1997) considers this fact as an
indication of behavioural pre-adaption of the tarpan to domestication. Never-
theless, genetic and phenotypic variability for ‘domestic type’ behaviour might
exist in the ancestor tarpan populations and might provide the necessary basis
for successful behavioural selection and domestication. As experiments with
fox domestication show, radical transformation of behaviour may occur in less
than a dozen generations (Belyaev, 1979). It may mean that the initial but
crucial steps could be accomplished within a limited period. A diastema (a gap
between the front incisors and rear grinders) provided an opportunity for the
innovation of bridle and bit. Without them, managing a horse would be much
more difficult.
History of horse domestication
Clearly, the domestic horse could reach the Middle East only by two ways (Fig.
2.2): over the Caucasus, or through the steppes and semideserts to the east
from the Caspian sea. Use of horses probably started spreading between 3500
and 3000 BC and reached the Middle East in the middle of the third millennium
BC. The earliest known clay figurine of a domestic horse (~2300 BC) was found
recently at Tell Es-Sweyhat, about 300 km northeast of Damascus (Bower,
1993). The horse reached Egypt close to the end of the Hyksos dynasty (~1580
BC) when it was considered a rare animal.
30
The horse appeared in southeastern Europe (Greece) at about the same

time, soon after 1900 BC (Bökönyi, 1984). Much later, in the time of Philip of
Macedon, the father of Alexander the Great (430–354 BC), horses still were
imported extensively into Greece from the kingdom of Scythia, the area of
modern Romania, Ukraine and south Russia (Clutton-Brock, 1987). The Greek
mythological figure of the man–horse Centaur shows the spread of horse-
riding culture in ancient Greece and particularly in its northern neighbour
Scythia, where these skills were highly developed and significantly affected
contemporary arts. The horses on Scythian artefacts are characteristically large
and Arabian type in their conformation (Clutton-Brock, 1987). From this time,
expansion of the horse into the major western civilizations spread rapidly, with
the recognition of its military usefulness.
The domestic horse penetrated eastward at least by the early first
millennium BC. A Scythian horse wearing a ritual mask was found in the frozen
tomb at Pazyryk in the Altai mountains, dated to the 5th century BC (Zeuner,
1963; Rudenko, 1970). There are indications that horse riding appeared in
the Altay-Sayan region as early as 1500 BC (Bökönyi, 1984). In this case,
Sarmatians and other seminomadic people who lived eastwards from the Ural
mountains and Caspian Sea might have possessed domestic horses.
It is well known that the steppes of modern Kazakhstan, southern Siberia
and Mongolia were the places where the ‘horse culture’ reached its highest
development. For the nomadic tribes that lived there, it was a way of life
compatible with vast territories and natural conditions. These tribes rode
horses, milked them, fermented ‘kumyss’ (an important part of their diet), ate
horse meat and used their hides.
There is no historic evidence that the domestic horse was used in China
before the second or third centuries BC. In 102 BC, Emperor Wudi sent a
huge military expedition to Middle Asia (‘Fergana’) to obtain ‘heavenly horses’
(Zeuner, 1963; Olsen, 1988). However, there are indirect indications that
Scythians had contact with China long before this time. Silk and a bronze mir-
ror found in the Scythian Pazyryk tomb in the Altai mountains confirm contacts
between China and Scythia in about 500–400 BC. These data may indicate that
the domesticated horse reached China through the Altai region as early as
500–400 BC. It seems likely that the domestic horse reached Mongolia by a
similar but more northerly route.
World history would be quite different without the domestic horse.
Interestingly, wheeled vehicles were in use on the Russian steppes by 3650 BC
(Haywood, 1997), but military chariots were introduced only in the 16th
century BC in Egypt. Egyptian cavalry and horse-drawn chariots were first
mentioned in the biblical description of Exodus, when the whole army was
swept away by the waves of the Red Sea. The domestic horse became an
increasingly powerful component of Eurasian civilizations from the middle
of the second millennium BC (The International Museum of the Horse 1998.
Lexington, Kentucky http://www.imh.org/imh/imhmain.html).
Horse transport enabled humans to increase the speed at which they
could move across land, in a way that none of the animals domesticated earlier
31
had provided. That inherited differences occur in gaits (footfall patterns) of

horses and in no other domestic animal is probably also an indication of the
significance of ridability to its domestication. From the early centre (or centres)
of domestication, horses spread in all directions (Bökönyi, 1984). People
migrating into new territories brought their domestic animals, including
horses, with them. Since the horse was a major means of transportation, horses
were also spread along major trade routes, and probably gained new homes as
captured booty from skirmishes with invaders.
Genetic Studies of Domestic Horses and Przewalski’s Horse

Morphology and historical information classically have been used to describe
the relationships of breeds. More recently, studies of objectively determined
genetic markers have been used to understand the fundamental relationships
of breeds to one another and to other equids, particularly Przewalski’s horse,
the most closely related species. An inherent problem in genetic comparison
conclusions concerning domestic and wild horses is that a Mongolian domestic
mare is included in the pedigree lineage of many extant Przewalski’s horses
(Kus, 1997). Although the other 12 surviving species founders for Przewalski’s
horse are not considered to represent domestic horse hybrids, this point is not
known with certainty.
Chromosomes
The genus Equus is characterized by rapid karyotype evolution (see Chapter

9). Rapid evolution of satellite DNA in equids (Wijers et al., 1993) may be a
factor in their rapid chromosome evolution (Wichman et al., 1991; Bradley
and Wichman, 1994). The karyotype of the domestic horse is composed of 64
chromosomes (13 metacentric autosomal pairs, 18 acrocentric autosomal pairs
and a pair of sex chromosomes). That of Przewalski’s horse is very similar, but
the diploid number is 66 (12 metacentric autosomal pairs, 20 acrocentric
autosomal pairs and a pair of sex chromosomes). The difference appears
to involve chromosomal fission or fusion (depending on the direction of
evolutionary change) of ECA5 (E. caballus chromosome 5).
The karyotype difference between Przewalski’s and domestic horses may
have alternative evolutionary scenarios. According to the first one, the tarpan
had 64 chromosomes at the time of domestication, which explains why
domestic horses have 64 chromosomes. The possible difference between the
tarpan and the takh may be a result of fixation of the Robertsonian trans-
location in the tarpan if the ancestor of both subspecies had 66 chromosomes.
The second proposal is based on the assumption that the Robertsonian trans-
location occurred in the very early stages of domestication, essentially in one
herd of tarpan that originally had 66 chromosomes. Due to random events,
only homozygotes for this translocation survived. All domestic horses would
32
originate from this single herd. However, if the common ancestor of both wild
subspecies had 64 chromosomes then a fission event of metacentric or sub-
metacentric chromosomes might increase the number of diploid chromosomes
from 64 to 66 in Przewalski’s horse (Ishida et al., 1995). Hopefully, future
investigations will provide information to rule out one of these proposals.
All Przewalski’s horses that have been studied have the same diploid
karyotype of 66 chromosomes. All horse breeds so far studied have a diploid
set of 64 chromosomes, except for the Caspian pony, a rare group of horses
found in the northern part of Iran around the Caspian Sea, which shows poly-
morphism in the diploid number of chromosomes (Hatami-Monazah and
Pandit, 1979). Out of 17 studied animals, 11 had 64 chromosomes while six
had 65 chromosomes, demonstrating heterozygosity for centromeric fission in
one of a pair of metacentric chromosomes. None had 66 chromosomes. The
G-band pattern of these chromosomes indicated close resemblance to both
E. caballus and E. f. przewalskii. The fertility of mares in the group was low,
about 40%, as expected for heterozygosity for a Robertsonian translocation.
The stallions had a low sperm count and poor sperm motility. Possible expla-
nations for this chromosomal polymorphism in Caspians could be natural
hybridization of domestic and Przewalski’s horses in the past or it could
have been produced by a spontaneous, independent event involving the
same chromosomes as the karyotype difference between Przewalski’s and
the domestic horse.
Nuclear genes detected by immunogenetic and biochemical techniques
Starting in the late 1960s and continuing to the early 1980s, genetic studies of
horses were based on immunogenetic and biochemical markers developed for
parentage verification of domestic horses registered by breed societies (see
Chapter 5). Development of these tests involved extensive research with a few
major breeds (e.g. Thoroughbred, Arabian, Quarter Horse, American Standard-
bred and Swedish Trotter) but subsequently the tests proved highly effective
for examining parentage questions in any breed – and for looking at genetic
similarities among breeds and with Przewalski’s horse. Investigators with
access to genetic material from Przewalski’s horse applied these gene assays
to that species (Braend, 1979; Kaminski, 1979; Ryder et al., 1979; Scott, 1979;
Putt and Whitehouse, 1983; Bowling and Ryder, 1987; Bowling and Dileanis,
1990; Patterson et al., 1990; Fincham et al., 1992). These studies generally con-
firmed a significant level of similarity among breeds and between E. caballus
and E. f. przewalskii compared with other Equidae species, and, for several
loci, genetic variants were present in some Przewalski’s horses that were not
found in domestic horses.
The first highly effective parentage test developed for horses, still used by
many breed registries throughout the world, consisted of a battery of tests
detecting blood group and blood protein polymorphisms developed by collab-
orating laboratories belonging to the International Society for Animal Genetics
33
(ISAG) (described in Bowling, 1985; Bowling and Clark, 1985; and see Chapter
5). Several comparative studies of breeds and Przewalski’s horses have been
conducted based on the parentage test battery. Bowling and Ryder (1987) used
18 polymorphic loci to investigate five breeds of domestic horses and
Przewalski’s horse. The genetic distance between the breeds of domestic
horses and Przewalski’s horse was estimated as 0.3 or slightly greater, while
the domestic breeds clustered rather closely at distances of about 0.1 or lower.
Interestingly the average heterozygosity for Przewalski’s horse did not differ
significantly from the values calculated for several domestic breeds.
Dubrovskaya et al. (1992), using a smaller set of polymorphic systems and a
different group of domestic breeds, came to a similar estimation of genetic
distances. Surprisingly, the genetic distance between Przewalski’s horse and
the Shetland pony was rather small, possibly reflecting not only the real
relationships between these two populations, but also results of genetic drift.
The cluster analysis grouped several phenotypically quite different indigenous
breeds from the eastern part of the former USSR, such as the Akhal-Teke and
Yakut horses.
This unexpected conclusion was confirmed recently in the study by
Tikhonov et al. (1998) based on a much larger set of breeds and on a more
powerful set of polymorphic loci than used by Dubrovskaya et al. (1992)
(comparable with the parentage panel described by Bowling and Clark, 1985).
In the Tikhonov study, indigenous breeds with such distinctly different
phenotypes as Akhal-Teke and Yakut show high levels of relatedness. Rogers
coefficient of similarity between these two breeds was equal to 0.681. Even
more surprising is that the similarity of Arab and Yakut horse was about
0.725. However, these data do not contradict the discussion concerning the
spreading of horses from a horse domestication centre in Scythia. Tikhonov
and colleagues expressed the view that Yakut and several autochthonous
breeds of Middle Asia had significant association with the ancient horse that
moved eastwards from the centre of horse domestication.
Przewalski’s horse consistently takes an outgroup position in the
dendrograms of domestic horses based on nuclear genes (Bowling and Ryder,
1987; Dubrovskaya et al., 1992; Tikhonov et al., 1998). This is an additional
argument apart from morphology, karyology and behaviour that Przewalski’s
horse did not contribute to the gene pool of the domestic horse.
Molecular polymorphisms – mtDNA and microsatellites
Polymorphisms in DNA sequence have also been used to decipher the recent
evolution of horses. The first studies involved mitochondrial DNA (mtDNA)
(George and Ryder, 1986). Comparisons of Przewalski’s horse and domestic
horse mtDNA cleavage maps (based on shared restriction enzyme recognition
sites) yielded estimates of divergence from 0.27 to 0.41%. Using an average
estimation of divergence rate for mtDNA of 2% per million years, it can be
assumed that the common ancestor for Przewalski’s and domestic horses lived
34
about 100,000 years ago. Ishida et al. (1995) confirmed data presented by
George and Ryder and provided new information concerning evolution of
equids, particularly for domestic and Przewalski’s horses. From the sequence
of the variable region of the horse mtDNA (D-loop segment), they concluded
that ‘the lineage of the Przewalski’s wild horse is not located at the deepest
branching among the E. caballus sequences’ in the neighbour-joining trees
they constructed. The observed topology of the trees clearly contradicts the
origin of the domestic horse from Przewalski’s horse. However, it is difficult to
reconcile the topology of the phylogenetic trees constructed by Ishida et al.
(1995) with comparative morphological, karyological and behavioural
data and with trees constructed by others. On the dendrograms of Bowling
and Ryder (1987), Tikhonov et al. (1998) and Dubrovskaya et al. (1992),
Przewalski’s horse shows early separation between wild and domestic horses,
while that of Ishida et al. includes Przewalski’s horse within the branches of
different breeds of domestic horses.
Oakenfull and Ryder (1998) determined the mtDNA D-loop sequence in
surviving Przewalski’s horse pedigrees using representatives of the four extant
matrilineal mitochondrial sources. Only two sequences were found, one of
which corresponded to that of Ishida et al. (1995). The other sequence differed
from the first, but both were certainly more similar to the published sequences
of three Thoroughbreds and a Mongolian horse than to other equids, corre-
sponding to the close relatedness found from nuclear gene studies for domes-
tic and wild horses. There is no other information suggesting that the mtDNA
sources in surviving Przewalski’s pedigrees are derived from domestic horses.
However, Przewalski’s horse and domestic horse hybrids are viable and fertile.
The contradiction between the mtDNA and nuclear DNA studies may be an
indication that in addition to the known introgression event that occurred
within a captive breeding programme, introgression also occurred in the wild.
Dinucleotide tandem repeats in horse DNA (microsatellites) in non-coding
regions of undefined genes have been described (e.g. Ellegren et al., 1992;
Marklund et al., 1994; and see Chapter 6). Microsatellites can be assayed
subsequent to polymerase chain reaction (PCR) fragment amplification using
semi-automated procedures for efficiency of sample testing. Frequency data
for microsatellite fragment sizes (allelic markers) of Przewalski’s horse and
domestic horses were reported by Breen et al. (1994). While there was consid-
erable overlap among variants observed in both species, some alleles
appeared to be present in the wild species, but not in domestic horses.
Worldwide Distribution of the Domestic Horse

The current estimated global population of domestic horses is 62 million
(FAOSTAT Database 1998), consisting of approximately 500 ‘breeds, types and
varieties’ (Mason, 1996). Classically, a breed is a distinctive set of animals
associated with a restricted geographical area in which it was developed to
meet human needs under particular local conditions (an autochthonous
35
breed). Increasingly often, horse breeds are defined by societies or registries

that record pedigrees and maintain a stud book for a selected subset of horses
based on geographical origin, phenotype or function. Horses registered with a
breed society constitute about 10% of the global population (Bixby et al.,
1994). Horses not associated with breed societies include feral horses and the
majority of those working in transport and agriculture. Autochthonous breeds
not constrained by stud book regulations potentially constitute a significant
genetic resource, often overlooked.
Attempts have been made to organize horse breeds into major sub-
divisions, for example based on physical size and proportions (pony, light
horse or draught horse), or on temperament (coldblood, warmblood or hot-
blood), reflecting perceived evolutionary relationships. However, no such
system provides a robust, intellectually coherent classification scheme in
which each contemporary breed would have an unequivocal assignment.
Notwithstanding the difficulties in arriving at a comprehensive classification
scheme, from time to time the above terms are useful to describe certain sub-
sets of horses. For example, ‘European warmblood’ has become the accepted
descriptor for a group of horse breeds, not so much defined by temperament
as by related origins, physical appearance and use.
Stud books define the gene pool of a breed and the rules for managing it
Horse breeds defined by stud books represent a diverse collection of options

for assembling and managing a gene pool. In most countries, there is no over-
riding authority that oversees compliance with a single stud book model to
define and maintain a breed, such as exists for purebred dogs. The rapidly
accumulating and widespread evidence concerning the poor genetic health of
many dog breeds provides a dramatic example of the importance of consider-
ing genetic implications of stud book policies, both at the stud book inception
and during the maintenance phases. Horse breeds may appear to be less
phenotypically distinctive than dog breeds, perhaps a reflection of the histori-
cal relatedness of many breeds and more recent crossbreeding schemes. For
horses registered with a breed society that allows crossbreeding, the potential
for generating heterozygous genotypes may contribute to overall breed health,
but compromise the predictable genetic breeding uniformity of individuals.
Some horse stud books are under the authority of a government agency
(e.g. Spanish Purebred horse (Andalusian)), but most stud books are main-
tained by and subject to the legal obligations of a private corporation. The
keepers of the stud book (generally, the elected or appointed Directors of the
Breed Society) determine the registration rules. The rules may be changed by
the current authorities when deemed essential for breed viability. In the last
few decades, authorities have had to make decisions about whether to allow
assisted reproductive technologies (ART) (such as artificial insemination, trans-
ported cooled semen, frozen semen and embryo transfer) which have poten-
tial to affect the genetic future of the breed. While many breeds have endorsed
36
these technologies, a notable exception is the Thoroughbred, for which stud

books worldwide have agreed only to register animals conceived by ‘natural
cover’ and delivered by their own (genetic) mother.
Stud book breeds suit a variety of purposes. The founder populations
usually have been selected particularly on appearance (‘type’) and utility.
Selection may also be based on geographical origin (Arabian, Connemara, Ice-
landic, Kiger), colour (Appaloosa, Paint), gait (Tennessee Walking Horse, Paso
Fino), racing speed (Thoroughbred, American Standardbred) or relationship to
a single stallion (Morgan, Shagya). Crossbreeding initially may be allowed (and
recorded in pedigrees) for several generations to build up a viable breeding
nucleus. Subsequently, many stud book authorities close registration to any
but the offspring of horses already registered with the society. In the case of a
closed stud book (e.g. Arabian or Thoroughbred), the breed today is based on
a selected set of founders and there are no (or extremely few) options to
increase diversity in the gene pool. One possibility to expand the gene pool is
reciprocity with stud books in other countries. Even if breed stud books in
different countries are based on the same founders, genetic differences due to
the mutation process, recombination and genetic drift probably will develop
provided the populations remain separated for a sufficient length of time.
Breed societies that have elected to keep their stud books open usually
restrict crossbreeding to horses registered with specified stud book authorities.
The breeds allowed for outcrossing most commonly include Thoroughbred
and to a lesser extent Arabian, such that modern breeds with open stud books
may be losing their distinctiveness (Bixby et al., 1994). Crossbred horses in
open stud books may be placed in a separate section (e.g. Thoroughbred
crosses in the Appendix section of the Quarter Horse stud book) but may
advance to regular registry status after meeting performance or breeding
standards. Due to the pedigree restrictions of most breed societies, there is
little opportunity for proven useful gene combinations from unregistered
horses (e.g. feral horses) to be added to their gene pools. However, new horse
breed societies continue to emerge (e.g. National Show Horse, Azteca, Tiger),
permitting breeders to take advantage of gene sources and combinations not
otherwise accommodated by extant breeds. This continuing development of
breeds is not nearly as common among other domestic animal species but, for
horses, there appears to be sufficient interest and economic incentive to do so.
For the most part, the offspring of a pair of registered (stud book
recorded) parents of the same breed will also be eligible for registration in the
same stud book, but some breed societies have defined restrictions. For Euro-
pean warmbloods, foals may be recorded in a ‘foal book’, but not attain full
breeding registry status until they pass a series of requirements, including
physical inspection, performance and breeding tests. Particularly for colour
breeds, foals that do not have the defining colour may be assigned to a
separate section and may not be allowed to participate in breed shows, but
their offspring are fully eligible for regular stud book status if they meet
the colour and pedigree requirements. Even ‘non-colour’ breeds may have
‘colour’ requirements. For example, until recently, Morgan foals could not be
37
registered if they were of cremello or perlino colour (i.e. ~25% of foals arising
from the inter se breeding of palomino or buckskin parents) or had ‘excessive’
white markings (genetics not defined). Those registration restrictions were
lifted in 1996 for Morgans, but similar ones are in place for Quarter Horses.
Breeds defined by stud books are young compared with the length of time
that horses have been domesticated. Breeds with the longest pedigree records
include Lipizzaners (since the early 1700s) and Thoroughbreds (since the
late 1700s) (both breeds from acknowledged crossbred sources). Arabians are
considered to have been a recognized breed for longer than either Lipizzaners
or Thoroughbreds, theoretically without any crossbreeding, but for most Arab
horses the bulk of the recorded pedigree consists of lines that trace to desert
sources representing only 100 years or less of written records, and no line can
be carried back before 1800.
Examples of horse breeds
Examples of modern horse breed diversity are provided here by riding horse,
draught horse, pony and mixed-use breeds. Breed information, chosen to
illustrate the kinds of information available about the genetic history of breeds,
was obtained from comprehensive material provided by breed registries,
Edwards (1980) and Hendricks (1995). The breeds selected provide back-
ground for the genetic distance comparisons that follow later in this chapter.
Arabian (AR)
The Arabian as a breed has no origin in recorded history. Desert nomads in the
Arabian peninsula developed a moderately sized horse noted for such beauty,
stamina and conformational strength that for centuries horse breeders went
to the Arabian desert to import horses for improvement of local stock. The
Thoroughbred (TB) and continental cavalry breeds are the noteworthy result
of this process. Historically, a few breeders in Europe and Egypt imported ARs
not only for crossbreeding, but also to establish AR breeding programmes.
Most modern AR pedigrees trace to desert imports from about the mid-1800s to
the early 1900s. AR stud books are maintained throughout the world. The
international gene pool of ARs is essentially closed, but it is not homogeneous.
Stud books could still be acquiring new genetic material from other countries.
ARs have been particularly successful in events requiring endurance, but are
primarily bred for competitive show ring events in which excellence is judged
subjectively. In traditional classification schemes for horse breeds, ARs are
typically presented along with TBs as a standard example of the hotblood or
light horse. The breed data for this chapter are derived from horses registered
with The Arabian Horse Registry of America.
Iberian (IB)
Horses of the Andalusian (Purebred Spanish horse) and Lusitano breeds are
riding horses that have been developed in Spain and Portugal, respectively,
38
from historically similar autochthonous Iberian peninsula breeding elements.

Differences seen today can probably be attributed to relatively recent differ-
ences in selection emphasis. For example, most Andalusians are grey, with
occasional examples of other colours except chestnut (while chestnuts occur,
they are not considered acceptable as breeding stock). Any solid colour is
acceptable in Lusitanos, including chestnut. While both breeds are used as
riding horses, the Lusitano is an integral part of the Portuguese bull-fighting
tradition and is selected primarily for excellence in this sport, while the Pure-
bred Spanish horse is selected for beauty and sound, functional conformation.
Iberian horses historically have been used as a source of strength and elegance
for breeding stock improvement at European state studs and are highly valued
for those same traits today. The stud book of the Purebred Spanish horse is
maintained for horses worldwide by the Cria Caballar, a branch of the Spanish
military. Lusitanos have a more restricted worldwide distribution. In the USA,
horses of each breed and their combinations are registered by The Interna-
tional Andalusian and Lusitano Horse Association and the breed data for this
chapter are derived from those horses.
Lipizzaner (LI)
This breed was developed in central Europe, in an area associated variously
with Italy, Austria or Yugoslavia, depending on national border changes
established by peace treaty agreements. Lipizzaners are distributed around
the world, although the number of horses overall is not large. The American
Livestock Breeds Conservancy (ALBC) classifies LIs as rare. The predominant
colour for LIs is popularly referred to as ‘white’, although that colour would be
recognized by geneticists as being produced by the gene for grey colour
whose epistatic action (see Chapter 3) causes the progressive and gradual
lightening of the dark hair of the foal coat. LIs are riding horses characterized
by great strength. Today, LIs are best known for their association with the
Spanish Riding School in Vienna, the oldest riding school in the world, and for
their excellence in classical riding disciplines (dressage). Archduke Charles,
son of Emperor Ferdinand I, established a stud farm at Lipizza in 1580 that
exchanged horses with the court stud of his brother at Kladrub and with
other state studs. The LI has one of the oldest stud books, dating to 1701. The
genetic elements of LIs, in addition to autochthonous horses, include IB,
AR, Danish, Neopolitan and Kladrub sources. Breeding traditions emphasize
paternal and maternal line founder elements and attempt to preserve all the
extant pedigree sources. The breed data for this chapter are derived from
horses registered with United States Lipizzan Registry.
Miniature (MI)
The ideal for this breed is an animal that is a miniature version of a standard
horse but measuring no more than 34 inches at the withers (base of the mane).
While animals are seen that simulate this ideal, most tend to reflect their
pony origins. Miniatures are too small for riding but they can be used for
light driving. They are particularly valued as companions and for show ring
39
competition. In addition to small size, these horses are known for their great
variety of colours and patterns – indeed it is reasonable to propose that all the
colours and patterns distributed among various horse breeds can be found in
MIs. Their earliest origins are unrecorded and subject to various interpreta-
tions, as with other breeds pre-dating stud book records. There is no compel-
ling evidence of a recent relationship with any horse-sized breed, despite
physical resemblance of some animals, for example to ARs or TBs. Certainly
some MIs are of relatively recent descent from Shetland ponies meeting MI size
requirements. Another source is from the breeding programme of the Falabella
family in Argentina. Pedigrees of MIs may be relatively short, since the breed
association is relatively new, and horses meeting size requirements may be
accepted for registration without a pedigree. The breed data for this chapter
are derived from horses registered with The American Miniature Horse
Association.
Morgan Horse (MH)

All horses of this breed trace to one stallion, a horse owned in the late 1700s
by a Vermont school teacher named Justin Morgan. The breeding origins of
this stallion are not documented reliably. Mixtures of TB, AR, Dutch Draft and
Welsh Cob breeding have all been suggested, but nothing can be proved. He
was bred to the variety of mares available locally and his descendants demon-
strated tractability and versatility, from weight-pulling, to saddle and harness
racing, and use as a utility saddle horse – all by the same horse. A registry was
established in 1909 incorporating in many cases pedigrees with elements
tracing back 100 years. In the early decades of the registry, crossbreeding with
such breeds as AR, Standardbred and American Saddlebred, followed by
back-crosses to MHs, was allowed. At present, the registry is closed. The gene
pool of this breed is expected to be quite diverse, despite descent from a
single sire. Reasons for this include the variety of mare lines used in the estab-
lishment of the breed, the more recent use of crossbreeding, and selection
practices based on somewhat subjective characters such as physical type
which have a low heritability. MHs provide an example of a horse breed that
logically should be classified as a warmblood, since it has elements of
hotblood and coldblood breeds. However, the term ‘warmblood’ is applied
now to mixtures of European breeds with TBs and it is likely that there
would be some objections to the inclusion of MHs in the warmblood category.
The breed data for this chapter are derived from horses registered with the
American Morgan Horse Association.
Norwegian Fjord (NF)

Horses of this breed are used as small draught horses and as riding and driving
horses. They are hardy horses of ancient origin and today are of a distinctive
colour (dun), although the uniformity of pattern was imposed relatively
recently (selective breeding programmes dating from the late 19th century).
The predominant colours – red, brown and grey dun – are produced by the
interactions of the basic coat colour genes with the Dun gene. To maintain
40
hardiness and diversity of the gene pool, registration is denied for horses
conceived from breeding between first generation relatives. The breed data for
this chapter are derived from horses registered in the USA with the Norwegian
Fjord Horse Registry.
Paso Fino (PF)

This gaited (lateral rather than diagonal footfall pattern) riding breed is being
developed in the USA in a relatively recent effort from Caribbean and South
American sources. The horses descend from Barbs, Iberian horses and Jennets
brought to the New World by Spanish explorers and colonists as long as 500
years ago. The PFs have a natural lateral gait, a characteristic of most of the
world’s riding horses prior to the 17th century, that contrasts sharply with the
square trotting gait seen in most horses today. This gait is extremely comfort-
able for the rider and is relatively non-tiring for horses to perform. In the USA,
these horses are used primarily for pleasure riding and showing. The breed
data for this chapter are derived from horses registered with the Paso Fino
Horse Association.
Percheron (PN)
This draught horse was developed in northern France, from crosses of oriental
stallions with local mares of undocumented, but ancient origins. These horses,
along with other European draught horses, were widely exported in the mid-
to late 19th century to provide the breeding basis for agricultural horsepower,
particularly for the USA. While breed numbers declined dramatically with the
advent of agricultural mechanization in the early years of the 20th century, in
the last few decades the number of foals registered has been increasing so
that this breed is no longer considered rare. The horses are still popular for
agricultural uses, for show ring competition and for crossbreeding with TBs to
produce competition sport horses. The horses today are black or grey, with
minimal white markings. The breed data for this chapter are derived from
horses registered with the Percheron Horse Association in the USA.
Thoroughbred (TB)
The recorded origins of this breed trace to the use in the early 1700s of
imported ‘eastern’ (‘Arabian’, ‘Barb’ or ‘Turk’) stallions with English mares
to beget horses for racing. Weatherby’s General Stud Book (GSB), Vol. 1,
appeared in 1808. Registered TBs must trace in all lines to horses registered in
the GSB or in similar TB stud books maintained outside Great Britain. Thus,
this breed, originally a crossbred, has had a closed stud book for nearly 200
years. Individual TBs may excel at jumping, cross-country racing and dressage,
but for the most part these horses have been selectively bred only for gallop-
ing speed. In traditional classification schemes for horse breeds, TBs typically
are presented as a standard example of the hotblood or light horse. The breed
data for this chapter are derived from horses registered with The Jockey Club
in the USA.
41
Trakehner (TK)
This breed was developed in the 18th century as a cavalry horse from Prussian
local horses of various types including heavy horses, augmented with selected
TBs and ARs. The TK is one of the breeds traditionally referred to as a
warmblood because of its origins from mixed breed types, including TB with
continental European autochthonous breeds. The breed was almost destroyed
during World War II, but, through the efforts of dedicated breeders and
German federal government support, it has been revived as a vigorous and
highly regarded breed, particularly valued for its abilities in sport horse com-
petitions, including jumping, dressage and cross-country events. The breed is
distributed worldwide. It is also used as a breeding element in other European
warmblood breeding programmes. The breed data for this chapter are derived
from horses registered with the American Trakehner Association in the USA.
Genetic similarity studies of breeds provide information to assess genetic

relatedness
The early breed comparison studies were based on easily identified allelic
differences in protein-coding genes. With the rapid development of techniques
for identification of DNA sequence variation, assays of highly polymorphic
microsatellites as markers of non-coding genetic sequence have become
available. A microsatellite-based alternative parentage test that can be applied
to blood or other biological samples, including hair roots, teeth and bone, has
been developed and provides a standard, readily assayed battery of molecular
markers for descriptive breed data (Bowling et al., 1997). A new generation of
breed comparisons can now be carried out. The more comprehensive the
genome coverage, the more likely it is that genetic similarity measures will
reflect the relatedness of breeds and allow us to provide reasonable assess-
ments of the early stages of breed developments.
A population analysis of allelic frequency data for ten breeds is presented.
The analysis is based on tests of over 50,000 horses for 22 loci of blood group
and protein polymorphisms and 16 loci of microsatellites, includes loci repre-
senting 18 autosomes, the X chromosome and six loci whose autosomal
assignment at present is not known (Table 2.1) (for a discussion of the loci, see
Chapters 5 and 10). For each locus, estimates of the total gene diversity (HT)*,
the coefficient of gene differentiation (GST)* and average gene diversity (HS)*
are provided for domestic horses (Table 2.1). The high gene diversity (HT)
values overall reflect the selection of moderately to highly polymorphic loci to
provide power for parentage testing. The measures HS and GST provide an
estimate for the partitioning of the variation within and between breeds. The
* HT is the expected heterozygosity of an individual produced by random mating within the total population of
horses, disregarding breed; HS is the expected heterozygosity of an individual produced by a random mating
with a subpopulation (breed); GST relates HT to HS. It is a measure of loss of diversity within subpopulations
compared with the total population of horses.
42
Table 2.1. Loci used for analysis of breed differences and data for construction of dendrogram.
Estimates of the total gene diversity (HT), the coefficient of gene differentiation (GST) and average
gene diversity across breeds (HS) are provided for each locus.
Locusa Chrb Alleles HT GST HS
Blood groups EAA 20 12.4 0.740 0.139 0.638

EAC U 2.4 0.467 0.099 0.421
EAD U 25.4 0.889 0.079 0.819
EAK 2 2.4 0.115 0.115 0.102
EAP U 3.4 0.512 0.036 0.494
EAQ [8] 6.4 0.667 0.152 0.566
EAU 24 2.4 0.429 0.156 0.362
Average 7.4 0.546 0.111 0.486
RBC proteins AP U 2.4 0.076 0.018 0.074
CA U 6.4 0.137 0.071 0.127
CAT U 3.4 0.357 0.161 0.300
HBA 13 5.4 0.530 0.119 0.467
PGD 2 3.4 0.293 0.106 0.262
PGM 5 3.4 0.202 0.034 0.195
GPI 10 5.4 0.094 0.129 0.082
Average 3.9 0.241 0.091 0.215
Serum proteins ALB 3 3.4 0.451 0.090 0.411
C3 7 5.4 0.450 0.061 0.423
ES 3 12.4 0.504 0.124 0.442
GC 3 2.4 0.161 0.060 0.151
PLG 31 2.4 0.327 0.116 0.289
TF 16 15.4 0.766 0.097 0.691
PI 24 25.4 0.876 0.089 0.798
XK 10 4.4 0.173 0.097 0.156
Average 8.5 0.463 0.092 0.420
Microsatellites ASB17 2 22.4 0.871 0.080 0.801
VHL20 30 10.4 0.830 0.094 0.752
HTG10 21 12.4 0.845 0.067 0.788
HTG7 4 5.4 0.606 0.124 0.531
HTG4 9 8.4 0.687 0.092 0.624
AHT5 [8] 11.4 0.809 0.083 0.741
AHT4 24 11.4 0.809 0.076 0.747
HMS6 4 8.4 0.759 0.074 0.703
HMS3 9 11.4 0.822 0.078 0.758
HMS7 1 10.4 0.803 0.093 0.728
HMS1 15 8.4 0.664 0.040 0.637
LEX3 X 14.4 0.859 0.076 0.794
LEX33 4 12.4 0.834 0.089 0.759
ASB2 15 14.4 0.847 0.111 0.753
CA425 [28] 11.4 0.670 0.051 0.636
HTG6 15 11.4 0.622 0.181 0.510
Average 11.8 0.771 0.088 0.704
Average (38 loci) 7.9 0.567 0.094 0.514
aLociidentified here by abbreviations are explained and referenced in Chapters 5 and 10.
bChr:chromosome; U: unassigned to a chromosome; brackets designate provisional assignment.
More information on chromosome assignments is provided in Chapter 10.
43
higher values for HS (within-breed variation) and the lower values for GST
(between-breed variation) show that most of the genetic diversity found is
shared among breeds. Notice that, at least among the loci chosen here, micro-
satellites are slightly less effective in distinguishing between breeds (lower GST
values) than the gene loci of the conventional test (blood groups and protein
polymorphisms). The ten breeds of horses (described in previous paragraphs)
have been chosen to provide a sampling of physical types and uses, breed
origins and pedigree structures. Estimated average heterozygosity values for
each breed and for Przewalski’s horse are provided in Table 2.2. The breeds
with the oldest pedigree records (TB and LI) have the lowest heterozygosity
values, and the newer breeds (based on the age of the stud books) (PF and
MI) have the highest values. Average heterozygosity for Przewalski’s horse,
despite the very small number of founders (13) recorded in the stud book
(Kus, 1997), has values comparable with some of the domestic horse breeds.
Genetic distances (D) among these breeds and Przewalski’s horse, based
on 38 loci, were calculated using DISPAN (Ota, 1993) (Table 2.3). As in other
genetic distance studies, Przewalski’s horse provides the most dissimilar of the
paired comparisons for any breed, shown here with a value of at least 0.308.
Between domestic breeds, no distance measure exceeds 0.214 ± 0.05 (TB
versus NF), which seems appropriate considering the lack of a documented or
even anecdotal connection between these breeds. Also, the very close distance
value between TK and TB (0.041 ± 0.01) is expected considering the contem-
porary use of TBs in TK breeding programmes (but not vice versa).
As a means of visualizing these distance data, a dendrogram was con-
structed based on a neighbour-joining algorithm (NEIGHBOR) using PHYLIP
(Felsenstein, 1993) (Fig. 2.3). The arrangement agrees reasonably well with
anecdotal and published information available for these breeds and with
Table 2.2. Estimated average heterozygosity at 38 loci (listed in Table 2.1) for ten
breeds of horses and Przewalski’s horse, arranged from lowest to highest values.
Breed or taxon Estimated average heterozygosity (±SD)
TB 0.461 (0.047)
LI 0.473 (0.042)
PZ 0.474 (0.044)
AR 0.478 (0.045)
IB 0.491 (0.046)
TK 0.511 (0.043)
NF 0.531 (0.039)
PN 0.535 (0.041)
MH 0.537 (0.042)
PF 0.551 (0.045)
MI 0.579 (0.038)
AR, Arabian; IB, Iberian; LI, Lipizzaner; MI, Miniature Horse; MH, Morgan;
NF, Norwegian Fjord; PF, Paso Fino; PN, Percheron; PZ, Przewalski’s horse;
TB, Thoroughbred; TK, Trakehner.
44
03 April 2000 10:36:01
Table 2.3. Standard genetic distances (±SD) between ten breeds and Przewalski’s horse based on 38 polymorphic loci (listed in Table 2.1).
MH NF PF TB TK AR LI PN IB MI
Genetic Aspects of Domestication
NF 0.109±0.02
PF 0.057±0.01 0.124±0.02
TB 0.114±0.03 0.214±0.05 0.129±0.03
TK 0.069±0.01 0.152±0.04 0.094±0.02 0.041±0.01
AR 0.078±0.02 0.175±0.04 0.099±0.02 0.105±0.02 0.065±0.02
LI 0.113±0.02 0.194±0.05 0.126±0.02 0.202±0.05 0.155±0.03 0.139±0.03
PN 0.079±0.02 0.115±0.03 0.092±0.02 0.194±0.04 0.150±0.03 0.156±0.03 0.132±0.03
45
IB 0.107±0.03 0.168±0.03 0.092±0.02 0.170±0.04 0.137±0.03 0.109±0.03 0.199±0.04 0.139±0.03
MI 0.091±0.02 0.092±0.02 0.083±0.02 0.182±0.04 0.141±0.03 0.151±0.03 0.136±0.03 0.089±0.02 0.137±0.03
PZ 0.345±0.08 0.354±0.08 0.323±0.08 0.382±0.09 0.382±0.09 0.394±0.09 0.394±0.09 0.344±0.08 0.389±0.09 0.308±0.07
Breed abbreviations as in Table 2.2.
A3759:AMA:First Revise: 20 January 1999 CHAP-2

45
Fig. 2.3. Thirty-eight loci of genetic markers (blood groups and proteins as well as
microsatellites) were used to construct this dendrogram for ten breeds and Przewalski’s horse
based on a neighbour-joining algorithm using NEIGHBOR in PHYLIP (Felsenstein, 1993) and bootstrap
resampling of 100 data sets. Bootstrap values are provided at branch points.
previously published dendrograms using fewer loci and less extensive genome
coverage. As in previously published dendrograms based on nuclear genes,
Przewalski’s horses remain as an outgroup to the domestic horse breeds. MI
and NF horses form a cluster, set off from the other breeds. The remaining
breeds form a somewhat loosely defined cluster, with the closest relationship
being between TBs, TKs and ARs, and the others branching off from this set.
This arrangement probably reflects the similarity in early origins of most
breeds of domestic horses, with the evident phenotypic distinctions being
produced by rather minor collections of genetic differences, as suggested by
the population data analysis discussed above and in Table 2.1. Perhaps a
better method to discriminate breed relationships (as compared with species
46
relationships) will be provided when we can construct dendrograms based not

on breed-based allelic frequency comparisons, but on allelic compositions of
individuals within breeds, such as recently presented for cattle by MacHugh
et al. (1998). Such studies are more likely to reflect genetic disequilibrium
effects that doubtless play a significant role in the comparatively recent
formation of breeds.
Addressing questions of introgression between domestic breeds
Discussions about horse breed purity have a long-standing history. Indeed,

registered horses are often referred to as ‘purebred’, certainly implying a
notion of purity, although the genetic meaning of that term is not clear. Parent-
age verification programmes, designed to address questions concerning first-
generation pedigree errors, have only been available for about 25 years. Prior
to that time, pedigrees were based on sire and dam assignments provided by
the owners. Pedigree errors could not have been detected objectively, except
when genetic exceptions to coat colour rules occurred (see Chapter 3, this
volume) and owners or registries recognized them. As horse owners become
knowledgeable about genetics, they are putting pressure on breed registries to
address rumours about particular examples in past generations of prescribed
introgression from other breeds.
Using the well-characterized loci that have been identified to be effective
for domestic animal parentage, testing has been used to investigate intra- as
well as interbreed similarities and differences, as previously shown in this
chapter. Most of the genetic variation within a breed is present in other breeds.
Rare variants that are confined to one or a few related breeds are found (e.g. a
D system phenogroup in Caspian ponies by Cothran and Long, 1994), but no
breed-specific markers (akin to species-specific markers) have been identified.
That is to say, no variants have been found that are present only in a single
breed and possessed by every horse in that breed. Genetic differences
between breeds for the most part are allelic frequency differences, originating
from differences in selection schemes, founders or random drift, i.e. differ-
ences in breed histories, but not necessarily differences in earliest origins.
Certain alternative pedigree proposals involving past generations may
be addressed productively using mitochondrial and Y chromosome DNA
haplotypes (polymorphisms of linked markers), which would be unaffected
by genetic processes of segregation and recombination that confound the
tracking of autosomal genes through extended pedigree lines. Mitochondrial
haplotypes, strictly maternally inherited in the tail female line of the pedigree,
have been used to resolve maternity controversies without access to biological
material from the horses in question (Bowling et al., 1998). Assays for Y
chromosome haplotypes, inherited strictly in the tail male line of the pedigrees
of males, are not yet available for horses, but probably will be developed.
Certain pedigree problems in remote generations could thus be addressed by
stud book authorities if there were a compelling need to do so. It will be
47
important that well-intentioned plans acknowledge the genetic principles that

govern the likelihood for the transmission of factors through generations, the
lack of biological definition for a breed, the role of crossbreeding in the
development of nearly all breeds and the ancient shared origins of domestic
horses. All these factors combine to hinder the simple detection of most cases
of proscribed crossbreeding in remote generations.
Future Prospects for Domestic Horses

All domestic animals in the last 100 years have been subjected to great pres-
sures to evolve to meet the changing needs of a mechanized, commercialized,
globalized planet. While horses may still have a working role in today’s
society, with the development of combustion engines this role worldwide has
become a minor one. Horses are still used for working with beef cattle world-
wide, and by nomads and in subsistence agricultural societies, particularly in
parts of eastern Europe, Africa, Asia, Central and South America. One of the
emerging prominent uses for many breeds of horses is for competitive perfor-
mance events or as personal sport companions (racing at short distance by
trot, pace or gallop; long distance racing; jumping; precision riding; weight
pulling; ranch task competition; pleasure riding; pleasure driving, and so
forth). Increasingly the horse’s aesthetic value becomes a major aspect of its
importance. As with breeds in other domestic species, some horse breeds may
be threatened with extinction because they do not appear to meet a current
need. Various breed conservation groups have identified threatened breeds
and subpopulations and provide active encouragement for breeders to con-
serve them in order to preserve genetic diversity (see Chapter 14, this volume).
The genetic health of breeds and of the species in general appears to be excel-
lent, and the variety of phenotypes and traits available seem sufficient to meet
the challenges of the next several centuries.
Acknowledgements
Our thanks to C. LaBounty and M. Williams for preparing allelic frequency
data and to M.C.T. Penedo for preparing the population data analysis of the
ten breeds and Przewalski’s horse. We also thank M. Bowling for editorial
assistance with preparation of this chapter.
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University of California, Davis, CA 95616–8744, USA; 2Animal

26 A.T. Bowling and A. Ruvinsky

No other domestic species has been used so widely as a means of transport in

Origin of the Domestic Horse

While horses present a great spectrum of morphological differences, including

Genetic Aspects of Domestication 27

28 A.T. Bowling and A. Ruvinsky

Fig. 2.2. Area of horse domestication and likely directions of migration.

Genetic Aspects of Domestication 29

Reasons, pre-condition and the initial steps of horse domestication

30 A.T. Bowling and A. Ruvinsky

Shifts in genetically determined behaviour may cause changes in the

History of horse domestication

Genetic Aspects of Domestication 31

The horse appeared in southeastern Europe (Greece) at about the same

32 A.T. Bowling and A. Ruvinsky

had provided. That inherited differences occur in gaits (footfall patterns) of

Genetic Studies of Domestic Horses and Przewalski’s Horse

The genus Equus is characterized by rapid karyotype evolution (see Chapter

Genetic Aspects of Domestication 33

Nuclear genes detected by immunogenetic and biochemical techniques

34 A.T. Bowling and A. Ruvinsky

Molecular polymorphisms – mtDNA and microsatellites

Genetic Aspects of Domestication 35

Worldwide Distribution of the Domestic Horse

36 A.T. Bowling and A. Ruvinsky

breed). Increasingly often, horse breeds are defined by societies or registries

Horse breeds defined by stud books represent a diverse collection of options

Genetic Aspects of Domestication 37

these technologies, a notable exception is the Thoroughbred, for which stud

38 A.T. Bowling and A. Ruvinsky

Examples of horse breeds

Genetic Aspects of Domestication 39

from historically similar autochthonous Iberian peninsula breeding elements.

40 A.T. Bowling and A. Ruvinsky

Morgan Horse (MH)

Norwegian Fjord (NF)

Genetic Aspects of Domestication 41

Paso Fino (PF)

42 A.T. Bowling and A. Ruvinsky

Genetic similarity studies of breeds provide information to assess genetic

Genetic Aspects of Domestication 43

Locusa Chrb Alleles HT GST HS

Blood groups EAA 20 12.4 0.740 0.139 0.638

44 A.T. Bowling and A. Ruvinsky

Breed or taxon Estimated average heterozygosity (±SD)

A3759:AMA:First Revise: 20 January 1999 CHAP-2

46 A.T. Bowling and A. Ruvinsky

Genetic Aspects of Domestication 47

relationships) will be provided when we can construct dendrograms based not

Addressing questions of introgression between domestic breeds

Discussions about horse breed purity have a long-standing history. Indeed,

48 A.T. Bowling and A. Ruvinsky

important that well-intentioned plans acknowledge the genetic principles that

Future Prospects for Domestic Horses

Genetic Aspects of Domestication 49

Belyaev, D.K. (1979) Destabilizing selection as a factor of domestication. Journal of

50 A.T. Bowling and A. Ruvinsky

Felsenstein J. (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed

Genetic Aspects of Domestication 51

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