Published in The Canadian Horse Annual '98

Using Genetics to Pinpoint Endangered Canadian Horse Breeds

Molecular Genetics Can Help Identify Genetically Unique Horse Breeds for Conservation Purposes

Anouk M.P. Behara, Dave T. Colling1 and John P. Gibson
Centre for Genetic Improvement of Livestock
Animal & Poultry Science, University of Guelph
and 1Mann Equitest, Guelph, Ontario

This past century has seen a rapid decline in numbers within many breeds of horses. The mechanical revolution has outdated the usefulness of horses for agriculture and transportation. Changing trends and a more global approach to horse breeding have contributed to the shrinking numbers such that today many breeds, once popular and prolific, are now listed as critically endangered.

Breeds which have few breeding animals can suffer a loss in the amount of genetic variation present within the breed. What this means is that less genetic variation exists between animals in the breed. This can be useful to an extent in that it increases the overall homogeneity of the breed, such that most animals within a breed are likely to look, behave or perform similarly. The down side to this genetic homogeneity is that the breed is less able to adapt to new selection pressures, either environmental or human-mediated. For instance, less genetic variation might mean that the breed is less able to withstand a new disease strain, because the genes which may have provided disease resistance have been lost.

Another possible consequence of small numbers of breeding animals is an increase in the level of inbreeding. In genetic terms, an inbred animal is more likely to have inherited two alleles at any gene (see sidebar: A Primer in Genetics) that are identical. As such, the probability that an animal will have inherited two copies of a 'deleterious' allele is increased. A classic example would be Severe Combined Immunodeficiency (SCID), a recessive disorder of concern in Arabian horses. Affected foals are unable to fight infections and die within a few months after birth. In order to be affected, a foal must inherit two copies of the SCID allele. Since the probability of inheriting any two identical alleles is increased for inbred animals, the frequency of horses born with SCID is higher in an inbred population than in a non-inbred population.

In general, the consequences of excessive inbreeding include a greater occurrence of genetic diseases, a decline in reproductivity and overall hardiness, and at worst, extinction of the breed.

As part of a global project organized by the Food and Agriculture Organisation of the United Nations, we are using DNA markers to identify genetically isolated breeds as a high priority for conservation. Our research project focuses on the Canadian Horse (see sidebar: Le Cheval Canadien) with the intention of providing a realistic framework applicable towards conservation efforts directed at other endangered breeds. An important part of the Canadian historical scene for over 300 years, the number of Canadian Horses has declined to the point of creating concern about the level of genetic variation and inbreeding within the breed.

For our study, we are making use of current molecular genetic techniques to compare the amount of genetic variability within rare and more common breeds in order to establish if rare breeds have suffered from a critical decline in genetic variation. Once we have determined the amount of genetic variation within our target breed, we can make recommendations as to whether or not the stud books should be opened in order to increase the amount of variation within the breed. The next step is to work out the genetic relationships between breeds so that we can establish which breeds are most closely related to our target breed. Should the opening of the stud books be considered necessary, we can then suggest that this be done in a limited fashion, allowing only those breeds which are genetically similar to our target breed to be contributors.

To date, we have analysed DNA from 903 horses from 11 breeds of horses common in Canada, including the Canadian Horse. These data were generated for development of parentage testing systems by Mann Equitest Inc. of Guelph, Ontario. The eleven breeds included in this analysis were (the short form and number of horses analysed for each breed is given in brackets): Appaloosa (APP, 65); Arabian (ARA, 93); American Saddlebred (ASB, 55); Belgian (BEL, 54); Canadian (CAN, 33); Miniature Horse (MIN, 126); Morgan (MOR, 98); Quarter Horse (QHH, 95); Standardbred (STB, 98); Thoroughbred (TBD, 94); and Tennessee Walking Horse (TWH, 92).

We used the DNA data (see sidebar: Microsatellite Markers) to compare both the overall level of genetic variation in different breeds, as well as the level of inbreeding. According to preliminary analysis, the level of genetic variation in the Canadian horse is about midrange for the 11 breeds surveyed, indicating that the Canadian Horse has not suffered a loss in genetic variation due to it's small population size. The level of genetic variation in the 11 breeds is shown as the black bars in the graph in figure 1. The white bars depict the average level of variation of individual horses within the breed (the average occurrence of two identical alleles at any gene). This can be used to give us a measure of the overall level of inbreeding in the breed. The lower the white bar in relation in relation to the black bar, the more highly inbred the breed.

Figure 1From Figure 1, we can see that the Canadian horse does not appear to be more highly inbred than more popular breeds. Of note is the relatively low level of individual variation in Arabian horses (compared to what one might expect given the amount of within breed variation depicted by the black bar), suggesting a higher average level of inbreeding within the breed. As the Arabian breed does not suffer from small numbers, the greater degree of inbreeding may be a result of line breeding practices.

Our second analysis involved the use of the same DNA data to work out the genetic relationships between the 11 breeds, based on the degree of genetic similarity between breeds.

These relationships are depicted in pictorial form in figure 2. The 'tree' shows how the breeds are related in a fashion similar to a pedigree diagram. The horizontal length of the branches between breeds represents the genetic distance between the breeds, and more closely related breeds cluster together in the diagram. For instance, the Thoroughbred and Standardbred breeds cluster together, and if one were to measure the total length of the horizontal lines joining the two breeds, one would see that the distance is much lower than that between say the Belgian and the Thoroughbred.

Figure 2From the figure, we see that breeds known to be closely related (such as the Thoroughbred and Standardbred) cluster together, while the Belgian, Miniature and Canadian are more distantly related to the remaining breeds, which are of race and riding type. This shows us that the Canadian, bred in isolation for so long, does still appear to be genetically distinct from the popular race and riding horse breeds, reinforcing the need to consider the conservation of this breed a high priority.

Our work is continuing with the addition of more DNA data as well as additional breeds to our analysis. We are in the process of searching for DNA or tissue samples from the French breeds believed to be ancestral to the Canadian Horse. These are the Selle Franšais, Trotteur Franšais, Trait Breton, Postier Breton and French Barb. Anyone having knowledge of where to obtain such samples can contact either of the authors at the Centre for Genetic Improvement of Livestock, University of Guelph.


This research is being performed in conjunction with Mann Equitest Inc. of Guelph, Ontario and is partially funded through the Equine Research Centre in Guelph, Ontario. The generation of all microsatellite data was funded by Mann Equitest Inc.


Deoxyribonucleic Acid. This is where genetic information is stored.

Bundles of DNA which store genes in cells. Horses have 32 pairs of chromosomes. One chromosome out of each pair was inherited from the sire and the other from the dam.

The fundamental unit of heredity. A stretch of DNA which usually codes for a particular feature. Some genes are non-coding, and can be used for the analysis of genetic relationships and variation.

Alternate versions of genes exist, which are called alleles. For instance, for the eye colour gene, there are brown and blue colour alleles. Every individual carries two alleles for each gene, one inherited from each parent. An individual may carry two identical alleles, or two different ones.

Microsatellite Markers
Microsatellites are non-coding genes, each with many different alleles. For particular genes, we can determine which alleles a horse carries, which forms a horse's genotype at that particular gene. By genotyping a horse at a number of different genes, we can generate a unique genotype for each horse, which can be used to exclusively determine a horse's parentage. We can use this same genetic information to measure the amount of genetic variation within breeds as well as within individuals, and to establish the genetic relationships between breeds.


Le Cheval Canadien

The predecessors to the Canadian Horse (le cheval Canadien) began to arrive in New France in 1647. These horses were shipped by order of King Louis XIV in order to facilitate the settlement of the nobility in the new colonies. While the exact ancestry of the Canadian is unknown, they are most commonly thought to have arisen from crossings including Arab, Breton and Norman breeds. The horses adapted well to the Canadian climate and are considered by many to be the best acclimatized horse in Canada, earning them the nickname "Little Iron Horse". The number of horses rose substantially over the first 100 years following settlement, during which time the breed is believed to have remained completely isolated from outside influence.

By the end of the 19th century, industrialisation had led to the decline of the breed's numbers to critical levels, such that concern exists about the level of inbreeding in the breed today. Although concerted efforts by breeders have resulted in the Canadian breed presently numbering at around 3000 horses, it is still classified as critical on the endangered breeds list of the American Livestock Breeds Conservancy.