Population Genetics and Diversity Study

Conservation Assessment and Management Plan (CAMP)

Background

The Arabian horse originated with migrating Bedouin tribes in the greater Arabia Deserta, an area roughly encompassing today’s countries of Iraq, Jordan, Syria, Saudi Arabia, Bahrain, the Arab Emirates, Oman, and Yemen. Western accounts from the 1700s onward attest to the Bedouin practice of breeding within a closed gene pool of horses whose provenance was known to the tribes. Horses so bred were called “asil.” While the first Arabians taken to the West were used principally to develop other breeds, a few studs maintained lines traceable entirely to Bedouin sources. Such studs in most of Western Europe and Russia were decimated by war in the 19th and early 20th centuries.
Two major programs that developed outside the countries of origin during the 1800s survived into the 1900s: that in Egypt and the Blunt program at Crabbet stud in the UK. The Egyptian program evolved with the changes in political structure as described below and continues today. Studs in Egypt and the U.K. provided horses for other breeders around the world, supplemented by a few direct desert exports such as those obtained by the Davenport expedition of 1906 and gifts of horses from Saudi Arabia to Westerners involved in oil development efforts in the early and mid-1900s.

Heritage programs and the asil horse

Beginning in the 1950s and ’60s, a few breeders in the U.S. became concerned with the potential loss of this presumptive asil gene pool, as evidence developed that most of the horses being bred in the West and registered as “Arabians” included non-Arabian ancestors. Mrs. John E. Ott and her daughter Jane created The Blue Arabian Horse Catalog to document the horses then in the U.S. that descended entirely from Bedouin stock. Their efforts were expanded by the formation of Al Khamsa, Inc. in 1974. In parallel with these efforts, the Asil Club (based in Germany) began to document extant horses of entirely Bedouin origin, principally those remaining in Europe. In Egypt, the breeding programs that had originated with the Pashas in the 1800s continued through the founding of the Royal Agricultural Society’s purebred Arabian program in 1914, its renaming as the Egyptian Agricultural Organization, and later incorporation of the Inshass horses of Kings Faoud and Farouk. The closed gene pool of “Egyptian” Arabian horses populated programs around the world; it continues in Egypt where it constitutes the longest-documented closed herd of presumed asil horses outside of the countries of origin.  In 1969 The Pyramid Society (based in the U.S.) took on the role of perpetuating horses from this herd.
For the past 35-40 years, breeders who adhered to the concept of breeding with this presumptive asil gene pool pursued a type of conservation breeding by limiting matings to those between horses who fit the asil definition. Over time, breeders collaborated informally and developed sub-populations based on defined founder groups. What began in the U.S. as “Blue List” breeding (matings among horses catalogued by the Otts) has transformed into distinct heritage groups. The largest of these, identified by their heritage names (in ascending order of extant population size, with average annual foal production shown) are:

  • Blue Star (a subset of the horses identified by the Otts); 10 foals
  • Davenport (traceable to the 1906 importation, with the potential addition of two horses from the same geographic area that were imported to the U.S. for the 1893 World’s Fair); 35 foals
  • Heirloom (horses from the Egyptian programs prior to the formation of the RAS Arabian horse breeding section in 1914); 40 foals
  • Sheykh Obeyd (horses from the Egyptian programs including the RAS and EAO programs but generally prior to the incorporation of horses from the Inshass stud); 40 foals (in addition to most of the Heirloom foals)
  • Straight Egyptian (defined by The Pyramid Society and generally including most, but not every foundation animal from the Heirloom and Sheykh Obeyd groups, with additional founders from the Inshass stud); 500 foals (in addition to most of the Heirloom and Sheykh Obeyd foals)

Each of these heritage groups has sub-populations that include/exclude specific founder horses, with the understanding by some breeders that maintaining sub-populations within the group is beneficial to long-term conservation (the late Dr. Ann Bowling and Michael Bowling have had a profound impact in this regard). There are a small number of other founder horses that have been interbred with horses from the groups described above, but their annual foal production numbers are small and declining (fewer than 50 per year).

Current status

During the first 75 years of the 20th century, most asil horses were bred from a wide range of available asil stock, with matings constrained by logistics of distance and lack of information on available horses. The heritage groups had not developed. During the past 30 years, this trend has completely reversed. Most horses are bred within defined heritage groups, while the population of asil horses that incorporate a broader group of founders has become quite small. Of the recent (since 2000) average annual foal crop of 700, fewer than 50 represent crosses among these heritage groups. Unlike most populations where broad cross-breeding is practiced, with the trend toward theoretical uniform heterozygosity, the reverse is currently true for the asil population.
Contemporary breeders who hew to a concept of conservation breeding within the historic asil definition have no framework based on the science of population genetics within which to make breeding decisions. Most seek to produce a desirable animal (by their own definition of quality and adherence to Bedouin type) by breeding a stallion of heritage group A to a mare of heritage group A. There has been no systemic documentation of the extant herd in total and no determination of genetic diversity within or across groups that could lead to a conservation plan based on the developing principles of population genetics as applied to closed-herd breeding. The heritage groups have never been evaluated, using contemporary genetic tools, to determine their viability or efficacy for future cross-breeding. It is unknown whether some groups are already so inbred that further extension of the group will actually contribute to lost diversity (the reverse of the intent for maintaining such groups), or whether the sub-population structure of a given heritage group will allow that group to continue for some time.
Some heritage groups are absolutely unique in their founders; other share some founder animals. No work has been done to evaluate the shared-founder groups to determine if, de facto, additional sub-groups have arisen but are not recognized because they do not correspond to the historical events that framed the defined heritage groups. Determining the genetic diversity of sub-groups, both those of unique founders and shared founders, would likely be critical to a conservation plan.
The Arabian horse population experienced a huge increase in breeding during the 1970s-’80s and a precipitous decline during the past 15 years. Such a decline is expected to continue, or even accelerate, given current economic conditions. This argues for immediate action on the project described below, as the asil population is likely experiencing a genetic bottleneck that may substantially reduce the number of retained founder genes.
The Institute for the Desert Arabian Horse was formed, in part, to support research with the goal of conserving the asil horse internationally based on collaborative efforts. The Institute’s Board of Directors are breeders from various heritage traditions concerned about the population trends and the lack of a scientific basis for the nominal conservation programs that have evolved. There are other breeders who are sufficiently far-sighted that they support scientific assessment of the diversity of the herd and development of a conservation plan. It will be the Institute’s role to engage these breeders in implementing a conservation plan.

Project concept

The Institute for the Desert Arabian Horse wishes to undertake a research project leading to development of a conservation plan for the asil horse outside of its countries of origin. While species survival plans have become the norm for endangered wildlife, conservation plans for rare breeds of domestic livestock are only recently being developed. Because the Arabian horse is a domestic animal with some historic landrace characteristics, the Board of Directors of the Institute is seeking academic research partners with relevant expertise and interest in conducting such a project and developing such a plan. The initial efforts would be limited to evaluating the extant herd and offering breeding schemes for stock within North America (this herd is well-documented). Subsequent efforts could incorporate international stock, much of which derives from Egyptian and/or North American intermediate ancestors (the Institute is engaged in a separate census project to  identify and document the asil horses outside of North America).
The goal is similar to that found in wildlife species survival plans: to retain 90-95% of the gene diversity for the next 100 years.
There would be two major phases: first, to characterize and analyze the structure and diversity of the extant population; and, second to develop conservation breeding plans/models. The first phase is intended to answer these fundamental questions:

  • What are the relatedness/diversity characteristics of the extant herd?
  • What are the trends and likely outcome if there is no intervention or new knowledge applied to breeding schemes?
  • Are the heritage groups and sub-populations useful for future breeding schemes? If not, what sub-population structure would be useful?
  • Would the population benefit from specific breeding schemes to achieve the goal of retaining 90-95%% of gene diversity for the next 100 years?

Based on a layman’s understanding, the Institute Board of Directors can imagine the following possible elements. These are intended only as the basis upon which to have further discussion with researchers.

Phase I – Characterize and analyze the structure and diversity of the extant population
1.  Identification of unique dam lines
During the 1990s, the late Dr. Ann Bowling, University of California Davis, conducted pioneering research to identify discrete dam lines using the D-loop hypervariable region of mitochondrial DNA. Through her work, 16 historical lines, identified to 13 different haplotype sequences, have already been characterized. Dr. Cecilia Torres-Penedo has continued this work. The Institute has provided samples to Dr. Torres-Penedo that identified an additional historical line as sharing one of the 13 sequences found by Dr. Bowling. We are working with Dr. Torres-Penedo to characterize the remaining 25 dam lines in the U.S., and further work on samples from unique lines found in other countries is anticipated.
2.  General characterization of diversity in the extant population, based on pedigree
The intent is to characterize the asil group broadly – to identify the current gene diversity, effective population size, founder contribution, and founder representation. One of the issues in such analysis is determining whether it is necessary to work from foundation horses or whether later-generation animals can be used to simplify the analysis, without losing the granularity needed to evaluate diversity.
3.  Determination of sub-populations, diversity within and between sub-populations, and their usefulness for future breeding
This includes consideration of unique sub-populations and evaluation of sub-populations that share some founders. For the latter, it may lead to identification of sub-populations not previously identified as heritage groups. It will be important to evaluate gene diversity within identified heritage groups and their sub-populations to determine whether or how such diversity can be retained so the sub-population can continue to be a reservoir of genetic material for the future. This element might also involve determining the loss or gain of diversity resulting from removal of one or several sub-populations.
4.  Projection of future population diversity based on recent practice
Determine the trend in diversity, perhaps by calculating Founder Genome Equivalents and Effective Population Size at some interval over the past 50-60 years. (The largest heritage group last added founder animals in 1945; other, unrelated heritage groups added horses as late as 1961). The purpose is to identify whether and to what extent diversity is being lost by past and on-going breeding practices. This may include extinction probabilities as well.
5. Comparison of quantitatively determined expected diversity, using pedigree information, with diversity determined by using molecular markers
Microsatellite and PCR research is allowing for comparison of expected allelic diversity with that determined in the lab. It would be useful to test some of the calculated relatedness values determined in the above-described elements against data from microsatellite and/or PCR, as that could influence the construction of future breeding plans that are premised on calculated values of heterozygosity.
The best applicable mathematical model(s) will need to be identified. The sub-population structure may influence the weighting of within- versus between-group diversity. Relatedness determinations will need to take into account that some of the sub-populations are highly inbred and therefore standard inbreeding calculations may not reveal sufficient differentiation because the commonality of most-frequent ancestor is more than 5 generations back in the pedigree. For example, 6 sons and 11 daughters from a dominant 1934 sire were imported to the U.S. The true dominance of that sire is not discerned only by looking at imported animals as founders, or by calculation of inbreeding in less than 6-8 generations.

Phase II – Development of conservation breeding plans/models
This phase will likely not be undertaken until elements 1-4 in Phase I are substantially complete. Researchers involved in Phase I may be expected to offer recommendations as to the construct of Phase II.
Institute resources
The Institute for the Desert Arabian Horse can provide database pedigree information and some information technology assistance to convert data from the Institute database to a form usable by researchers. It also will form an Advisory Group for the project, composed of breeders who have substantial knowledge of the structure of the heritage groups. The purpose of the Advisory Group is to assist researchers in understanding the foundation, historic changes/development, structure, and anomalies of each of the heritage groups and their sub-group structure. The members also can serve as information bridges to the breeder population that will be encouraged to understand the results of Phase I and engage in conservation practices consistent with the recommendations from Phase II.