Thoroughbred horses as unique research subjects

Thoroughbred horses as unique research subjects:

An Ideal Model for Studies of Inheritance and Selective Mating

By Loren Bolinger

I have been a Thoroughbred horse breeder for over 36 years in New
Mexico. I have a passion for selective mating, historical research,
and improvement of the breed. I believe that improvement to the
breed can be made by breeders through selective mating. Many horse
breeders since the founding of the breed have had an anecdotal belief
in maternal inheritance. In 1894, Charles Bruce Lowe classified and
ranked Thoroughbreds by matrilineal lineage and each family's success
at elite races. His was also the first widely publicized [among
Thoroughbred horse breeders], systemic attempt to document and prove
maternal inheritance and the validity of certain forms of selective
mating. During the 1960's biologists discovered the importance of
the mitochondrial genome and established incontrovertible proof of
the second system of biological inheritance - maternal inheritance
through DNA located in the cytoplasm of the ovum. Mitotyping is the
term used for methods that identify the true matriline of the
individual under examination. Errors in Thoroughbred parentage
classification of many historical individuals' lineages have
propagated through entire branches of their family trees to the
present GSB, and even when known, have never been possible to verify
and corrected.

Now that there are accurate, reproducible, and cost effective
techniques, it is especially important to breeders to verify and
correct matrilineal lineages. Any sort of reasonable attempt at
breed improvement through selective mating depends on accurate
lineages.
Goals include reconnection of the lost American, Australian Colonial,
Argentinean families with their English roots [and other unidentified
members of the current Thoroughbred breeding population]. Another
goal is to untangle, separate, and correct the misidentified,
incorrectly recorded English lineages that occurred primarily in the
1800's. Yet another goal is to assess the connection between
mitochondrial inheritance and the expression of performance traits.

Dr. Phillip W. Danielson, University of Denver and Dustin Mark
Gilbert, our research assistant, are skilled and highly trained in
DNA forensics. Dr. Danielson conducts training seminars for law
enforcement and investigative personnel in crime scene procedures.
Their protocols and procedures are accurate, rigorous, comprehensive,
and reproducible. The mitotyping we use produces cutting edge
accuracy and reproducibility [better than 99.9 per cent accuracy].
They have trained me in mtDNA collection, data collection, and
fieldwork. Our DNA technology is far cheaper, faster, and more
accurate. We are using the same procedures used in criminal
forensics. Our lab is currently processing about 35 - 50 samples per
week with only one research assistant.

1. Our laboratory procedures used for processing buccal swabs, blood,
and hair samples incorporates duplicate methods used by the US Jockey
Club for parentage verification and registration. Our hope is to
eventually gain access to the DNA repository of the Jockey Club to
continue this important research.

2. Our procedures and protocols are compatible with those used by Dr.
Emmeline Hill reported in Animal Genetics, August 2002 [pp. 287-294].
We have verified and reproduced results as reported in "History and
Integrity of Thoroughbred Dam Lines Revealed in Equine mtDNA
Variation."

Why the Thoroughbred
The Thoroughbred horse represents an unusual research opportunity
with potentially far reaching implications for all species. Nearly
all plants and animals chosen for research are relatively randomly
mated, wild mated, mated without human-caused selection, or mated
with selection for simple or single gene traits. Often,
inappropriate "selfing" or other radical selection practices are used
in the laboratory and often on strains of animal models completely
divorced from the real world.

In contrast, among all domesticated animals, the Thoroughbred is
mankind's longest lived and most successful, selective-mating
experiment. It has had a relatively consistent goal over
approximately three hundred fifty to four hundred years - the test of
the winning post. That the selective mating strategies have been
successful can be assessed by the physical changes in the organism
since its founder stock. The phenotypes of the modern day
Thoroughbred, evolved over about 350 - 400 years, can also be
compared against those of other breeds of horses. This particular
breed, developed through specialized selective mating, performance
testing, and culling, is unique among all domesticated animals.

It is generally agreed that multi-factorial genes (and possibly)
maternal inheritance control traits involved with elite performance.
Research into inheritance of multi-factorial traits has been
extremely difficult and complex. Traits inherited through the
mitochondrial genome are not well understood. The Thoroughbred
brings a unique genetic background that is better suited to the
unraveling of the conundrum of understanding complex traits. It is
unique in the organization, selection, and culling of its lineages
and individuals. Historically, all forms of selective mating
experiments have been tried.

The large body of Thoroughbred horse breeders is highly motivated to
improve horse breeding techniques yet for the most part biological
research has ignored the Thoroughbred. The horse among domesticated
animals has had a far stronger economic impact today than the
proportionate research dollars spent on its behalf would indicate.
The North American Thoroughbred industry has an economic impact as
reported in the Wednesday, June 29, 2005 electronic edition of the
Thoroughbred Times of $39.2 billion , an economic impact study in
Australia revealed the contribution of the Australian Horse Industry
was estimated at 6.3 billion in 2001 , and in Great Britain, in 1999
[most recent year], it was estimated that the economic impact of the
British horse industry was about 2.5 billion, second largest economic
activity in the British countryside only to farming , yet
Thoroughbred breeders have received little attention from the
biological sciences. We are basically still using crude, eighteenth-
century selection practices and/or many breeders are governed by non-
genetic issues such as commercial appeal, fad, and fissionability.
[The element of uncertainty added by misclassification of lineages
should be unacceptable to horse breeders intent on breeding the very
best individuals possible incorporating selective-mating methods with
correction, verification, and finally accuracy of lineages using
scientific objectivity from the genomic era. An unacceptable
variable can be easily eliminate by modern biological science.]
Current Progress
Dr. Emmeline Hill [et al 2002] and Dr. Phillip Danielson [Gilbert,
Bolinger et al 2005 preliminary] have shown that mitochondrial DNA
analysis is an easy, cost effective, accurate, and reproducible way
to identify and characterize horses by their families or maternal
lineages.

Analysis by both groups [above] has shown large discrepancies in the
GSB [General Stud Book] classifications. Most errors seem to have
arisen from misclassification of horses very early in the bloodlines
of the Thoroughbred.

There seems to be far fewer founding mares [matriarchs] than
originally believed due to convergence of many families into one
haplotype and the fact that diverging families seem to result from
misclassification rather than multiple founding mares or mutations.

Lastly, the founding mare population was more than likely small due
to the very limited and controlled breeding by the early English
founder breeders in the initial stages of the species' development.

With our limited, current database, our first goal is to continually
gather more data, especially on families that have not yet been
sequenced.

The next step while we continue to enlarge our database would be to
begin tracking down American, Australian, Argentinean, and other lost
bloodlines and connecting them back to their English ancestors.

Extremely valuable horses are being created with 19th century
selection methods. Far too much wastage and injuries occur, and
needless, catastrophic breakdowns occur. In the amazing explosion of
the current Genomic Era, it seems relevant to employ biological
discoveries in breed improvement, conservation, humane treatment, and
preservation of the Thoroughbred. The possibilities exist that
significant progress can be made to reduce unsoundness and wastage in
the Thoroughbred through breakthroughs in scientific selective
mating.

We wish to understand the contribution toward elite athletic
performance that comes through maternal inheritance - the
mitochondrial DNA contained in the cytoplasm that is inherited only
through the tail-female lineage. In order to accomplish this
objective, the accuracy of the lineages must be first restored or
corrected. Until this is done, selective mating schemes are useless.
If I didn't have the help of a top genetic laboratory and one of the
best forensic geneticists in the United States, Dr. Phillip
Danielson, this project would never have been possible.

My personal aim is to disclose the pure research, hopefully, if it
has any merit at all, published in a scientific journal and on the
TBHeritage website, like the other matriline discoveries. The goal is
to be able to produce practical results that breeders can apply, not
ivory tower research that only gathers dust and cobwebs and only
satisfies intellectual curiosity. I'm a pragmatist, I wholeheartedly
believe in maternal inheritance with respect to performance traits,
have put my limited resources where my mouth is, and incorporated my
beliefs in my breeding program. I am satisfied [at my level of
participation in the horse breeding business] the results I am
getting. It would be very satisfying to have biological evidence to
back up my passion for breeding horses.

Yours truly,
Loren
Loren Bolinger
Running Horse Farm LLC
7102 Ilfield Road Southwest
Albuquerque, New Mexico 87105-7046
505-873-2220 Voice
505-877-4443 FAX
e-mail: lbolinger1@comcast.net