First Method of Selective Breeding

The First Method of Selective Breeding

By Loren Bolinger, June 16-17,2006

Matching mating partners by their anatomical proportions preceded pedigree matching as a primary selective breeding method for improvement.

Judging individuals by their physiological structure: conformation, symmetry, or form, then breeding those individuals that seem most physically compatible became the first method of selective breeding domesticated livestock. These basic agrarian methodologies then became the starting point for the early English founder breeders.

Selectively breeding individuals by their visual compatibility or conformation is the basis of phenotypic matching [selection based on anatomical proportions, judgement of conformation, or perceived biomechanical efficiency]. It preceded another method of selective breeding in which mates were chosen by their relationships, ancestry, lineages, or family trees.

“Shape is the principle point to have regard to in order to amend faults of sire or dam; and almost every person who likes a horse, and has any experience, knows what good shapes are. The grand secret is to know when they are properly put together, and to discover where the screw is loose in the machinery which renders the whole useless.”
- The Book of the Horse, Samuel Sidney, (circa 1875), Cassell, Petter, Galpin & Co., London, Paris, & New York, page 262.

Anatomical selection had to be the first selection method practiced by breeders, since at the time of the early English founder breeders, ancestry and parentage were often problematic issues. The founder breeders in their passion for the new sport of horse racing began their attempt to create a new breed of horse - the Thoroughbred racehorse with this method. At the time, the newly imported, Oriental founder stallions' parentage was usually unknown. The earliest native English and/or Irish Hobbye mares often had dubious, incomplete, or unknown parentage. The most successful form of breeding selection was based on the test of racing - attaining the winning post - combined with keen assessment and judgement of conformation. Finally, those individuals failing to measure up were usually culled. These became the biological tools that drove the early development of the Thoroughbred.

Among agriculturalist of these early times [pre-industrial England], the anatomical proportions of all farm animals were intently judged; farming success depended on accurate assessment of the qualities of all stock. Intense evaluating by all agriculturalists of all livestock is a farming practice that goes back before the Roman Empire and even earlier. Indeed even every human’s survival was highly depended on the qualities, yields, and efficiency of all manner of husbandry. It's natural that the physical proportions of the horses of this new sport of racing would be judged just as intently for their suitability to race and win.

Ranking the conformation of breeding stock, judging, measuring, and recording physical proportions, evaluating compatibility of form between potential parents was an all consuming preoccupation in an agrarian society. Almost all agriculturalists of the [pre-industrial age] 13th century onward were quite familiar with judging the physical appearance of domesticated plants and animals: "beauty of form" [Wood, Orel, page 76]. Livestock judging persists even today not only in farms and ranches, but also in the state and county fairs, 4-H Clubs and Future Farmers of America. Developing a keen eye for conformation and other outward manifestations of phenotype was a very important attribute in an agrarian society. It was only natural that animals judged more attractive and deviated less from a mutually accepted [agreed] standard would be considered more valuable and more desirable.

[Wood, Orel, page 76, quoted] Marshall 1790 [The Rural Economy of the Midland Counties] wrote that the qualities of "beauty of form", "proportion of parts", "flesh", "fatting quality" are "found to be heredity... ...depending in some considerable degree at least, on BREED, or what is technically termed BLOOD, namely on the specific quality of the parents". However, little was said beyond the parents to the grandparents or more remote [deeper] ancestral members. Wood, Orel write that "no consideration was given to the matter of pedigree." ...and... "Ancestry was much more to be considered when exploiting an established race than when creating a new one." [Wood, Orel, page 76]

Initially, ancestry, family trees, or parentage beyond one or two generations of domesticated animals was not as well known or nor as important a consideration as the physical manifestations of phenotype: conformation, temperament, etc. At the time of the beginnings of the breed, there was little regard for ancestry among livestock breeders. Only when the early English founder breeders began their creation of the Thoroughbred horse, did parentage of the members of the new breed, gain new importance and scrutiny. The parentage of the Eastern Oriental imports, for the most part, was unknown. Most breeders felt that the female made no heredity contribution and was merely a vessel of parturition. The lack of naming many mares is an indicator of their disregard. Therefore, beyond her sire, the parentage of the early broodmares was usually less known than the more highly regarded sires.

Some of the most successful of the early breeders were more enlightened. Their appreciation of broodmares and their possible heredity influence paid their breeders dividends. The more prescient breeders became aware of the importance of the female, that patterns in lineages had importance, and recognized the radical concept of maternal inheritance, probably through the practical observation that certain, rare mares became exceptional producers independent of the sire to which they were bred. Early, successful female runners also contributed to an appreciation of the contribution of the female. After all, if you owned an elite female racehorse, wouldn't you greatly anticipate her progeny over more ordinary females?

Horses with ancestry that traced directly from the best-regarded progenitors of the founder stock had higher value among horsemen of the era. This provided incentive to record early pedigrees and to incorporate aspects of ancestry in selection. As breeders became aware of the value of certain lineages, techniques such as pedigree matching developed. As differing matching schemes were tried and evaluated, a body of knowledge and pragmatic beliefs formed a series of refined approaches to the selective mating of racehorses.

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

Proving a Point with Statistics

Proving a Point with Statistics

[finding enlightenment or not, dazzling with
data and/or engaging in costly self-delusion]

By Loren Bolinger

Solving a problem requires enough understanding to formulate the
right questions. If you cannot ask the right questions you will
never find the right answers just as if you don´t look in the right
places you´ll never find the solution. So, if you´re intellectually
curious, you count stuff, measure various things with various types
of yardsticks, classify into different groups based on objective
similarity, make labels for your groups, massage the data with all
sorts of sophisticated mathematical algorithms - hopefully to attain
a bit of enlightenment. Oh yeah, and while doing all this, don´t
forget to include contemplation, commonsense, logic - you know, using
the brains you were given.

If your goal is objective and pragmatic enlightenment that can be
usefully applied as, for example, in horse breeding, the accuracy and
integrity of the collected data must be as close to beyond reproach
as possible. I mean if you´re just trying to win your argument at
any cost, just manipulate or ignore the data all together. Proving
your point often implies that the answer is already known and you are
merely selecting data that supports your position. That is neither
scientific inquiry nor objective. If your motives are less than
pure, you could just select the data that proves your point and
ignore the rest. Failure to record all relevant data, flawed,
incomplete, or incorrect data, is worse than useless, it is
unconscionable. Inaccurately classifying data sets into useless
[incompatible] groups, manipulating the data incorrectly or
mistakenly all produce corrupted results that prove nothing. There
are no places for overt or hidden agendas that might cause undue
influence in the creation of a living creature. Objectivity must
sweep aside all spin. Arbitrary selection based on intuition is
acceptable only if it leads to objective results. Failure to be
objective and accurate in evaluating breeding data, pedigree
information not only leads to erroneous interpretations but
invalidates the justifications for any selective matings based on
such erroneous data. You risk making meaningless and absurd the
goals, objectives and selective matings guided by such erroneous
interpretations made during your career as a breeder. [A breeder
deliberately create a living creature partially of his own
specifications, largely from his thoughtful considerations for the
process of selective mating, the principles, guidelines, and
practices of breeders that have gone before. He grapples with the
harmonies of anatomical proportions, various measures of
compatibility between sire and dam, powers in near and distant
ancestors, prepotency in the sire, proper proportions of inbreeding,
combinations of bloodlines, weighing ratios of sex-balance, assessing
the contribution of matrilineal descent, environmental influences.

Albert Einstein observed, "whoever undertakes to set himself up as
judge in the field of truth and knowledge, is shipwrecked by the
laughter of the gods," could very well be applied to Jack Werk and
others like him. Whether they are those who manipulate and/or misuse
racing/breeding statistics, misunderstand, or misinterpret the
numbers they stand or fall based on their faithfulness to eternal
objectivity.

Blind, ignorant reliance on statistical studies
without verification of the study itself or its
mathematics leads to the laughter of the gods.

Such a horse breeder may find enlightenment
or not, may be dazzled with data, attempt to
dazzle others with the same data, and/or
engage in costly self-delusion.

While some indices such as "dosage" are without biological merit or
usefulness in the selective mating of racehorses, even those measures
specifically developed by knowledgeable horsemen and scientists to
objectively gauge racing performance must be taken with a grain of
salt. As I have pointed out many times, these population statistics
derived measures do not apply to the individual except only as a
general guide. It is wrong to give them more credence than that.
Among those most relevant to breeding and selective mating, many of
the most credible indices commonly used to gain insight into the
genetic worth of horses, breakdown or fail under certain
circumstances. For example, Standard Starts Index (SSI) and Average
Earnings Index (AEI) are very much less useful or applicable as
measures of performance merit in regional areas where purse
structure, racing styles, etc. are often quite different than in
major racing venues. These indices were developed for and are useful
as a performance gauge with major runners racing for major purses at
the most prestigious race tracks.] The indices were constructed on a
weighted basis, but the weighting scheme breaks down as a valid
comparison when applied across all racing venues.

Depending on your integrity and/or your ability to set up the
intellectual conditions, situations, or queries that will provide as
much as possible of the answer to the question, you may or may not
reach enlightenment. As I said before, if you don´t know how to ask
the questions you will never find the answers. Supposing that the
data is clean, then there are the problems of how to interpret: just
what does it mean and just how may it be applied as a selection
factor in selective mating? There are the difficulties of not
understanding what information you´ve obtained, misunderstanding the
meaning of the information, coming to the wrong conclusion through
misinterpretation, or even ignoring the obvious conclusions.

Then there is complexity of inheritance. Multifactorial traits such
as performance traits may involve thousands of genes. On the
surface, it seems impossible that anything a horse breeder could do
would have much of an effect on inheritance or triggering the
expression of performance genes. Yet the results of the early
English founder breeders are there for all to see. Wise, selective
mating by expert agriculturists [early breeders] using methods that
may go back to the time of the Roman Empire revealed that some traits
can be approximately manipulated through selection. They invented a
breed of animal whose phenotype and genotype visibly responded to
such breeding selection in less than one hundred years. The proof of
this is the dramatic changes in the rapidly developing Thoroughbred
from its founder stock. Some may argue that a performance plateau
may have been reached for the breed, but to many horsemen that´s
irrelevant in light of their love for the horse, the wonderful nature
of the modern Thoroughbred, and the dramatic differences between the
today´s horse and its origins.

Some critics suggest that analyzing the inheritance of the good
horses without the controls of analysis of the bad horses is
committing bad science. I disagree; failure is failure regardless of
the cause. Often the causes of failure cannot be determined. I
don´t need to learn how to breed bad horses, I need to discover the
principles of breeding good horses. Even under the best of
conditions, with the very best horses, there will be inexplicable
failures. A breeder must glean what he can from each failure,
disregard any her obsession, and move on. Each breeder has only one
lifetime to affect the gene pool of the Thoroughbred, so if your
intent is to breed a good horse, you need to sort through the chaff,
find the right needle in the haystack, and execute your planned
selective matings.

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

Selective Mating Definition

Selective Mating [of Thoroughbreds] Definition

By Loren Bolinger, January 30, 2005 version, edited 6/11/2006

“…since the writings of Charles Darwin and Francis Galton … domestication is the selective and purposeful breeding of animals in captivity to produce animals adapted to human-made environments. ”

Selective mating for the Thoroughbred is defined as the intentional selection of mates to be bred based on the collective and harmonious combination of certain, specific, genealogical patterns of ancestors, temperaments , and their anatomical proportions that are most likely to produce the expression of performance traits in the offspring. The parents of a mating, breeders believe, should have demonstrated racing performance. Often, other goals of selective mating practices include minimizing and or repairing genotypic and/or phenotypic faults or flaws so that the resulting progeny are improved or less flawed than the parents. Another, often ignored factor is the responsibility to cull stock that fails to meet expectations in performance and anatomical proportions to minimize the number of failures that enter the breeding population.

Selective mating is the process by which intentional selection of individuals with desired traits or characteristics are mated in a systematic way such that those traits or characteristics have a higher likelihood of being transmitted to their offspring and subsequent generations in a breeding program. The purpose is to increase predictability and transmission of desired traits and to reduce variability.

In the process of selective breeding, intentional decisions made by the breeder in which those individuals having traits that allow them to exhibit superior racing performance and transmit those traits to their progeny are identified and preferred over those less able to win and transmit winning traits to their progeny. In the course of the number of generations of race horses that a breeder will produce in his lifetime, as his knowledge and confidence increase, there can be a progressive tendency for the astute breeder's entire breeding stock to upgrade or increase their [cumulative or] overall degree of winning performance.

Reinforcement
The expression of desired traits and characteristics is primarily accomplished through inbreeding reinforcement. Powerful, positive reinforcement factors include the duplication of ancestors, combination of ancestors, or patterns of ancestors in order to cause expression of overt and latent traits carried within the genome. Reinforcement can also be accomplished through genomic combination [combining sirelines, ancestors, and/or matrilines (female families). Conformation Fault Compensation is the repair and/or improvement of parental flaws in the offspring and among some bloodlines can be an additional, desirable attribute of nicking. Phenotypic combination occurs when parents with compatible phenotypes are mated. Phenotypic similarity, as with symmetry is a golden rule of nature and breeding racehorses. Sophisticated mating selection is often based on sex-linkages of certain ancestors or can be based on the desired sex of the target, itself.

Sex-Linked Selection
Sex-linked selection methods are those in which mate selection is based on the sex of specific ancestors in the pedigrees of the mates and/or the sex of the target individual. In a number of selective mating methods, the sex of specific ancestors and/or the sex of the target is important to achieve the desired results or increase the probability of obtaining the desired results. Coordination of the sex of ancestors in selective mating schemes is usually made in conjunction with the duplication of key ancestors. Increasing probabilities of obtaining prepotency and the resulting expression of performance traits by early breeders was most successfully accomplished through sex-linked inbreeding of certain ancestors. These ancestors were commonly acknowledged [recognized] by many breeders as having desirable, heritable characteristics and a predisposition for passing their characteristics on to subsequent generations compared to the mean for the breed.

A potential problem of sex-linked selection is that the sex of the TARGET cannot at this time be predetermined or pre-selected. The breeder may select methods optimal for producing a male but incorrect for a female or vice versa, then have the incorrect sex foaled for the method chosen.

Selection, avoidance, and culling
Selection, avoidance, and culling involve the continued elimination, avoidance and/or attenuation of undesired traits and characteristics in breeding stock that leads to poor performance or increased variability [that is, a lower likelihood].

The Breeder's Rejection and Culling Process
During the selection of mates, decisions must be made by the breeder that identify and reject breeding stock that have the semi-independent variables of poor ability to win and low ability to transmit winning traits to their progeny. In this way the breeders’ chances of success are vastly increased. By rejecting those perceived to be unfit, the probability of production of progeny exhibiting superior racing performance will improve. Better racehorses produced by the breeding program obviously improve the breeders’ chances of economic survival and satisfaction. By being highly selective over his lifetime of breeding horses, the breeder's efforts have a progressive tendency to increase the overall degree of successful performance in his offspring.

Maternal Inheritance and my Mitotyping Project

My interest in maternal inheritance has been longstanding. My
mitochondrial DNA study project has been contemplated for over
fifteen years before I got brave enough to think I might be able to
make some kind of positive contribution in knowledge toward the
Thoroughbred that I dearly love. It was Charles Bruce Lowe whose
writings and difficulties gave me inspiration and confidence to at
least make the attempt. An abortive attempt was made in 1997 with
Dr. Ann Bowling, but she suddenly passed away at the age of 41 from a
cerebral hemorrhage.

I have prepared myself by operating a Thoroughbred breeding farm for
36 years, immersing myself in pedigree theories, conducting breeding
experiments on my farm, breeding research, biological research, and a
background of extensive historical research. My planned matings
using pedigree patterns, inbreeding, balanced-sex inbreeding,
techniques learned from successful breeders, and voracious reading of
Hewitt, Lowe, etc. has produced very satisfying and successful
runners in a regional setting.

Our mtDNA study was started by, financed by, and matured with a horse
breeder interested in selective mating, maternal inheritance, and the
expression of performance traits. I have tried to NOT bring to the
table the baggage of stubborn opinion or "know-it-all" closed
mindedness. I hope I have the open mindedness that objective science
requires. Academic pursuit of knowledge while important is parallel
to the potential benefit of pragmatic application of modern,
biological science for the horse breeder's benefit. In this genomic
age we are still applying eighteenth century, archaic breeding
practices.

Mitochondrial investigation must be more than a tool of identity in
order to be incorporated by the interested horse breeder in his
breeding program. I am happy and willing to acknowledge the great,
groundbreaking contribution made by Hill, Cunningham, Bowling, et al.
I have no intent to duplicate their efforts - why would I want to do
what has already been done?

Our interest in identifying matrilines is just an initial step
because how can legitimate research be done if you cannot identify
that which you are studying? How can you trust any conclusions if
you don't know from where you started? Obviously, therefore, the
research must start with identity. In approximately 20 -25 percent
of the samples we have sequenced so far, the mtDNA haplotype is in
disagreement with the recorded lineage of the individual. The Jockey
Club had no parentage verification prior to 1987 other than an honor
system dependent on the integrity of Thoroughbred breeders.
Registration relied on written and diagrammatic descriptions of
external markings similar to those used by state and federal live
stock inspectors with other domesticated animals. From 1987 until
2001, parentage verification was determined through nuclear DNA from
a sample of blood in addition to the written and diagrammatic
descriptions (except for an unsatisfactory attempt to use nasal swabs
for DNA verification in 1994-95). The integrity of lineages is
crucial to any rational selective breeding scheme. Mis-
identification of Thoroughbred lineages has lent an unwelcome and
unpredictable variability to selective mating schemes causing
inexplicable and unexpected failures from some matings selected by
experienced and expert breeders. Mis-identification of lineages
invalidates any thoughtful, objective attempt at breeding selection.

Our ultimate objectives are not the same as previous researchers. We
have better equipment [Transgenomics WAVE technology], a state-of-the-
art, forensic genetics laboratory, at least 8x better accuracy with
our methods compared to previous methods, far cheaper and quicker
processing, etc. At this time, we are building our own DNA database.
Access to the hair and blood samples retained by The Jockey Club
would be a researcher's dream.

In Mendelian inheritance, the nuclear DNA is the scaffolding or
structure. There are little differences at the level of DNA between
a horse, a human, or a hamster. What goes on is going on beneath.
Researching the nuclear genome is so large and complex that it would
take millions of dollars and far more elaborate facilities, years,
and resources to make any kind of meaningful contribution - Inquiry
into nuclear inheritance is far beyond my limited means.

The much smaller mitochondrial genome of "Equus caballus" [ACCESSION
X79547] is 16660 bp [base pairs] in size. It is monoclonal [that is
it replicates or clones from dam to progeny. The mitochondrial
genome does not split, divide, and recombine as in nuclear
processes]. It is somewhat simpler to understand and research.
PLUS, it has to do with maternal inheritance, which is where my
interests have laid for thirty years. Long live the ladies!
Yours truly, Loren

Running Horse Farm LLC
7102 Ilfield Road Southwest
Albuquerque, New Mexico 87105-7046
505-873-2220 farm
505-604-2221 cel
lbolinger1@comcast.net
-or-
lbolinger@gmail.com

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

Mitotyping Project

Mitotyping Project
By Loren Bolinger 9/14/2005

Unlike previous scientific inquiries, my first impulse was to present
our project directly to the typical Thoroughbred breeders across the
USA and internationally. The Internet and several breeders' e-mail
discussion groups proved useful to query a wide range of breeders
directly at minimum cost. I was curious as to the interest of other
Thoroughbred breeders to my passion and obsession. I also thought
that it would be more likely to pick up a wider range of unusual
matrilines, scientifically interesting, and suitable candidates for
sampling. Some of the matrilines are rare or obscure and more likely
to be found in the hinterlands. These rare matrilines may have
important relevance to our project.

One, very satisfying observation I've made, is the surprising numbers
of horse breeders sophisticated about maternal lineages,
mitochondrial inheritance, the Lowe family numbers of their horses,
and the potential of my mitotyping project to not only accurately
resolve known identity problems, discover unknown, longstanding mis-
identifications, but also for its application by horse breeders to
future selective matings. All horse breeders passionately want to
improve their stock. Accurate identification of lineage is crucial
to many selective breeding schemes.

The response to my mtDNA inquiry has been warmly rewarding to me
through the very large volume of e-mail and overall enthusiasm of
horse breeders internationally. I had planned to place small
advertisements in industry publications to get a wider range of
samples, but now must wait additional funding.

I have received tremendous grassroots response to what some might
regard as a rather obscure, technical inquiry. I can assure the
Jockey Club that my informal and anecdotal survey reveals that a
majority of Thoroughbred breeders are, in fact, tremendously
interested in the potential of mitochondrial research, more accurate
identification of maternal lineages and therefore, more accurate
identification of most all Thoroughbreds in the current population to
the current limits of modern scientific methods. The biological
knowledge and advances in scientific technologies are accelerating at
a mind-spinning rate - new discoveries coming almost day-by-day. We
are in a new golden age of genomic discovery. It would be unfair to
the breed we love to not take advantage of these advances to preserve
and conserve the Thoroughbred horse. For the most part, we still use
archaic selective breeding practices at a time when the biological
sciences are making major contributions the health and welfare of
humans and many species of domesticated and wild plants and animals.
If the knowledge learned from mitotyping could be used to reduce the
needless wastage and injury, minimize genetic defects and diseases,
conserve the breed for the future, while improving selective mating
techniques that produce the modern Thoroughbred racehorse, the effort
and expense would be well worth it. To my mind, it is a win - win
situation.

I strongly believe that ultimate responsibility for the
identification of the Thoroughbred lies with the keepers of the
General Stud Book, such as the Jockey Club and other international
keepers of the studbooks in their countries. They have the existing
recorded data, the authority, and the resources. There are an unknown
number of undiscovered haplotypes in lineages of the current
Thoroughbred population. One of my intentions is to attempt to
discover as many of the unknown haplotypes as my means allow; the
purpose being to make known the entire number of surviving haplotypes
comprising the modern Thoroughbred breed. I believe this is an
important project and I hope that my tiny mtDNA study will inspire
and encourage the appropriate authorities to create and fund an
international project to identify and verify all Thoroughbreds to the
limits of our technologies as far back as possible.

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

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