☛ AQHA Genetic Pool shrinks 1-10–15
AMERICAN QUARTER HORSE GENETIC POOL SHRINKS
WHAT CAN BE DONE ABOUT IT?
By Rick Dennis
Jan. 10, 2015
Recent articles in the American Quarter Horse Journal entitled “The Changing Landscape of Quarter Horse Genetics, Part 1 and Part 2,” really caught my eye because of two reasons: 1) I’m an American Quarter Horse breeder specializing in multiple-event reined cow horses and 2) I’m a Life Member of AQHA.
Part 1’s first paragraph essentially sets the stage for the present state of the breed in that it’s becoming more and more inbred, stating, “Talk to an equine geneticist long enough and you are bound to hear two assertions made about the American Quarter Horse breed that sound like opposites: First, it is one of the most genetically diverse equine breeds in the world and second, it’s becoming increasingly inbred.”
The second and third paragraphs of Part 1 outline the history of the breed and a factor causing this shrinking of genetics, stating: “Beginning in colonial America, the breed began from a diverse genetic base of largely Thoroughbred and Spanish blood that was added to and developed for roughly 200 years, focusing on producing quickness and durability. But fast-forward to the modern era of specialized American Quarter Horse performers, especially at the highest levels, and you find specialization in the horse-breeding herd too: specific groups of individuals used to produce those top performers.
That suggests there are narrowed gene pools in those subgroups and now a genetic study clearly shows it. A research team from the University of Minnesota has published its findings in an issue of the Journal of Heredity, “The American Quarter Horse: Population structure and relationship to the Thoroughbred.” The 2012-2013 study was partially funded by the American Quarter Horse Foundation.
The team analyzed six Quarter Horse performance subgroups identified as halter, western pleasure, reining, working cow horse, cutting and racing. The team pulled the top 200 performers for each group in 2009 and 2010, selecting by money-earned for the reining, working cow, cutting and racing groups, and by AQHA points earned for western pleasure and halter.
The team then eliminated half and full siblings, making the sample as diverse as possible. From the remaining horses, the team ran genetic and pedigree analyses on 24 random individuals in each subgroup.
“We genotyped them for about 65,000 genetic markers … and we pulled their five-generation pedigrees so we could compare what both sets of information told us about the relationships between the individuals,” said Dr. Molly McCue
What They Found
“The groups clustered into three genetic groups,” said Dr. McCue. “The racing Quarter Horses stood out on their own genetically, the pleasure and halter horses clustered together and the working cow, cutting and reining horses formed the third group. We were able to prove quite clearly that horses were in a specific genetic cluster depending on what performance group they came from.
“In the pedigree analysis, some groups shared no common sires, such as halter and racing, but other groups did, such as reining and working cow horse. Although popular sires within one group were rarely shared with another group, all the pedigrees reflected the common roots of the Quarter Horse.
“Additionally, pedigree analysis showed that the most common 15 sires across the groups were all direct tail-male descendants of Three Bars (TB), with several of those stallions showing more than one cross to the Thoroughbred in the first four generations.
“Inbreeding” refers to the mating of relatives and results in an “inbred” individual. The amount an individual is “inbred” can be estimated from its pedigree or genetic data. In a pedigree analysis, determining an individual’s “co-ancestry coefficient” gives an idea of how closely related individuals are on a pedigree page. Two individuals can be highly related without either of them being inbred, but if you breed two individuals with a high co-ancestry coefficient, their offspring will be inbred.
“Diversity quantifies the amount of genetic variation there is in a population. Typically, a highly inbred population has low genetic diversity.
“Using both pedigree and genetic analysis gives a more complete picture of a population’s relatedness, inbreeding and diversity. For example, the average Thoroughbred could very well exhibit a much lower genetic diversity in its genome than the average Quarter Horse, even though the Thoroughbred might show no repeated individuals in its five-generation pedigree.
As a point of reference, and to fully illustrate the long term adverse effects of inbreeding please refer to the following CBS article: “Amish Inbreeding Causes Genetic Mutation and Mental Retardation.”
Click for article on Amish inbreeding>>
“(In this study) the lowest genetic diversity within a sub-population was in the cutting and racing groups. The highest average inbreeding was found in cutting.
“When inbreeding was calculated from the pedigree analysis, the reining group had the lowest average inbreeding when it was calculated with genotype; the pleasure group was the lowest.
“Halter horses, on average, were about 3 percent inbred, although some individuals were as high as almost 27 percent inbred.”
“What’s more, the study found that, due to the contribution of popular sires, relatedness within the groups is on the rise. This increase in relatedness, or co-ancestry, is likely to lead to an increase in the number and extent of inbred individuals,” continued Dr. McCue.
Click to read Part 1>>
Analyzing the Quarter Horse Breeding Rules:
From this study, it’s clear that the present American Quarter Horse breeding rules require scrutiny to determine: 1) their contribution to this shrinking genetic pool and 2) the adverse affect each adopted breeding rule may or may not have on the breed itself. I wonder if the executives paid six figures at the AQHA and the Executive Committee members, especially the Stud Book and Registration Committee, had any forethought in the ramifications their expansive breeding rule adoptions would have on the Quarter Horse breed and industry over time?
As a private sector Risk Analyst, I’m commonly faced with the task of analyzing practices and concepts to determine either the detriment or usefulness an existing concept or practice has on an organization. In order to shed light on the topic, I examined two specific breeding rules adopted by AQHA: Multiple Embryo Transfer and Frozen Semen. I also examined the impact each adopted breeding rule may have on the breeding populous as well as a correlation of each one’s compliance with AQHA’s Mission Statement.
AQHA Mission Statement
Your Association adheres to the highest standards.
AQHA Mission Statement:
- To record and preserve the pedigree of the American Quarter Horse while maintaining the integrity of the breed and welfare of its horses.
- To provide beneficial services for its members which enhance and encourage American Quarter Horse ownership and participation.
- To develop diverse educational programs, material and curriculum that will position AQHA as the leading resource organization in the equine industry.
- To generate growth of AQHA membership via the marketing, promotion, advertising and publicity of the American Quarter Horse.
- To ensure the American Quarter Horse is treated humanely, with dignity, respect and compassion at all times.
Multiple Embryo Transfer
The first analysis and breeding rule comparison involved the Multiple Embryo Rule adoption. On one hand, the first statement of the AQHA Mission Statement asserts “maintaining the integrity of the breed and the welfare of its horses” but on the other hand, this AQHA breeding rule adoption and Dr. Mc Cue’s study raises challenges to the credibility of this profound statement concerning the integrity of the breed and welfare of its horses under their present approved breeding methods.
Past court testimony of Dr. Glenn Blodgett an AQHA Executive Committee member and in-line future AQHA President brings a challenge to this assertion. Dr. Blodgett’s sworn oath expert witness testimony, during the Kay Floyd V AQHA trial, fully illustrates and verifies this contradiction as well as the dangers and hardships the breeding mares were subjected to during an egg and embryo flush. The hypocrisy is fully realized when Dr. Blodgett, who at the time was the Chairman of the Stud Book & Registration Committee, the group who consider the proposed rules of registration and answer to no other committee, fully exposed these dangers and hardships on a horse while voicing his opposition under sworn oath testimony. However, Dr. Blodgett has been one of the most prolific users of multiple embryo transfer technology since 1985, long before the Kay Floyd v AQHA lawsuit.
Click for Dr. Glenn Blodgett Testimony>>
As a breeder, I have always been opposed to many of the breeding rule adoptions of AQHA, (i.e.) Multiple Embryo Transfer that allows a mare to produce multiple same genetic-type foals in a single breeding season instead of adhering to the “one-mare, one-foal” breeding theory, essentially limiting or maintaining the narrowing of the genetic pool by eliminating or controlling mass production of a single genetic type. By Dr. Blodgett’s testimony, this breeding rule also contradicts AQHA’s own mission statement, “To ensure the American Quarter Horse is treated humanely, with dignity, respect and compassion at all times.”
The magnitude of the mass expansion of a specific genetic line of horses by multiple embryo transfer is realized in past computations resulting from the analysis of seven (7) separate Quarter Horse Racing mares that produced 174 foals during a specified time, averaging 24.85 babies each. Such an expansion of a specific genetic line also has an adverse effect on the breed in that it further narrows the genetic pool, which under normal circumstances reduces the odds of inbreeding. In addition, this breeding technology also contributes to an over population of Quarter Horses.
In Part 2, of the article, Dr. Molly McCue specifically addresses the effect Multiple Embryo Transfer is having on the industry.
Click for Horse Genetics Part 2>>
What It Means
“We are changing the genetic landscape in the Quarter Horse within the top-level performance groups,” stated Dr. McCue. “This study clearly demonstrates that we’re concentrating the genetics within certain lines of Quarter Horses and we’re increasing inbreeding within particular performance groups.
“A horse’s conformation affects his ability to perform certain tasks. Read more about this interesting concept in AQHA’s Form to Function report.
Click for “Form To Function” Report>>
“Longstanding breeding practices likely contribute to that. Habits such as “popular sire syndrome,” which is the tendency for many breeders to breed to a top-performing stallion, or the use of assisted reproductive techniques such as frozen semen and embryo transfers can greatly amplify one individual’s genetic impact. Even the practice of always breeding the ‘best to the best’ can contribute to increased inbreeding in a subpopulation.
“Any time we take a single individual and increase its ability to generate offspring, that is going to decrease the genetic pool that is reproducing.
“Additionally, when you increase inbreeding and reduce diversity, you increase the incidence of undesirable genes making an appearance.
“A good example is the incidence of HERDA (hereditary equine regional dermal asthenia) in cutting horses. It’s very frequent within this subpopulation, which might be the result of decreasing diversity and/or the ‘popular-sire’ effect. A previous study revealed that 28.3 percent of cutting-bred individuals carried the recessive gene for HERDA.”
A textbook example of the advantages of the “Frozen Semen” breeding rule, as it relates to a specific classification of horse, can be illustrated by examining the history of an AQHA Quarter Horse Racing member Frank “Scoop” Vessels and his history-making stallion First Down Dash. Mr. Vessels, an avid Quarter Horse Racing breeder, died in a plane crash on Aug. 11, 2010. On Nov. 28, 2010, a press release from the AQHA announced that First Down Dash died on Thanksgiving Day at the Vessels Breeding Farm in California.
Under the old rule, frozen semen could only be available until the end of the year the stallion died in. However, thereafter, the AQHA quietly changed the frozen semen breeding rule to extend a stallion’s frozen semen indefinitely. This extension makes a dead or sterile horse immortal, so-to-speak. Even though he died in 2010, according to the AQHA records, in 2012 he sired 68 foals.
Breeding dead horses from the grave and sterile horses that should be culled, (i.e.) removed from the genetic pool at death or sterility, are still introducing their genetic lines in today’s breeding market. The normal course of a breeding sire is that he is born, lives, reproduces and dies. Afterwards, his progeny carries on the genetic line from generation to generation. By allowing the reintroduction of a dead or sterile horse’s genetics over the years simply means he could be breeding with horses that already carry his line of genetics, further shrinking the genetic pool and possibly causing a concern of inbreeding and disease among the industry.
A more prudent option would be to seek a genetic out-cross instead of an in-cross. A plausible question for the AQHA powers-that-be emanating from the frozen semen breeding rule is: “Why are stallion owners with live horses having to compete for a fair market breeding share against deceased or sterile horses that should have been removed from the breeding roster at death or sterility?” At this stage of the breeding game, wouldn’t it be more responsible for AQHA to design a genetic breeding profile similar to the “Magic Cross” that breeders have used for years to breed performance horses, to minimize or eliminate the in-breeding concept identified by Dr. Molly McCue’s study.
Dissecting the Recent Select Yearling Sale:
For a look at today’s diversity, or lack thereof, in the cutting horse, the 50 horses auctioned off during the NCHA Select Yearling Sale, held Dec. 9 during the NCHA Futurity, were put in a data base. The yearlings were the highest of the six sales, averaging $71,655, carrying a $53,000 median (halfway between the highest- and lowest-selling horse), and the high seller brought a whopping $255,000. This sale was chosen as it represented the best-of-the best of today’s upcoming cutting horses.
Twelve stallions were represented, with every stallion having Three Bars represented on both the top and bottom sides of their pedigrees, mostly through Doc Bar. Of the 47 dams represented, only four didn’t have Three Bars on both sides of their pedigrees. The results were amazing.
Tracking included how many times the sires of the horses selling went back to Three Bars, along with the dams of the horses selling – then those figures were added together to get a total and that total was ranked by the median, which is half-way between the highest and lowest total, with the highest total representing the most Three Bars in the pedigree and the least diversity.
The highest median (meaning the least diversity) went to yearlings sired by Spots Hot, with four going under the gavel (included were horses that sold and horses that didn’t, using their last bid). The median for those four head was 12.5, meaning that the yearlings went back to Three Bars, both on the top and bottom side, 12.5 times. The highest was 13 and the lowest 10. As an individual Spots Hot goes back to Three Bars three times on the sires’s side and three times on his dam’s side, for a total of six.
His sire Chula Dual went back to Three Bars through his sire Dual Pep, out of Miss Dual Doc by Doc’s Remedy by Doc Bar by Lightning Bar by Three Bars. Chula Dual’s dam, Smart Fancy Lena, is sired by Smart Little Lena by Doc O’Lena by Doc Bar. Smart Fancy Lena’s dam, Docs Fancy Peppy, is out of Docs Fancy Pants by Doc Bar.
Spots Hot’s dam, Sweet Shorty Lena went back to Three Bars three times, with her sire Shorty Lena being sired by Doc O’Lena by Doc Bar and her dam, Quixotes R Sugar by Son O Sugar by Sugar Bars by Three Bars and dam Zan Ote by Doc Quixote by Doc Bar.
Next was Metallic Cat, whose offspring went back to Three Bars a median of 11 times with the highest being 11 (4 of them) and the lowest 8.
The individual sale horse with the highest individual score, a 16, was Miss Stylish Katz, selling for $152,000. She was sired by High Brow Cat out of Miss Stylish Pepto by Peptoboonsmal. She went back to Three Bars three times through her sire High Brow Cat and 13 times through her dam. Miss Stylish Pepto went back to Three Bars nine times through her sire One Stylish Pepto and four times through her dam Miss Silver Poppy who was sired by Dualin Gun out of Docs Poppy King.
The highest-selling yearling, Tappin A Cold Brew, bringing $255,000, was sired by Smooth As A Cat out of Tapt Twice by Dual Pep. Smooth As A Cat went back to Three Bars four times through Doc Bar and Tapt Twice also went back to Three Bars four times through Doc Bar for a total of 8. Smooth As A Cat had a median of 8.
Click for Yearling Sale chart>>
With all of this information in mind, wouldn’t it be beneficial for the AQHA and the Quarter Horse Industry to take a step back and rethink and reexamine the impact these two breeding methodologies are having on the American Quarter Horse and its members and adjust accordingly instead of providing breeding rules that may be harmful to the breed and cater to the rich and affluent members of the association? Coincidentally, the rich and affluent are the only ones who can afford such extravagant breeding methods anyway.
In conclusion, I would recommend to AQHA, pursuant to my Risk Analysis of the multiple embryo transfer and frozen semen rules, that these two rules in their present form and use is in direct conflict with AQHA’s Mission Statement and is a direct contributor to the shrinking of American Quarter Horse genetics as stated in Dr. Molly McCue’s study.
Also, who was the officer in charge of Breed Integrity during these rule changes? I believe it was Tom Pereschino, Executive Director of Competition and Breed Integrity, who in the last IRS 990 was shown as receiving a salary of $181,187, which included a $7,873 bonus and is a $25,440 increase from the prior year.
Until Next Time, Keep ‘ Em Between The Bridles!
Copyright 2015, Rick Dennis, all rights reserved. ©
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