TABLE OF CONTENTS
Part 1: Breeding for Breakdowns »
Part 2: The Rise of the Ill-Fated Gene Pool »
Part 4: On the Brink of Extinction? »
Written and Researched
by JANE ALLIN
"As the 20 horses were being loaded into the starting gate for the (2008) Kentucky Derby, with Eight Belles ― standing in post position five ― poised to make her bid to become only the fourth filly in history to win America's most important race, Ellen Parker, a thoroughbred breeding consultant and analyst in Kentucky, said quietly to her husband, "I just hope this filly doesn't break down." 
Eight Belles was euthanized on the track at Churchill Downs, just minutes after she finished second to Big Brown.
Eight Belles broke her cannon and sesamoid bones which led to her ankles collapsing, said Dr. Larry Bramlage, the on-call veterinarian for the American Association of Equine Practitioners. This is the same type of break suffered by 2006 Kentucky Derby winner Barbaro in his off hind. It eventually lead to his death after numerous surgeries and treatments, all which failed to save the horse's life.
PHOTO CREDIT: BRIAN BOHANNON / AP
What Parker was referring to is the bane of horse racing in today’s syndicated commercially-driven industry where money, greed and short-term gains preside over the welfare of the horse. A shift in the industry in recent decades and the maniacal frenzy for speed at the expense of durability and soundness has all but decimated a once genetically diverse and robust species.
Over time, especially in the last four decades, the manipulation of the gene pool of the Thoroughbred and relentless inbreeding at the hands of unscrupulous breeders has created inherent weaknesses in the bloodlines that have led to dangerous flaws in physical conformation. In the tragic case of Eight Belles, Parker had identified a series of foreboding crosses stemming from a line notorious in the Thoroughbred breeding world for unsoundness.
"What so concerned her on the eve of this Derby, what she found so disturbing, even infuriating, traced to her unshakable belief that Eight Belles was carrying in her DNA the seeds of her own destruction.
"Specifically, in the pedigree of this speedy gray filly, Parker had seen the same kind of dangerous crosses ― in her case, lines of known unsoundness triply crossed behind an unsound sire line – that she believed had contributed to the racetrack breakdowns and deaths of such prominent horses as Ruffian and Go For Wand, of George Washington and Pine Island, and even of Barbaro.
"Indeed, when Ellen Parker first perused the bloodlines of Eight Belles, she saw a danger clear and present: a family tree that bore three branches of the extremely brilliant but unsound racehorse Raise a Native, who was a very muscular chestnut, heavy on the front end, who had won all four of his starts before he broke down in front and limped off to stud." 
As it happens, today’s Thoroughbred population is so saturated with the blood of Raise a Native’s sire Native Dancer ― speed at the expense of endurance ― the threat to the viability of the breed is in question. For example, all of the starters in the past three Kentucky Derby's (2008, 2009 and 2010) carried the gene pool of Native Dancer, many of them multiple times. [3, 4]
Moreover, the blood lines of the current 2011 Derby contenders are equally infused with Native Dancers volatile genes, some of which ominously parallel the pedigree of Eight Belles in terms of the degree inbreeding and multiplicity of crosses.
This proclivity for the Native Dancer bloodline is not limited to North America but rather persists throughout the entire global Thoroughbred industry.