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While there are a number of geneticists around the world, collecting, compiling and analyzing genetic data on the Thoroughbred race horse, Victory Rose has developed a working relationship with ThoroughGen, LLC, with whom we’ve had analyze our stallions, mares and progeny’s DNA. This is an evolving science that is growing by leaps and bounds. In another 5 years or so, our belief is that everyone will be using this science and wondering how we ever muddled through without it??? Genetic testing is not meant to replace other traditional methods of choosing race horses and mating pairs. It is best used to enhance and improve on pedigree analysis, conformation assessments, nicking selections and good horse management. The following document outlines the basic premise of the use of Genetics in the breeding shed and selection of race horses.

Identification of Performance-Related Polymorphisms in Horse Using Genome-Wide Association

Otherwise known as;
Identifying performance genes, common in successful race horses and breeding stallions

Hundreds of millions of dollars are spent annually by Thoroughbred owners hoping to breed or buy the next champion. More tens of millions are spent on training and racing these same horses. Yet, the current state-of-the-art “scientific” and analytical underpinnings of the decision-making process (which horses will be bred and which ones should be trained for racing) are virtually the same as theories and methods that were applied one hundred years ago. Direct genotype information changes this static market dramatically by providing validated, predictive information that will improve the likelihood of success in purchasing, breeding, and deciding which horses are best to train and race. All other mating and pedigree research is based on the probability of a sire and broodmare sire passing specific, genetic, alleles to their offspring. This is primarily speculation, and at best an indirect assessment, since it is based on inferred genetic information. Instead, if a buyer wishes to know the actual gene variants that were passed from the sire and dam, direct DNA sequencing of the stallion and the mare is the only possible way to get this information.

How the models were created

Association mapping (finding common genes) is a powerful approach to identify genes affecting complex traits. It has dramatically improved our understanding of complicated human conditions such as Alzheimer’s disease, cardiovascular impairment and even traits as complex as behavior. The same approach can be used successfully in thoroughbred horses to identify gene variants that affect performance and therefore increase the power to pick winning horses or to choose the best possible breeding combinations. The logic behind association mapping was relatively simple; cluster individuals into ‘good’ and ‘bad’ performing groups, genotype all the individuals within those groups across the entire genome, and then test for allele (gene variant) frequency differences among the groups.

The models that have been created represent a study in population genetics, based on genetic differences between good horses and bad horses, both on the racetrack and the breeding shed. These are probability scores, thus choosing a horse from the top group seems to have a significantly better chance of success than one from the bottom group. For example, if a racing groups’ success rate is normally 20% (which is actually higher than the average or norm) out of 20 horses they buy, four horses should be good. Clients who have added genetic testing have that number up to 40% and even 50%, which would represent 8 or 10 good horses out of 20. If an owner can improve their success from 4out of 20 to 6 out of 20, it seems obvious this is money well spent

Applications for genetic testing

Racing and Individual Breeding Score: As mentioned above, the initial use for this model was to predict racing potential. Over the last three years, ThoroughGen tested more than 1000 horses and the model appears to be very robust. It is separated into two categories, class and optimal distance. On the class scale, the horses scoring high are more genetically similar to elite horses, while horses scoring low share a genotype with horses that are usually sub-elite. The distance scale is more straightforward, with horses lower on the scale found in a very high % of sprinters, and horses scoring high on the scale being more genetically similar to horses that run two turns. We have tested yearlings for the past three years and have been able to predict the eventual racing level and distance (as two and three year olds) in over 70% of yearlings tested. It seems pretty obvious the huge advantage this testing gives not only the buyer at auction but as an aid to the breeder in making culling decisions. I’ve included a few samples of this scoring.

Sample test results;

mare

name

sire

class

distance

# sprint allele

# dist allele

energy

real paranoide

 

 

46

75

0

0

b

 

summer paranoia

SS

72

42

0

0

 

 

a real siberian

SS

76

95

0

0

 

 

paratarib

MUQ

92

21

0

0

 

shebang

 

 

85

42

1

1

a

 

bang banger

LA

92

42

1

0

 

 

global magician

GLOB

76

74

1

1

 

 

sea of magic

SOS

50

100

0

1

 

lady’s champagne

 

 

51

42

0

0

a

 

summer champagne

SS

89

75

0

0

 

 

13 lady's champagne

SOS

34

100

0

0

 

 

summer lady

SS

90

21

0

0

 

Stallion Markers (Gene Allele Variants): After compiling and comparing, using association mapping, large numbers of successful and not so successful stallions, geneticists have be able to identify the gene allele variants or “Markers” that successful sires share. By ranking a stallion’s % of these “markers” on a scale of 0-100, a breeder can get a pretty accurate idea of whether a young stallion will be a success at stud. It’s long been a mystery in our industry why many elite race stallions were complete flops in the breeding shed and visa versa. We now understand that the genetic “Markers” that make a great race horse, have nothing to do with the “Markers” that make for a superior breeding stallion. While a stallion can be well endowed in both categories, it’s not a given. The following outlines, statistically, the importance of breeding to a stallion with at least a 50 ranking on the Stallion Marker profile.

The median "% stakes winning offspring" from stallions that ranked "high" (50-100) on the ThoroughGen scale is 8%, while the median % stakes from the horses that scored "low" (0-49) is 4%. This in itself appears to be very informative and supports the model nicely. So, just from categorizing the stallions into two groups based on their genetic profile, we see a doubling of the % stakes winning offspring.

Within those groups:

84% of horses in the 0.5-1.0 range had greater than 6% stakes winners, while only 19% of the 0-0.49 group reached 6% or better stakes winners. Therefore, stallions that score high on our scale have a 4 times better chance of producing stakes-winning offspring.

30% of the 0.5-1.0 stallions had greater than 10% stakes winners, while only 4% of stallions in the 0-0.49 group reached 10% or better stakes winning offspring.

Stallions that scored between 0.95-1.0 on our scale (very elite) had a median % stakes winners of 9%.

Further, 96% of stallions that tested between 0.95-1.0 on the scale had at least 6% stakes winning offspring. Finally, 43% of these genetically elite stallions have over 10% stakes winning offspring, so almost a one in two chance of hitting the 10% mark based on the roughly 350 stallions we've tested to date.

Breeding pair assessment (Breeding cloud): One more application for genetic testing is an application by which a broodmare owner can make hypothetical crosses with a number of stallions to identify the best possible breeding pair. This is far more informative than just nicking or pedigree analysis because the actual genotype of each horse is used to compile every potential offspring with the probability of each outcome. This as compared to traditional pedigree assessments, which are based only on inferred genetic alleles, which may be passed from parent to a potential offspring. The breeding cloud won’t replace traditional methods of narrowing down the list of potential suitors for a mare. It will, however, substantially improve the odds of making the best choice between these potential mates. For the 2014 season, Victory Rose will provide a Breeding Cloud test for all interested clients, using a $300 booking fee to cover the expense of the test, which comes off the price of the stud fee.

Summary

This is just a summary of what is now being offered with genetic testing and it will likely continue to improve and expand. This science has been used for years by the Sheiks and very wealthy in our industry. It’s finally gotten affordable enough for the rest of us to use and puts us on a much more even playing field.

It can’t be stressed enough that this is not a quick pick, microwave approach, to picking race prospects or mating pairs. Genetics must be used in conjunction with lots of good traditional hard work and studying. But it does give owners a big advantage over just using traditional methods alone.
 

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