Pedigree Query

In the British Channel 4 documentary on the TB which is internet linked in the Inbreeding and biomechanics thread the last segment was a very brief interview (many two sentences) with Emmeline Hill. In those two sentences she mentioned that they had discovered gene controllers not only for speed and precocity versus stamina but also for elite performance.

Elite Performance?! Where can I find this paper?

Would a stallion owner ever do something like this or would it be way too expensive or too inaccurate given the number of sperm per ejaculate? Take a sperm sample and test 100 or 1000 sperm for the "elite" genes. Get a percentage of "elite" to non-elite sperm and market the stallion based on that?

If all the test is good for is for foals on the ground, it will save breaking and training costs, but what will happen to the ones who don't pass the genetic tests?



I can't quite see how one could do a comparable test on eggs.

The Thoroughbred Pedigree and Genetic Symposium held in KY for the last two years goes into great detail about the "Myostatin Gene". After sifting through the scientific jargon, my understanding of the Myostatin Gene is that all thoroughbreds carry the gene. Their are 3 variations of the gene, CC which is precosious, speedy, sprint type, CT which is middle distance, and TT which is later developing and stamina type. Apparently the testing has overwhelmingly confirmed the genes accuracy. I believe the test is available and cost around $1000. What I found interesting was because of the combinations of the expression of the gene, meaning if CT was mated to CT, the offspring would have a 25% chance of being CC, 50% chance of being CT and a 25% chance of being TT. So full brothers could be polar opposites, one could be CC, a sprinter, and one could be TT, a distance runner.

vineyridge wrote:Elite Performance?! Where can I find this paper?

Here.

PZ, you understand these things.

I'm reading the paper you linked. Have only gotten to page 2, but am puzzled about the huge difference in quality between their Elite and Other groups. I can see using an RPR of 115 for the Elite. But their Other were pitiful performers: RPR of 73 or less and non-winners ever. Did they choose such plodders because the difference was SO extreme that it made finding what they were looking for easier? Why not use Elite and the general rest of the population for Other?

Blue Feather, this is a different paper with newer research.

vineyridge wrote:I'm reading the paper you linked. Have only gotten to page 2, but am puzzled about the huge difference in quality between their Elite and Other groups. I can see using an RPR of 115 for the Elite. But their Other were pitiful performers: RPR of 73 or less and non-winners ever. Did they choose such plodders because the difference was SO extreme that it made finding what they were looking for easier? Why not use Elite and the general rest of the population for Other?

Their sample set was selected for diversity of pedigree. Arguably, that could account for some of the dramatic difference betweent the elite and non-elite. There are several aspects of the study that could be (and have been) criticized, including the fact that the db here was their source for NorthAm race rcds. (This is an open-edit db that is not error-free, whereas official race records are available free from more than one source.) Bottom line - see the last page (62) three of the authors have a commercial interest in TB genetic testing, a field in which several companies, including Hill's Equinome, are engaged in intense competition. This study doesn't conducted for purely academic purposes and should be regarded accordingly.

Thanks Vineryridge, time to catch up.

Viney,

You might also like to look here....

http://performancegenetics.com/how-it-works/

Our study was completed on primarily North American horses.

Bryon, I can see a rather large hole.

Horses start their careers and begin to move through them as two year olds. For many of them, their whole subsequent history is determined by two year old results. This has been true for as long as racing has focused on futurities (2 year olds) and the three year old year. Many North American horses don't race after their two or three year old years, and this is something that has become much more common recently. If your model is less predictive for two year olds and younger, it would appear to me to lose a good bit of its usefulness. Wouldn't it be very, very rare for an owner to wait until the 3 year old year to confirm that his/her horse was worthy of training for the very top classes of race? And given how much of the Kentucky Derby money qualifier comes from racing in the 2 year old year, wouldn't that mean that some of your Elite horses don't get entries?

Our Elite horses RARELY race past three.

Not saying that what you are doing isn't very interesting and useful, but if it were more accurate for babies to two, it would be lot more interesting and useful.

Thanks for the link: HERE.

Will the C:C / C:T / T:T-classification based on the genetic test developed by Dr. E. Hill of Equinome (see http://www.equinome.com/) influence the "Chef"-classification in Dr. S. Roman's "New-Dosage-System"?

vineyridge wrote:Bryon, I can see a rather large hole.

Horses start their careers and begin to move through them as two year olds. For many of them, their whole subsequent history is determined by two year old results. This has been true for as long as racing has focused on futurities (2 year olds) and the three year old year. Many North American horses don't race after their two or three year old years, and this is something that has become much more common recently. If your model is less predictive for two year olds and younger, it would appear to me to lose a good bit of its usefulness. Wouldn't it be very, very rare for an owner to wait until the 3 year old year to confirm that his/her horse was worthy of training for the very top classes of race? And given how much of the Kentucky Derby money qualifier comes from racing in the 2 year old year, wouldn't that mean that some of your Elite horses don't get entries?

Our Elite horses RARELY race past three.

Not saying that what you are doing isn't very interesting and useful, but if it were more accurate for babies to two, it would be lot more interesting and useful.

Vineyridge,

I am a little confused by some of the terms you have used and I think that you might have misunderstood what is being said. Firstly, while expression may alter as it interacts with environment, the genes themselves don't change from the time that they are born until the time that they die so we can test a foal as soon as it is born and see where, at least in terms of genetics, that it lies in the model. Your statement that the 'model is less predictive for two year olds and younger' leads me to believe that you may think that the DNA changes somehow. It doesn't. Correct me if I have misrepresented you here.

Secondly, the reason why any prediction model is not going to be able to reliably predict early two year old racing is that the competition that the horses generally face at that time is very weak. We are talking about races like the Cinderella, Churchill Downs Debutante, Tremont, etc. These types of races are sometime won by horses that we predict as potentially elite, but often won by horses that we don't predict as potentially elite and these horses that win these types of races usually fall of the radar pretty quickly.

As an example, we predicted Necessary Evil as a sub-elite horse, she scored right in the middle of the model in terms of class but as a sprinter. She didn't test out as elite on our model, and I don't think that we got her wrong. If she was going through a sale, we certainly wouldn't have put a purchaser off buying her, as she was well out of the non-elite category, but she wouldn't be one that we would go out and recommend. Posse on the other hand, scored out as an elite on the model (he is in the top 5% of the model in terms of class actually). He was a good two year old that trained on at three to compete consistently at graded stakes level which is what our model is trying to identify.

If you are going to create a prediction model, you need to focus the model on what you are trying to predict. We took the view that most people are interested in buying horses that race late in their two year old year at consistent graded stakes level and compete at three and hopefully beyond at the highest level. We created the model to identify this type of horse and it does this very well. We didn't create the model to find horses like Necessary Evil that are out early in their career and for one reason or another, never heard from again. For some people that is a good horse, but for our clients that is not the type of horse that they would like us to identify for them.

Perhaps I misunderstood what this quote means:

Where the Performance Genetics prediction model is most accurate is the prediction of the racehorse as a three year old and older. This type of horse requires a unique combination of cardiovascular capacity and genetic profile to achieve elite status as a three year old and older, regardless of the ultimate distance that the horse is best suited to and we have built the model specifically to identify these types of horses.

Viney,

What it means is that you can't be everything to everyone. Nobody can design a prediction model (unless they did multiple models and weighted them) that would completely predict outcomes, especially in performance of racehorses. There is too much variability. Just think about the differences between a horse like Necessary Evil, an early two year old on dirt, and say Better Talk Now, a late maturing distance turf horse. There is a lot of difference between these two types of horses, and say your center point, a horse like say Curlin.

If you build a model to try to predict Curlin, the outliers like Necessary Evil and Better Talk Now are going to confound. As good as Necessary Evil and Better Talk Now are, and we would love to have owned them, we took the view that our clients were not aiming to buy these types of horses. They want to buy a Curlin. So we built the prediction model around trying to identify that type of horse.