Buckpasser in the X

[Pan Zareta]

Competing companies certainly want to play down the importance of the X chromosome while at the same time pushing their own agendas which involve research on autosomes. They certainly would not want to discover any major variants on the X chromosome because that would only give another boost to the already great amount of interest in the so called superlative X.

That's almost as absurd as the idea that the "best" of Buckpasser's X can "somehow" be passed along through one of his sons. (Why let biological fact get in the way of what you want to believe?)

No one studying the TB genome in the academic and/or commercial sectors regards Haun as a competitor. I dare say many of them outside North America have probably never heard of her or her hypothesis and they're certainly not going to ignore genetic variants of more than minor relevance to superior performance, wherever they may be.

[Jeff]

It would be absurd for any breeder to disregard anything that plays even a slight influence in the breeding of a superior race horse. By PZ's own admission Stan's x theory at best plays some small slight role or has some slight influence. When the difference between winning and losing is a nose or a nano second, every little bit helps.

[stancaris]

DDT: In the thread The Mares In Great Sires on page 4 you responded to Byron Rogers on Oct 20th, 2011 at 8:49 PM in the discussion about the X Factor as follows:

"I do not care to bicker with you about this, but it is still a theory and you offer no scientific facts to disprove it, just opinions." Something is going on with the X chromosome and every elite colt produced receives an X from his dam and most of those genes have a chance for expression without the help of the Y."

Another of your quotes that you said to Brogers follows:

"You certainly did not involve yourself with these types of businesses without the thought of making a profit, whether or not your prediction came true. I believe your bias overcomes your logic when it comes to any matter that might cast a shadow on what you do for a living."

It is clear that you are in agreement with me that Brogers statements can be taken with a grain of salt because he is in the business of selling genetic discoveries on chromosomes other than what might be on the X chromosome. I agree with you that his bias overcomes his logic when it comes to matters that might cast a shadow on what he is selling for a living and the X factor is one of those matters. And my idea that the X chromosome is important is also one of those matters that casts a shadow on someone selling performance genes on other chromosomes.

Brogers himself said that there are variants on the X chromosome that relate to elite performance. Without a doubt. They just have nothing to do with heart size. He also said that one of these X variants reached statistical significance and then went on to say that particular variant is not even in the top ten in importance.

I think it is an extremely difficult thing to rate these variants in any way shape or form. For example if one variant strengthens muscles and another builds strong bones how can you ever say that one is more important than the other?

[DDT]

Stan

Those statements were made prior to my understanding and acknowledging the fact that Haun's theory is not correct. I told you before that at one point in time I also was a believer in the X factor and published an article to that effect, and I also told you where to find it. I have never denied the fact that I was a believer at one time. In addition, I am not the person that uses Rodgers' statements for any purpose whatsoever. I informed you more than once that now I believe that mtDNA has a lot to do with superior performance, and when I say there is something going on with the X chromosome that is what I mean, not the genes carried on it.

I have also come to believe that a larger than normal spleen may be the advantage Haun's research points to and not the heart or in conjunction with a larger than normal heart.

DDT

[Pan Zareta]

I think it is an extremely difficult thing to rate these variants in any way shape or form. For example if one variant strengthens muscles and another builds strong bones how can you ever say that one is more important than the other?

For starters, by quantifying frequency of occurrence of those variants in the sample population sorted by record, earnings, distances, surfaces, age, gender, etc, and that would just be the tip of the analytical iceberg.

Genome-wide scans are a recent tool for analyzing TB performance, not possible before the equine genome sequencing was finished in 2007 and the first equine SNP chip became available a year or so later. The thread referred to in your post was begun nearly two years ago. Information was presented therein that was completely novel to many thread contributors. A certain amount of initial healthy scepticism was to be expected but reasonable people eventually recognize and assimilate credible and useful information that's pertinent to their fields of interest.

[stancaris]

Pan Zareta: In the Mares in Great Sires Thread on Page 8 the last post by you occurred on Nov. 9th, 2011 at 4:16 PM.

In that post you responded to a question I asked. I asked you, "Is it your view that the X Chromosome is important in establishing leading broodmare sires.?"

You responded by saying, "In my opinion the nature of X chromosome transmission is what makes the sire's dam critical to his success as a broodmare sire. She contributes 100% of the X chromosome he passes to his daughters."

Wow! in 2011 in your mind the X chromosome was critical to broodmare sire success but now in 2013 it only plays a minor role at best.

[Pan Zareta]

You responded by saying, "In my opinion the nature of X chromosome transmission is what makes the sire's dam critical to his success as a broodmare sire. She contributes 100% of the X chromosome he passes to his daughters."

Wow! in 2011 in your mind the X chromosome was critical to broodmare sire success but now in 2013 it only plays a minor role at best.

I meant critical in the sense that the a male must have one complete and fully functional X chromosome but in the clarity of hindsight I can see how that statement might be misinterpreted, especially by you.

[stancaris]

Pan Zareta: Here is an interesting question regarding genomic research. Where can we get information about the one variant on the X chromosome that Byron Rogers mentioned was related to elite performance and reached statistical significance despite the fact he ranks it below the top 10 in importance? What was the function of that variant gene on the X that related to elite performance? This would be very valuable info but the big question follows: Is a company that is doing that kind of research willing to post that information since it may be selling it to breeders who are dreaming of getting that champion racehorse?

Are there other variants on the X that were discovered by other companies that reached statistical significance regarding elite performance or was that the only variant ever discovered by genomic researchers that was found on the X and reached statistical significance?

[hpkingjr]

Pan Zareta: Here is an interesting question regarding genomic research. Where can we get information about the one variant on the X chromosome that Byron Rogers mentioned was related to elite performance and reached statistical significance despite the fact he ranks it below the top 10 in importance? What was the function of that variant gene on the X that related to elite performance? This would be very valuable info but the big question follows: Is a company that is doing that kind of research willing to post that information since it may be selling it to breeders who are dreaming of getting that champion racehorse?

Are there other variants on the X that were discovered by other companies that reached statistical significance regarding elite performance or was that the only variant ever discovered by genomic researchers that was found on the X and reached statistical significance?

Great questions but at the end of the day I would expect anyone doing the research to try to make a profit from it. My gut is if any researcher finds a performance enhancing gene there will be a test available shortly after the announcement.

[Pan Zareta]

My gut is if any researcher finds a performance enhancing gene there will be a test available shortly after the announcement.

..and a peer-reviewed report, sometimes associated with a patent application.

There's no shortage of available evidence about the genetic variants regarded as most relevant to performance success. There is less information in the public domain about the many variables of lesser relevance to same. However, what is available there is consistent with what was reported to Stan in 'The Mares in Great Sires' thread. It certainly justifies the conclusion that the X is of some minor relevance to broodmare sire success (though having nothing to do with heart size, as Haun hypothesized) but not that it "dictates" such success as Stan proposes in the first post of this thread and elsewhere.

[stancaris]

Pan Zareta: You referred to the thread The Mares in Great Sires as information that substantiates your conclusions in the following quote "it certainly justifies the conclusion that the X is of some minor relevance to broodmare sire success." And then you so conveniently misquoted my first statement made in the first post of this thread. I did not say dictates alone. My statement was as follows: This data regarding Buckpasser may indicate that his X chromosome may dictate or contribute to his success as a broodmare sire.

It is your opinion that the X plays a minor role in broodmare sire success. I differ on that conclusion. I have presented evidence regarding many different kinds of statistics that indicate the X chromosome plays an important role in broodmare sire success:

1. The Pattern of Sex Linked Inheritence referred to by Alan Porter and Anne Peters in their book Patterns of Greatness II with specific page references to Buckpasser and Secretariat. In their final paragraphs on Buckpasser and Secretariat they strongly imply that sex linked traits of their dams, Busanda and Somethingroyal play an important role in their success as broodmare sires. These sex linked traits passed on to Buckpasser and Secretariat were carried on the X chromosomes of Busanda and Somethingroyal.

2. The fact that over the last 5 years 42% of the top 10 broodmare sires carry Buckpasser as their broodmare sire or second damsire. More specifically 34% of the top 10 carry either Buckpasser or Secretariat as their broodmare sire and 8% of the top 10 carries Buckpasser as his second damsire (that 8% being Danehill). Thats 5 years of data and over 10,000 runners, certainly not a cherrypicked sample as you so often critiqued.

3. David Dink's analysis of statistics regarding position in the pedigree in Racehorse Breeding Theories also supports the idea that the X chromosome is important to broodmare sire success.

4. The simple fact that great Broodmare sires like Buckpasser, Secretariat etc. transmit 100% of their X chromosome to ALL their daughters and NONE of their sons suggests that something significant is present on the X that is transmitted to the progeny of the daughters. It is the earnings of these progeny that rank the broodmare sire in the top 10. Sure there are other chromosomes that are also important in this regard but the X is the ONLY chromosome of a broodmare sire that is transmitted to all of his daughters but NONE of his sons.

5. When one looks at Northern Guest who led the broodmare sire list in South Africa 10 times one sees that he carries Buckpasser as his broodmare sire. Buckpasser's X chromosome surely played an important role in that success (not just a minor role).

The statements of Byron Rogers in the Mares In Great Sires should not be taken as gospel truths. He is selling research on horses and cannot be objective in his analysis. He certainly wants to push his agenda to make big bucks. . To say that the variant that reached statistical significance on the X chromosome is not even in the top ten in importance is questionable to begin with and since information on that variant is not available to the public I take what he says with a grain of salt.

[DDT]

Stan

You continue to say the same things over and over in an attempt to prove your conclusions, enough already. You simply ignore the fact that once all of these daughters go into production they do not pass on their X chromosome as it was received from their sire, they pass on a recombined version that could have very little of the original X or quite a bit, Mother Nature determines just how much. This fact alone puts a real damper on the suggestion that there is something significant present on the X chromosome going to broodmare sire success. You are entitled to your opinion as long as you remember it is only an opinion no matter how many times you reiterate it.

DDT

[Pan Zareta]

And then you so conveniently misquoted my first statement made in the first post of this thread. I did not say dictates alone. My statement was as follows: This data regarding Buckpasser may indicate that his X chromosome may dictate or contribute to his success as a broodmare sire.

Your statement "as follows" above is not a verbatim quote from the initial post of this thread. Your subsequent claims about the relevance of the X to broodmare sire success err closer to "dictate" than "contribute" and are supported only by circumstantial evidence that cannot prove what's happening at the genomic level, no matter how often it's reposted. Only genome-based evidence can even begin to do that. Not all such evidence that's available in the public domain and relevant to the TB has been underwritten by commercial interests.

Have you no scruples whatsoever about simultaneously citing (and overstating the case while doing so) Alan Porter's work as published in the mid 1990s in support of your beliefs while claiming that his partner in Performance Genetics "cannot be objective" about their current research? When you've reviewed all of the available genome based evidence relevant to the TB and from that can dispute their findings as reported in 'The Mares in Great Sires' thread, please do so. No source of information is so impeccable as to be exempt from well-informed critical scrutiny. Until then, however, it's your remarks that should be taken with the proverbial grain of salt.

[stancaris]

Pan Zareta: My original statement from my first post in this thread was as follows:
"It seems likely that X linked inheritance dictates or contributes to the success of Buckpasser as a great broodmare sire." I never really wavered from that post. I believe the X chromosome plays an important role in broodmare sire success.

You believe the X chromosome at best plays only a minor role in broodmare sire success.

You continue to use Byron Rogers statements in the Mares in Great Sires thread as absolute truths and also as definite proof that the X is at best of only minor importance to broodmare sire success.

The statements he made in that thread were biased. He is selling performance genetics to people who are willing to pay big bucks for that information. Mr. Rogers himself stated that there are variants on the X chromosome that relate to elite performance and one of them reached statistical significance. I surely would like to know the function of that variant gene on the X that reached statistical significance. And I would like to know how he can rank these variants with regard to importance.

Statistical significance does not mean importance; it means the variant is not likely to be due to chance. P values of .05 or lower simply mean the statisitic was not likely to be due to a random occurrence like flipping a coin 10 times and getting 8 heads in a row.

Just because Alan Porter and Ann Peters book in 1995 Patterns of Greatness is 19 years old does not make it obsolete or wrong. Those statements made about Buckpasser's dam, Busanda and Sec's dam, Somethingroyal hold true today. Could it be the X chromosome from those dams have something to do with broodmare sire success?

Oh, by the way, just a side note--- the winner of the Travers, Will Take Charge has Dehere as his broodmare sire and Dehere is a maternal grandson of Secretariat. The place horse Moreno has AP Indy as his broodmare sire and AP Indy has Secretariat as his broodmare sire. The show horse, Orb, has Unbridled as his broodmare sire and Unbridled has Buckpasser as his third damsire.

[Pan Zareta]

You believe the X chromosome at best plays only a minor role in broodmare sire success.

That's not what I "believe". That's what the available genome-based evidence indicates. In regard to which chromosome(s) is/are most/more important to performance success, unlike you I have no beliefs, opinions, biases, or reputation built on incorporating X passing positions as a factor in handicapping. If you're going to be meticulous about identifying the conflicting interests of others, you really should disclose your own as well.