Buckpasser in the X

[xfactor fan]

Couldn't say, about the eyes and ears, but what I've seen is that the forehand--neck,chest and withers seem to be passed together most of the time. And they seem to be X ,or pseudo X linked.

Here's what to look for if you want to look into this theory. And it is a theory, not holy writ, and the TB's aren't talking to me.

Test for X linkage. Basic assumption is that a collection of traits are located near each other on the X, so that when recombination does happens the region moves together.

Males will express only the one X they have. Sons of a stallion will not have their sire
s X, so they should not express the trait.

Daughters will have a copy of their sires X, and one recombined X with DNA from the maternal Grandsire plus recombined DNA from other maternal sires.

Males will resemble (forehand only) the maternal side of the pedigree, not the male.

Further linkage testing look for mares with several sons. There is the potential for two types of conformation, one following each X.


The theory predicts that the X first damsire will show up in colts 50% of the time. This is halved per generation.


Breeders who follow type to type matings muddle the results. The process works best using horses with distinctive conformation.

The Secretariat/Sir Gaylord/Somethingroyal/Princequillo/Papyrus conformation is everywhere.

Buckpasser or Ribot have a less common conformation.

Riverman has a very short neck.

Nureyev / Forli is pretty easy to spot.

It helps to look at conformation photos of stallions in racing trim, before they bulk up.

Good luck

[Linda_d]

H
Early on I started looking at mules. Most donkey jacks are about the same size and shape there being less variation in Donkey breeds than horses breeds. But Belgian Mules, don't look like Saddle Mules, or Arab mules, or Quarter Horse mules. Body type and over all size do seem to come from the dam. And anyone who says that all mules look alike hasn't seen many mules.

Here's an article about hinnies, the donkey mare x stallion cross, that seems to fit here: http://en.wikipedia.org/wiki/Hinny.

[stancaris]

Pan Zareta:

I started this thread by stating that 25% of the top 20 Broodmare sires over the last 3 years carry Buckpasser in the X passing position but only approximately 10% of horses from the general population carry Buckpasser in the X passing position. This translates into an impact value of 2.50 or one might say that Buckpasser is appearing in the X passing position more than twice as often as statistical expectation.

I then concluded that the data above supports the idea that the X chromosome is of major importance to that success. Doesn't that seem logical? How come you so conveniently never responded with any statements regarding the above statistics which I used to start this thread?

I am not alone in regards to thinking about the power of the X chromosome.

Jay Leimbach in an article entitled Broodmare Power in Genetics refers to the power of the X chromosome specifically in the 14th paragraph from the top in which he states, "So great broodmare sires Sir Gallahad, War Admiral, and Buckpasser might well have benefitted from an outstanding X chromosome which they transmit to all their daughters but none of their sons."

Alan Porter and Anne Peters co-authored Patterns of Greatness II and on page 191 in the section about Buckpasser they wrote:

"Finally, its worth considering just why Buckpasser was relatively unsuccessful as a sire of sires, and yet features as the broodmare sire of so many good colts, who subsequently became influential stallions. Can sex- linked inheritance from the superior mare, Busanda, have anything to do with it?"

On page 212 the last paragraph in their description of the great broodmare sire, Dr. Fager, they wrote:

"If Dr. Fager wasn't outstanding as a sire, he was certainly an excellent broodmare sire- something which those with faith in sex-linked inheritance might well have expected from a stallion out of such a great producing mare as Aspidistra. Over 67% of Dr. Fagers daughters have produced black type performers.

Rommy Faversham believes that the X chromosome is an important contributing factor to the success of a broodmare sire.

Another interesting description regarding the X chromosome is found in an article entitled (pdf) Sex Bias in the Thoroughbred- Pedigree Dynamics.

This article deals with Jungle Boys sons and daughters that raced from 1980-1990. It turns out that 67% of Jungle Boys stakes winners were fillies and only 33% were colts. Thats a pretty large sex bias. Could it be that the X chromosome has something to do with this pattern?

Brogers says that there is one variant on the X that reached statistical significance but its not in the top ten in importance. I really question how they possibly can rank these variants and once again can we read anything about this particular variant which he says is statistically significant but does not rank among the top ten in importance?

[stancaris]

Pan Zareta: I want to qualify one of my questions above? The question was how come you did not respond to my stats in the original post (the stats about Buckpasser in the X in 25% of the top 20 broodmare sires but is only found in the X in around 10% of the general population?

You did respond to that question and your answer was--- the high quality of the mares that were sent to Buckpasser allowed him to become a great broodmare sire. I ask, how come the high quality of the mares sent to Buckpasser didn't allow him to become a great sire of sires?

[DDT]

Stan

I would like to clarify my answering post to you about Buckpasser in the X passing position. I wanted to comment on why you were stating it that way, was it so the percentage would climb to 25% instead of 10%? What do you think the percentages in the breed as a whole and on the leading broodmare sires list was 10 years ago or 15 years ago?

As to why Buckpasser was not a sire of sires, how many superior running colts did he sire as opposed to his champion and superior fillies? There are other reasons for this but I care not to argue them with you.

DDT

[Pan Zareta]

I ask, how come the high quality of the mares sent to Buckpasser didn't allow him to become a great sire of sires?

First, you would have to provide the criteria you use to distinguish "great" from, say, "average" sire of sires. Plenty of Buckpasser's sons performed well on the track and entered the stud. He is still active in tail male. If by "great" you mean a sire deceased for several decades but still active in tail male at the top tier of TB breeding through descendants of multiple sons, such as Nasrullah, for one example, the answer is simple. No matter how well bred the horse the odds are overwhelmingly against that happening because the pressure against remaining in the top tier of the breeding population is weighted so heavily against males who are fewer in number in the total breeding population to begin with. Nasrullah's tail male descendancy has simply done better v. those odds than Buckpasser's but Buckpasser's has done better than most.

I am not alone in regards to thinking about the power of the X chromosome.

Stan, what have Jay Leimbach, Alan Porter, Anne Peters, and Rommy Faversham had to say about the X chromosome in the last few years since the equine genome was sequenced, SNP chips developed and applied to study of the TB genome? (I trust you do realize that Alan is a partner in Performance Genetics.)

Studying pedigree, comformation, phenotype, biometry, performance, etc. is useful and interesting and sometimes suggestive but never probative of particular modes of inheritance. The genome is probative.

Brogers says that there is one variant on the X that reached statistical significance but its not in the top ten in importance. I really question how they possibly can rank these variants and once again can we read anything about this particular variant which he says is statistically significant but does not rank among the top ten in importance?

Statistical significance is a universally accepted method of ranking relevance. For more information about the X SNP that's one of the 37 variants relevant to elite performance I'd suggest you contact Brogers or Alan Porter.

[DDT]

Stan

Just a few minutes of research reveals that Buckpasser had at least 17 sons that were pretty good runners and did well enough at stud. Silver Buck sired duel classic winner Silver Charm and Buckaroo sired Derby winner Spend a Buck. None of these sons received his X chromosome.

DDT

[stancaris]

Pan Zareta: You honestly feel that since genomic research has discovered variants on autosomes that are related to elite performance that all these geneticists are just going to change their mind and assign a lot less importance to the X chromosome's role in broodmare sire success. I have evidence to the contrary.

That article written by Jay Leimbach on Broodmare Sire Power was written in 2012. He still believes in the power of the X chromosome.

Rommy Faversham answered one of my emails two months ago in which I questioned him about the importance of the X chromosome for Broodmare sire success and he answered by saying it is very important for broodmare sire success.

I cannot state anything about Porter or Peters at this time. They may or may not have changed their mind about the importance of sex-linked traits for broodmare sire success. Since Porter is a partner in a genomic research firm his answer will be obvious.

I do not believe that the discovery of variants on autosomes that are related to elite performance in any way proves that the X chromosome does not play an important role in broodmare sire success. The only thing those discoveries of variants on autosomes proves is that there are codes on autosomes that are related to elite performance.

What about that article called Sex Bias in Thoroughbreds where they studied the sons and daughters of Jungle Boy and found 67% of his daughters were stakes winners whereas only 33% of his sons won stakes. Doesn't that seem to suggest that the X chromosome transmitted by Jungle Boy was superlative? That X was transmitted to all his daughters and none of this sons.



Brogers said the X chromosome has variants that relate to elite performance and one of them is statistically significant. It is possible that one variant can make a big difference in the phenotype. for ex one nucleotide base difference in the DNA molecule that governs blood cell shape can cause sickle cell anemia.

I surely would like to know what that variant does in the racehorse.
He says its not in the top ten in importance? How do they come up with that ranking. If its statistically significant, that's important.

I have done some research on Buckpasser in the X as a handicapping indicator and have found his presence to be statistically significant in the Derby and Belmont stakes. By the way, Orb and Revolutionary both have Buckpasser in the X passing position and finished first and third in this year's Derby.

[Pan Zareta]

Stan, Leimbach, Porter, Peters and Faversham are all professionals in the TB industry and at least two, maybe all, have academic background in the sciences (Faversham's an MD) but I'm pretty sure none of them are geneticists. Not that it's necessary to be geneticist to appreciate the import of the information that was provided to you in 'The Mares in Great Sires' thread. All that requires is understanding of the biological basis of inheritance, a modicum of common sense, and an open, unbiased, mind.

The article of Jay Leimbach's that you're referring to first appeared in Pedigree Post, Dec. 2007.

Given the tendency you've exhibited in various threads of this forum to parse facts and remarks out of context it seems prudent to take your statement about what Faversham (or anyone else) has told you with the proverbial grain of salt.

You apparently do not understand that the "variants" relevant to elite performance on the autosomes and the X are all SNPs, Single Nucleotide Polymorphisms, "one nucleotide base difference", one letter changed in the "codes"[sic]. You're just contradicting yourself by subordinating the "codes on autosomes" in one paragraph and emphasizing the "big differences" a change at a single nucleotide can make in a subsequent paragraph.

In regard to Jungle Boy, I find the skewed distribution by gender of his stakes winners probative of nothing. Sex-linked transmission is not the only possibly if there's some genetic mechanism, rather than random chance, coming into play there.

[xfactor fan]

To both stancaris and Pan Zareta.

As odd as this is going to sound, I suspect you are both correct.

I suspect that there is no specific mutation that can be detected by any current technology. Pan Zareta's point. However if a block of genes on the X controls conformation, and is in a region that doesn't easily recombine, this could be what stancaris is detecting via statistics.

One thing to look at is how did the book of mares bred to Buckpasser do with other stallons?

[Pan Zareta]

Just a few minutes of research reveals that Buckpasser had at least 17 sons that were pretty good runners and did well enough at stud. Silver Buck sired duel classic winner Silver Charm and Buckaroo sired Derby winner Spend a Buck. None of these sons received his X chromosome.

Further to the above-

Norcliffe got Champion Sprinter Groovy and MG1SW At the Threshold who got KD winner Lil E Tee
Buckaroo also got MG1SWs Roo Art and Lite the Fuse and MGSW Montbrook. All are/were popular and successful regional sires
Buckfinder got MG1SW Track Barron
Bucksplasher got MG1SW Buck's Boy
Spend A Buck got Brazilian Champion Pico Central
Silver Buck also got MGSWs Forever Silver, Time to Boogaloo and Silver Maiden

Etc.

[Pan Zareta]

I suspect that there is no specific mutation that can be detected by any current technology. Pan Zareta's point. However if a block of genes on the X controls conformation, and is in a region that doesn't easily recombine, this could be what stancaris is detecting via statistics.

That's not my point. My point is that genome-based evidence was presented here 18 months ago that conclusively refutes Stan's belief that the X chromosome may "dictate" or be anything more than a minor contributing factor to Buckpasser's success as a broodmare sire. Even without that evidence, anyone familiar with the published work on positive selection in the TB should realize it's ludicrous to ignore the autosomes in favor of the X.

If there's a block of genes in a recombination 'desert' on the X that control conformation, or anything else, there's no reason that any SNPs therein relevant to elite performance and therefore broodmare sire success would not have been picked up in the 70K SNP chip scan. If no such SNPs were detected then that block of genes is most likely stable across the TB population and has nothing to do with broodmare sire success.

[stancaris]

Pan Zareta: You are being dishonest with the statment you made above.

I NEVER said that the X chromosome is more important than any and all of the autosomes to Buckpasser's success as a broodmare sire.

The variants discovered on the autosomes do not prove that the X chromosome does not play a major role in broodmare sire success; they only prove that there are genes on the autosomes related to elite performance.

Are there any genes on the X that reached statistical significance? Yes, Brogers said there was one variant that did reach statistical significance
but it is not in the top ten of importance. That's a very vague kind of statement. A major contradiction: The variant on the X reached statistical signficance but it is not vital to the overall success of a racehorse.

Lots o Luck trying to decifer the meaning of the above especially when the research is not available to the general public.

[Pan Zareta]

I NEVER said that the X chromosome is more important than any and all of the autosomes to Buckpasser's success as a broodmare sire.

You've certainly inferred that but since you've never framed it in those exact terms I've edited the remark in the previous message.

The variants discovered on the autosomes do not prove that the X chromosome does not play a major role in broodmare sire success; they only prove that there are genes on the autosomes related to elite performance.

Are there any genes on the X that reached statistical significance? Yes, Brogers said there was one variant that did reach statistical significance
but it is not in the top ten of importance. That's a very vague kind of statement. A major contradiction: The variant on the X reached statistical signficance but it is not vital to the overall success of a racehorse.

Lots o Luck trying to decifer the meaning of the above especially when the research is not available to the general public.

There is nothing vague or difficult to decipher at all.

And relevant research WAS made available to the general public including you, at this forum 18 month ago, in the form of details of analysis of TB genome scans offered by someone who has no bias for or against any particular chromosome, just a vested interest in accurately identifying which areas of the genome are most relevant to elite performance. Paraphrasing those details in the simplest possible terms, there are 10 or more autosomal SNPs of greater statistical significance to elite performance and therefore broodmare sire success than the SNP on the X.

Genome-based findings are a specific and accurate basis upon which to identify genetic factors influencing elite performance and therefore broodmare sire success. Observations made from lists and pedigrees are not. The X chromosome is at most a minor contributing factor to broodmare sire success. It does not "dictate" broodmare sire success. It has no special "power" in that regard above and beyond the single SNP relevant to elite performance.

When do you plan to reply to DDT's post of Fri May 24 2013 3:19 pm? I too would like to know why you stated percentages the way you did.

[Jeff]

Stan,

Any commoner looking at a pedigree sees Buckpasser on the bottom side knows that's not a bad thing. It's common knowledge that Buckpasser daughters in a pedigree is a good thing.

Those pleading 'scientific' to deride the commonly known fact that Buckpasser in a pedigree is a good thing. Pretty much speaks for itself.

Stan, thank you for writing about Buckpasser, I always light-up to read anything about the great Buckpasser.

Jeff