Buckpasser in the X

[stancaris]

Pan Zareta: In True Nicks: Leading Commercial Sires: Who Will Carry On The Lines which was written by Alan Porter on Aug. 12, 2013 there is a group discussion about broodmare sires in which Byron Rogers responds to Sceptre on Aug 21, 2013 at 8:41.

Byron Rogers response is as follows:

"Almost all performance genes are located on chromosomes other than Y or X. The only reason I say that there is the potential for a Broodmare sire effect, and I believe they do exist, is that there are additional variants associated with elite performance that are on the X chromosome. Thus, daughters of these sires must get at least one copy of these variants (and thus have the potential to pass it on to their offspring) while the sons of these sires don't get it. This is why I think that the concept of an elite Broodmare sire, like a Buckpasser, has the potential to exist. That said, in regression models the X variants don't rank nearly as high as other variants on other chromosomes."

Rogers himself states that there are additional variants on the X chromosome that are associated with elite performance and even goes on to say that the pattern of inheritance from broodmare sire to daughters and none of the sons makes him think that the idea of the elite broodmare sire has the potential to exist.

His last sentence dealing with regression models and how they rank these variants is really up for debate. What is a regression model? How are these variants ranked? If its p value, then the ranking system has nothing to do with importance because p value only indicates that the variant was not due to chance. Variants with a p value of .05 are not necessarily less important than variants with a p value of .0000005.

[Pan Zareta]

Pan Zareta: In True Nicks: Leading Commercial Sires: Who Will Carry On The Lines which was written by Alan Porter on Aug. 12, 2013 there is a group discussion about broodmare sires in which Byron Rogers responds to Sceptre on Aug 21, 2013 at 8:41...........

(The quote taken from a comment posted to that entry in the Truenicks blog that wasn't quite rendered verbatim may be found in full original context here.)

Stan, the remarks in question are a de facto summary of the information provided to you by same source during the course of 'The Mares in Great Sires' thread. If you must ask what a regression model is how could you possibly have any informed opinion on whether their methods for ranking variants are "up for debate" or not?

[stancaris]

Pan Zareta: Byron Rogers recent quote from Aug 21, 2013 at 8:41 AM is different from his view that appeared in the Mares in Great Sires thread back in 2011.

Byron stated the following in that recent response to Sceptre on Aug 21,2013:

"The only reason I say that there is the potential for a Broodmare sire effect, and I believe they do exist, is that there are additional variants associated with elite performance that are on the X chromosome. Thus, daughters of these sires must get at least one copy of these variants (and thus have the potential to pass it on to their offspring) while, the sons of these sires don't get it. This is why I think that the concept of an elite Broodmare sire, like a Buckpasser, has the potential to exist."

In the thread The Mares in Great Sires, Rogers never mentioned anything about the basic pattern of sex linked inheritence from a sire to his daughter and then to their offspring. He never mentioned anything about the fact that a sire cannot pass on his X chromosome to a son. This basic pattern is crucial to an understanding of why X linked inheritence is important to Broodmare sire success. Sons of Buckpasser's daughters who receive variants that relate to elite performance on their X chromosome will express those good traits because they have nothing on their Y chromosomes to suppress it.

Rogers himself states that the Broodmare sire effect has the potential to exist because of this above sex linked pattern which involves the transmission of variants on the X chromosome that relate to elite performance. He never states that at best the X chromosome is of minor importance to broodmare sire success as you have so often reiterated.

OK, maybe their method of ranking variants is not debatable. Maybe I should just accept his statements about ranking variants as being absoultely true. But I would still like to know how these variants on the X chromosome were ranked. Why were other variants on other chromosomes ranked higher in importance? Is it possible to ascertain that information or is it kept as a secret.

[Pan Zareta]

Pan Zareta: Byron Rogers recent quote from Aug 21, 2013 at 8:41 AM is different from his view that appeared in the Mares in Great Sires thread back in 2011.

Byron stated the following in that recent response to Sceptre on Aug 21,2013:

"The only reason I say that there is the potential for a Broodmare sire effect, and I believe they do exist, is that there are additional variants associated with elite performance that are on the X chromosome. Thus, daughters of these sires must get at least one copy of these variants (and thus have the potential to pass it on to their offspring) while, the sons of these sires don't get it. This is why I think that the concept of an elite Broodmare sire, like a Buckpasser, has the potential to exist."

In the thread The Mares in Great Sires, Rogers never mentioned anything about the basic pattern of sex linked inheritence from a sire to his daughter and then to their offspring. He never mentioned anything about the fact that a sire cannot pass on his X chromosome to a son. This basic pattern is crucial to an understanding of why X linked inheritence is important to Broodmare sire success. Sons of Buckpasser's daughters who receive variants that relate to elite performance on their X chromosome will express those good traits because they have nothing on their Y chromosomes to suppress it.

Rogers himself states that the Broodmare sire effect has the potential to exist because of this above sex linked pattern which involves the transmission of variants on the X chromosome that relate to elite performance. He never states that at best the X chromosome is of minor importance to broodmare sire success as you have so often reiterated.

There was an obvious need for him to mention the specifics of X linked inheritance in the course of comments to the Truenicks blog entry but no such need in 'The Mares in Great Sires' thread here. During that thread he cautioned you on more than one occasion about "overstating" and "over-rating" the relevance of the X to performance/broodmare sire success, something you're still trying to do. "Minor" best describes the X's relevance in that regard per genome-based evidence reported by a variety of sources. It does not preclude those variants being of some advantage to broodmare sire success ("broodmare sire effect") when, first, environmental and more performance-relevant genetic factors conspire to place and keep a stallion in the top tier of the TB breeding population which is where elite broodmare sires are figuratively and most often literally born.

OK, maybe their method of ranking variants is not debatable. Maybe I should just accept his statements about ranking variants as being absoultely true. But I would still like to know how these variants on the X chromosome were ranked. Why were other variants on other chromosomes ranked higher in importance? Is it possible to ascertain that information or is it kept as a secret.

You've previously been referred to published findings from full TB genome scans. The main focus of these is usually certain autosomal SNP variants determined to be of highest relevance to racing performance. You've dismissed the findings, claiming the information has nothing to do with the X, ignoring the patently obvious implication that the most relevant variants are just not on it. If you want to know which variants on other chromosomes are ranked higher in relevance and why, have another look at the previously cited reports.

[stancaris]

Byron Rogers, himself, stated: "there are additional variants associated with elite performance that are on the X chromosome. Thus, daughters of these sires must get at least one copy of these variants (and thus have the potential to pass it on to their offspring) while, the sons of these sires don't get it. This is why I think that the concept of an elite Broodmare sire, like a Buckpasser, has the potential to exist."

I interpret that quote to mean that the X chromosome is important to broodmare sire success and played more than a minor role in the widespread success of the great broodmare sires: Secretariat and Buckpasser.

Autosomal variants certainly had an influence on the above greats as broodmare sires. Busanda's X and Somethingroyal's X were not just run of the mill.

[Pan Zareta]

Byron Rogers, himself, stated: "there are additional variants associated with elite performance that are on the X chromosome. Thus, daughters of these sires must get at least one copy of these variants (and thus have the potential to pass it on to their offspring) while, the sons of these sires don't get it. This is why I think that the concept of an elite Broodmare sire, like a Buckpasser, has the potential to exist."

I interpret that quote to mean that the X chromosome is important to broodmare sire success and no doubt played more than a minor role in the widespread success of the great broodmare sires: Secretariat and Buckpasser.

When everything that he's reported about the relevance of autosomal and X variants is taken into consideration your intepretation overstates the X's role in broodmare sire success. From his remarks in full original context the only reasonable and logical interpretation is that even the favorable X variants are dependent variables, dependent upon the presence of favorable autosomal variants and environmental factors before one or more of them may offer any advantage to performance and/or broodmare sire success.

Was sheer luck of the X recombination 'shuffle' the most important factor in Buckpasser's greater success as a broodmare sire v. his two ungelded half-brothers? An extremely unlikely scenario.

[stancaris]

Busanda's X chromosome was not just a run of the mill X and her son, Buckpasser, transmitted that superlative X to all of his daughters. None of his sons could get that X. The fact that Busanda generated three stakes winners from only 9 runners and one of them became Horse of the Year and leading broodmare sire 4 times is evidence supporting the idea that her X chromosome was important in that process. It did not just play a minor role.

Somethingroyal's X chromosome was not just a run of the mill X and her son, Secretariat, transmitted that superlative X to all of his daughters. None of his sons could get that X. Somethingroyal was a great broodmare who produced 4 stakes winners and 5 stakes placed runners from only 15 offspring that made it to the races. Among those stakes winning sons was the fabulous Secretariat, HOY and Triple Crown Winner, champion Sir Gaylord, Syrian Sea etc. Somethingroyal's X did not just play a minor role in that success.

Somethingroyal and Busanda were great broodmares and they gave us two Horses of the Year that went on to become great broodmare sires. The X chromosomes transmitted by Somethingroyal and Busanda to leading broodmare sires- Secretariat and Buckpasser respectively were not just ordinary genetic threads that played at best only a minor role in their great success. Secretariat and Buckpasser are found in the X passing position (as either the broodmare sire or the second damsire) in 42% of the top 10 broodmare sires over the last 5 years.

Somethingroyal and Busanda were awesome broodmares.

[DDT]

Stan

Sir Gallahad, III led the broodmare sire list 11 times, Princequillo led the list 8 times and Mr. Prospector led the list 9 times, so I guess these 3 stallions had a super X ala Buckpasser and Secretariat. In my opinion, environmental influences and exposure to quality books while standing at Claiborne is the primary reason for their success as broodmare sires, and of course you do know where Buckpasser and Secretariat held court do you not?

DDT

[Pan Zareta]

Prior to the availability of genome-based evidence the role of variants on the X in any kind success was unknown. Since such information has become available it's been reported that the variants most relevant to elite TB performance are on the autosomes, the overall diversity of which is somewhat greater than that of the X, but that there are still a few variants on the X of lesser relevance to elite performance, one of which reaches statistical significance.

Those facts do not support conclusion that the X is of greater than minor relevance to elite performance and therefore to broodmare sire success as defined by daughters' progeny earnings, or that the production records of Busanda and Somethingroyal (or any other outstanding broodmare) were attributable in any large part to the X, but neither do they preclude the possibility that X variants may afford some advantage between sires when other genetic and environmental factors favorable to success are roughly equal.

This does not "downgrade" the X's role in broodmare sire success since that role was heretofore unknown.

[stancaris]

The workings of genetics is not that simple that based on genomic research you can downgrade the X chromosomes of those great broodmares as having just a minor role in the broodmare sire success of Buckpasser and Secretariat.

There are genes on the X chromosome that regulate many important functions such as bone growth, muscle fiber strengthening etc.

There are genes on the X chromosome that turn off and turn on genes found on other chromosomes (imprinting genes that work only in one sex and not the other).

Position in the pedigree counts. Buckpasser and Secretariat have a profound influence on the leading broodmare sires over the last 5 years. 42% of the top 10 broodmare sires over the last 5 years carry one of the above great broodmare sires as either their broodmare sire or their second damsire. That means that 42% of the top 10 broodmare sires over the last 5 years are carrying either Buckpasser or Secretariat in the X passing position close up in their pedigrees. That's a large chunk of the top 10 leaders and is strong evidence that the X chromosome plays more than just a minor role in that success.

Buckpasser and Secretariat gave all their daughters 100% of their X chromosome. Busanda and Somethingroyal surely had more than a minor role to both of the above stallion's great influence as broodmare sires.

[DDT]

Stan

I do not believe that any person on this forum is denying the fact that ALL of the DNA passed on by Somethingroyal and Busanda to Secretariat and Buckpasser provided a major influence in their success as runners, stallions and broodmare sires. This discussion concerns their X chromosomes alone and whether or not the genes carried on the X are a primary influence on the success of these two as broodmare sires.

You continue to use the figure 42% when in fact you are talking about 4 representatives out of 10 which is actually 40%. You could say they are represented by 4 out of the top 10 broodmare sires for the last 5 years, but in your mind 42% makes a bigger impact. That is what you are all about Stan, sensationalism and argument instead of discussion of the true facts of the matter.

DDT

[Pan Zareta]

There are genes on the X chromosome that regulate many important functions such as bone growth, muscle fiber strengthening etc.

There are genes on the X chromosome that turn off and turn on genes found on other chromosomes (imprinting genes that work only in one sex and not the other).

Expression of imprinted genes depends on parent-of-origin, not the individual's gender. There are genes on every chromosome that regulate important functions and 'interact' with genes on other chromosomes. What defines the genetics of elite TB performance is not the genes per se. but variations of the code in and around them. No variation = no potential advantage/disadvantage, and there is less variability on the X to begin with.

[stancaris]

Pan Zareta: In True Nicks Leading Commercial Sires written by Alan Porter there is a discussion about variants on the X chromosome that are associated with elite performance. In that discussion Rogers states that there is a potential for the broodmare sire effect because of these variants and the fact that a sire transmits these variants on his X to all his daughters but none of his sons is the main reason he believes there is a potential for the broodmare sire effect.

Then Rogers goes on to state: "in regression models and neural networks the X variants don't rank as high as other variants on other chromosomes."

You said that I can readily find out from some sources exactly how these variants were ranked and how regression models and neural networks actually can be used to place these variants in order of importance

Could you tell me exactly where I can find out how these variants were ranked?

[Pan Zareta]

Could you tell me exactly where I can find out how these variants were ranked?

You're feigning ignorance-driven scepticism of valid analytical methods that you publicly accept and cite without criticism when you think the results confirm your beliefs. I've posted links before and there's way more than enough mind-numbing repetition in this thread already.

[stancaris]

Pan Zareta: How about other people who read this thread? Don't you think they also would like to know where they can find an article that explains how and why variants discovered on the X that relate to elite performance are ranked lower in importance to variants discovered on the autosomes that relate to elite performance.

My guess is that your bias on this matter has made you say something ridiculous like I am faking ignorance. Thats not the case. Where can we find an article that explains how the variants are ranked in importance? Does such an article actually exist?