Biomechanics, Inbreeding & Breakdowns

Understanding pedigrees, inbreeding, dosage, etc.

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Shammy Davis
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Postby Shammy Davis » Tue Jan 12, 2010 11:18 am


aethervox
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Postby aethervox » Tue Jan 12, 2010 12:14 pm

I definitely agree that there are multiple factors that make a great racehorse. So, what does a horse need to run fast and win races? (There's a very good summary of equine physiology at http://www.the-aps.org/press/aps/06/derby.htm)

Here's my opinion:

1. Good conformation.

Conformation would include stride length, which is an advantage to a horse because the longer the stride length, the more oxygen the horse takes into its lungs. It would also include girth size, as the lungs need room to expand as they take in air. It would also include bone size and hoof quality, as well as musculature and muscle types.

2. Good oxygen exchange, which includes, heart, lungs, spleen, nostrils

A large heart is an advantage because it can pump more blood. Also needed are lungs that can handle the blood pressure that the heart puts out.

There's an article at http://jeb.biologists.org/cgi/reprint/134/1/397.pdf that gives a good description of the reactions of a horse's heart and lungs during exercise.

3. Good attitude (i.e. will to win)

Even with the best conformation and the best oxygen exchange, if the horse doesn't want to run it doesn't mean anything. Man o' War's sister, Masda is a good example. She was 'wicked fast' when she wanted to run. Display, by Fair Play, is another example. According to the PQ database, he started 43 times, had 18 wins, 5 places and 1 show. He was also known as the most difficult horse to start and threw temper tantrums at the gate. Despite this, he was considered a great stakes horse and stayer. How many more races would he have won if he'd had a slightly better temperament?

IMHO, when you get a horse that is above average for all three of these factors, you get a champion.

For example, with Secretariat you had a horse who defied expectations. In the Derby, he ran each quarter mile faster than the one before, and still had enough energy to act up in the winner's circle. He had a long, energy efficient stride (there was very little overlap, i.e. time with two feet on the ground, in his stride which meant that he got the most propulsion from each individual leg). He had a large girth -- his saddle girths had to be custom made because the largest ones available commercially were too small. And, as was discovered during his autopsy, his heart was much larger than normal and it was perfectly healthy, so he was able to distribute more oxygenated blood to his body with each heart beat. No wonder he ran away from the field at the Belmont. :shock:

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Postby Shammy Davis » Tue Jan 12, 2010 12:42 pm

Don't forget SECRETARIAT'S quick recovery following races.

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diomed
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Postby diomed » Tue Jan 12, 2010 1:18 pm

Xfactor, regarding the difference in the female lines to Secretariat and Sham, you could be on to something here.
Lest we forget, Secretariat is from the same family as QH freak Dash For Cash.
Coincidence? I tend to think not.
MtDNA could very well be the freak factor here.
Also, if you look at Secretariat there is also a deep clustering of the same family #2 going on.
Does MtDNA mutate when reconnected with each other? Something to ponder.

I am one that believes that pedigree does give out clues.

Science does the rest.

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Pan Zareta
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Postby Pan Zareta » Tue Jan 12, 2010 3:32 pm

diomed wrote:Xfactor, regarding the difference in the female lines to Secretariat and Sham, you could be on to something here.
Lest we forget, Secretariat is from the same family as QH freak Dash For Cash.
Coincidence? I tend to think not.
MtDNA could very well be the freak factor here.
Also, if you look at Secretariat there is also a deep clustering of the same family #2 going on.


The only mtDNA haplotype identified to date in ff#2 is a haplogroup D type (specifically, sub-haplogroup D3 type). D is the most common haplogroup globally and within many breeds, including the TB. It was within samples from the most common TB haplogroup that Harrison & Turrion-Gomez (2006) identified three mtDNA haplotypes that have demonstrated better performance at speed/short distance. No surprise. Flight is the species' best defense, so it would be surprising if such aptitude was anywhere other than the most common haplogroup. (Only one haplotype therein demonstrated even a slight correlation with distance/stamina.) But whether Secretariat & Dash For Cash had one of those 3 haplotypes is unknown. There are a lot of different haplotypes within haplogroup D, and the 2006 study didn't fully define its sub-haplogroups, or correlate haplotypes with family #s.

Does MtDNA mutate when reconnected with each other? Something to ponder.


MtDNA has the 'equipment' to recombine, but does not normally do so in placental mammals since the sperm's mitochondria are used up at or prior to fertilization. Other types of recombination are possible, but equally or even more rare.

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Postby xfactor fan » Tue Jan 12, 2010 6:51 pm

Pan Zareta,

Are you using the nomenclature from the Hill study? They put Family 2 as belonging to the F group, and family 9 as either G, or A.

Or is the Hill study outdated now? Or has that set of family grouping gone the way of the Dodo?

Keeping up with the changes is a full time occupation these days.

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Pan Zareta
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Postby Pan Zareta » Tue Jan 12, 2010 9:10 pm

xfactor fan wrote:Pan Zareta,

Are you using the nomenclature from the Hill study? They put Family 2 as belonging to the F group, and family 9 as either G, or A.


The report by Hill et al. (2002) labelled as 'F' the mtDNA haplotype found in all samples from families 2,7,8,17,22 and one or more but not all samples from families 1 and 16. F was one of several haplotypes identified by the study that are part of clade aka: haplogroup D (nomenclature of Vila 2001, which was followed in the 2002 report for discussion of clades). Their haplotype G, found in some samples from family 9 is also in haplogroup D (sub-haplogroup D1, as defined by Jansen et al. 2002). Their other family 9 haplotype, labelled 'A', is in haplogroup A.

Or is the Hill study outdated now? Or has that set of family grouping gone the way of the Dodo?


Based upon a review of published reports re. mtDNA in other breeds, and analysis of TB samples in GenBank, I think the conclusion reported 2002 that all haplotype F TB's might share a common founder ~1650-1750 is premature at best and probably dead wrong. It ignores an indel common to the sequences from families 7, 17, and 22 (and also found in several other breeds). Also, there are multiple GenBank TB sequences identical to 'F' (as found in families 2,8, and 16) in the section of D-loop sampled for that study, but segregating at one or more base pairs elsewhere in D-loop.

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Postby xfactor fan » Tue Jan 12, 2010 11:27 pm

Thanks for the clear explanation of haplotypes vs haplogroups. Makes a lot of sense now.

I'll admit to scratching my head and wondering about why the classified everything as "F", when there were "segregating at one or more base pairs elsewhere in D-loop". This indicated that there were very deep differences in the populations, and one population of "F's" were probably only distantly related to the other population.

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Pan Zareta
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Postby Pan Zareta » Wed Jan 13, 2010 2:08 pm

xfactor fan wrote:I'll admit to scratching my head and wondering about why the classified everything as "F", when there were "segregating at one or more base pairs elsewhere in D-loop". This indicated that there were very deep differences in the populations, and one population of "F's" were probably only distantly related to the other population.


They didn't sequence the section of D-loop that tends to be more polymorphic in sub-haplogroup D3, and there was nothing in the 2002 report to suggest the sequences designated haplotype 'F' were not 100% the same, other than the fact that they reported finding 3 indels. Those indels were ignored for purposes of qualifying and comparing TB mtDNA haplotypes. You have to examine the sequences deposited in GenBank to find out where they are. One of them was betw bps 15528-15532 (a cytosine repeat) and found in samples from families 7, 17, and 22. Deletions and bp substitutions w/in that repeat have since been recognized as a valid point for segregating haplotypes in haplogroup D (see the report on Irish Draughts published by McGahern et al. 2007, for one example).

The D-loop sequence used to analyze TB haplotypes for the 2002 report was bps 15456-15837. The samples designated 'F' (but without the deletion) from all of fams. 2 and 8 and part of 16 are identical within that range with 13 GenBank sequences (2 TB) which are inclusive of 100% of the D-loop. But those 13 sequences segregate into as many as 13 different haplotypes downstream of 15837. The two TB samples differed by base pair substitutions and indels. In most haplogroups haplotypes can be reliably defined within the sequence used for the 2002 study. Unforunately, that doesn't appear to be true of sub-haplogroups D1 and D3, which is a problem b/c evidence suggests about ~25% of TBs are within that subset.

To return to the OT-
diomed wrote:Lest we forget, Secretariat is from the same family as QH freak Dash For Cash.
Coincidence? I tend to think not.
MtDNA could very well be the freak factor here.
Also, if you look at Secretariat there is also a deep clustering of the same family #2 going on.



Seven of 32 lines in his 5 gen. pedigree are ff#2. Five of those are via Imperatrice, and would be shared by Dash For Cash, albeit one generation further back.

Perhaps the breed has evolved to the point where complementary traits are somewhat more likely to be found in individuals with the same mtDNA haplotype, but that's pure speculation. If their was any particular theory behind the breeding of Secretariat or Dash For Cash (both 5 gen. outcrosses) it was most likely 'breed the best to the best and hope for the best', i.e. any concentration of a particular ff was incidental. If mtDNA is even part of the freak factor, it was b/c it and all other genetic and environmental factors were superbly complementary.

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Postby Shammy Davis » Thu Jan 14, 2010 5:44 pm

Forgive me, but Pan Zareta and XXF need to start speaking in layman's terms or my participation in this thread is awash.

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Postby Pan Zareta » Thu Jan 14, 2010 10:17 pm

Shammy Davis wrote:Forgive me, but Pan Zareta and XXF need to start speaking in layman's terms or my participation in this thread is awash.


I do apologize for the jargon. In (I hope) plain English, the points I was trying to make are:

(1)Family 2's mtNA haplotype *could* be unique to that family, contrary to conclusions drawn by and from the study published 2002 by Hill et al.

(2)*If* the family 2 haplotype correlates with any particular aptitude it's almost certainly sprint/speed not distance/stamina.

(3)MtDNA haplotype may be one small piece of the 'freak factor' puzzle, but I see no evidence that it's more important than any other genetic or environmental factors.

* * *

Fwiw, several pages of this thread ago I suggested a loose protocol for an extremely rough and unscientific evaluation of inherent soundness by analyzing the avg. # of starts and yrs. raced for foals of the more popular sires foaled ~1950. During the most recent blizzard, I spend a couple of days doing that. Overall, the most obvious trend that became apparent was that the avg. # of lifetime starts, starts/yr. and yrs. raced decreased over time for all the sires I looked at (Ambiorix 1946, Bold Ruler 1954, Native Dancer 1950, Nearctic 1954, and Round Table 1954). That smacks of change in the industry, not the gene pool.

Ambiorix hit the breeding shed first and among 27 of his sons (out of mares by *Blenheim, Count Fleet, Menow, and Nasrullah) average lifetime starts was 60.3, in 4.8 yrs. on the track. None of the other sires came very close to those avgs. Among the three 1954 models, the sons of Nearctic & Round Table had better avgs. than Bold Ruler's sons. But fewer of Bold Ruler's sons were gelded, so the interests of the breeding & sale ring $$ may have skewed his numbers. Even the oft-maligned (at least for the quality of his bone) Native Dancer got some warhorse geldings.

Nothing jumped out of these stats to shake my conviction that steroids have done far more to diminish soundness than any heritable trait present in the TB gene pool. That's my story & I'm stickin' to it. ;)

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Postby Shammy Davis » Thu Jan 14, 2010 11:16 pm

Pan Zareta: Nice story to stick too. Thanks for the statistics. It puts things into perspective.

XXF made reference to the family of SHAM as 9b. Interestingly, I just brought a mare to our farm out of the same family. She had 85 starts with over 60% in the money. Like SECRETARIAT, SHAM was not a particularly good sire. That might be because he was not sought after, I don't know. But, I think you agree it is an interesting comparison.

ALYDAR and AFFIRMED might also be an interesting study.

I think ZENYATA and RA are intriguing studies also although they are from different foal crops.

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Postby xfactor fan » Fri Jan 15, 2010 1:43 am

Shammy,

Putting more mtDNA info into basic English.

mtDNA is the little energy bodies that live in the cell cytoplasm. (Think of a chicken egg--mtDNA lives in the egg white, and the chromosomes live in the yoke.

When creating the sex cells, the egg gets chromosomes, and cytoplasm containing mtDNA. Sperm get chromosomes, but are "stripped down for speed" and shed almost everything including most of their cytoplasm, and mtDNA.

So female chromosomes and female mtDNA meet male Chromosomes and a embryo is created. So all horses and humans too, carry the mtDNA from their maternal parent.

What Pan Zareta and I were gene geeking about is the Hill study published in 2002, a very readable version of this study is up on the TB Heritage site titled "Who's your Moma" Parts 1, 2 & 3. Where Hill and company tested a decent number of horses, and found (surprise, surprise) that some large number of horses did not have the mtDNA they should have.

For example every horse from that traces their female back to Old Bald Peg, should have the type of mtDNA.

The Hill study tested one part of the mtDNA, and assigned letters to the different varieties of mtDNA they found. (haplotype )

Haplotypes are arranged in Haplogroups, which also have letter designations. Which I of course missed entirely when reading Pan Zareta's post. Hence my complete confusion, and the assumption that things had changed (again) while I wasn't looking. Genetics has a habit of doing that, the field is expanding so fast.

The second part of the gene babble was about how the testing was done. The Hill study looked at only one part of the mtDNA, and found a whole lot of the "F" haplotype. Which would suggest the same common female ancestor. However when other studies looked at other parts of the mtDNA they found a number of differences within the "F" group. So think of F1, F2, F3, and so on.

Given the time frame of mtDNA--changes are very slow--it is unlikely that any of the F sub types share a ancestor in the historical time frame of the TB.

Pan Zareta, thank you for taking the time to crunch the numbers, and applying some science to the breakdown topic. You mentioned a few warhorse gelding from each sire. Just looking at geldings might give a true picture of soundness, as it eliminates the financial pressure to retire horses for breeding, which skews the statistics. Something you probably have figured out.

Drugs and steroids in particular are high on my list of culprits. The only thing you have to do is look at the numbers of horses that breakdown in the US (drugs allowed) vs the rest of the world (no drugs)

However, whatever they did at this last Breeders Cup seemed to have worked. No breakdowns.

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Postby aethervox » Fri Jan 15, 2010 8:51 am

diomed wrote:Xfactor, regarding the difference in the female lines to Secretariat and Sham, you could be on to something here.
Lest we forget, Secretariat is from the same family as QH freak Dash For Cash.
Coincidence? I tend to think not.
MtDNA could very well be the freak factor here.
Also, if you look at Secretariat there is also a deep clustering of the same family #2 going on.
Does MtDNA mutate when reconnected with each other? Something to ponder.

I am one that believes that pedigree does give out clues.

Science does the rest.


What's intriguing to me is how similar the conformation of Dash for Cash was to Secretariat. See http://www.circledhorses.com/dfc_and_secretariat.htm for details, including a conformation diagram with measurments of Dash for Cash done by a sculptor who did bronzes of both horses.

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Postby Shammy Davis » Fri Jan 15, 2010 5:17 pm

aethervox posted: . . .
What's intriguing to me is how similar the conformation of Dash for Cash was to Secretariat.


I'm talking off the top here, but Somethingroyal had 16 plus or minus foals. Are there any connections that can be made conformation wise w/Dash for Cash and them?

Wasn't there a full or half brother to SECRETARIAT that just passed away? I recall looking at a picture of him. He didn't remind me one bit of Big Red.