The Official "Speed Gene" thread.

Understanding pedigrees, inbreeding, dosage, etc.

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vineyridge
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Postby vineyridge » Thu Mar 29, 2012 10:02 am

No saying that Nearctic was C/C. He came to Canada where he was bred to only 14 or 17 mares who were pure GSB. All the rest have "impure" lines to American TBs. It's entirely possible that his C from Nearco met Cs from NA mares and produced C/C stallions who then spread the gene widely. Or he could have passed a single C and the pure volume of his son's get spread it more widely.

I would guess that Nasrullah was bred to more "pure" GSB mares but I haven't looked. Just looking at his pedigree and race record, he's a far more likely candidate to have been a C/C.
Last edited by vineyridge on Fri Mar 30, 2012 9:18 am, edited 1 time in total.
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Postby diomed » Thu Mar 29, 2012 10:27 am

I thought it was confirmed that Nearctic was a CC though. If not, then that information should not have been published. I don't doubt that there are C carriers from the old general studbook. It's probably more available through American lines but I still believe that it could have come from England and I am sure there was more than one source.

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Postby Pan Zareta » Thu Mar 29, 2012 12:49 pm

The only published evidence in regard to Nearctic's genotype at the MSTN g.66593737 locus - "a significantly greater proportion of C/C horses [87% of 56 elite C/C] than T/T horses [68.3% of 41 elite T/Ts] traced to Nearctic....but there was no significant difference in the occurrence of the other Nearco-sired stallions in the ancestry of the C/C and T/T horses" (including Nasrullah and Royal Charger, descendants in tf of the "Flying Filly"). This is suggestive that Nearctic, or perhaps his most influential son Northern Dancer, were C/C, but it doesn't prove anything.

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Postby vineyridge » Fri Mar 30, 2012 9:16 am

There might still be a few Northern Dancer get alive, and if 1 of them were not either C/C or C/T, that would prove that Northern Dancer was a C/T. That wouldn't say anything about Icecapade or Explodent or Briartic or Nonoalco, of course, or about Nearctic.

I'm wondering where all the mares "suddenly" came from that provided a copy of the C allele to the stallions. Is it possible that C/T was the breed majority, and there was something in either racing or training in the UK that gave an advantage to T/T? That would explain why the C allele was 'suddenly available" to stallions carrying the C. It might not have just been the sudden influx of North American lines into the European gene pool.

And when they say "traced to", they just mean that there is one line in the pedigree to Nearctic. Could not some of the difference that they found in Nearctic as opposed to the other Nearcos have come from the mares he was bred to? I'm wondering if they had tested current "elite" North American horses, if the results would have been different.

Nasrullah and Royal Charger were a full horse generation before Nearctic; that might also make a difference in the percentages. Nearctic is STILL in the pedigrees of 68%+ of T/T horses.

Another question--JC requires DNA before registration now; they used to require Blood samples. Are the actual samples preserved or simply recorded and tossed? One suspects the latter, but what a boon to research if samples had been preserved.
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Postby brogers » Fri Mar 30, 2012 12:21 pm

vineyridge wrote: Another question--JC requires DNA before registration now; they used to require Blood samples. Are the actual samples preserved or simply recorded and tossed? One suspects the latter, but what a boon to research if samples had been preserved.


The hair samples are retained at UC Davis, but there are two wrinkles to the equation....

1) It is hair, which has a 'life' of about 3-5 years unless you flash freeze it. After that time it can be tricky to extract DNA from it as it is exposed.

2) Legally, the hair is collected only for identification purpose. That is what the Jockey Club collects the DNA on the basis of, nothing else. For anyone to do any type of analysis using that DNA, they would need to change the legality behind the collection of it.
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Postby Pan Zareta » Fri Mar 30, 2012 12:52 pm

vineyridge wrote:There might still be a few Northern Dancer get alive, and if 1 of them were not either C/C or C/T, that would prove that Northern Dancer was a C/T.


It would prove that Northern Dancer was either C/T or T/T.

And when they say "traced to", they just mean that there is one line in the pedigree to Nearctic.


It means that there is at least one line. Multiple occurences of Nearctic are not exactly unusual in the contemporary TB population.

Nasrullah and Royal Charger were a full horse generation before Nearctic; that might also make a difference in the percentages. Nearctic is STILL in the pedigrees of 68%+ of T/T horses.


I rather doubt that the age difference is as significant in this regard as the fact that Nasrullah & Royal Charger split their stud careers between the UK & NorthAm, whereas Nearctic spent his entire career in NorthAm, at Windfields, CAN.

In regard to blood & tissue samples, it's not uncommon for breeding farms to retain these.

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Postby xfactor fan » Fri Mar 30, 2012 7:28 pm

Given the high frequency of "C" in Quarter Horses---short sprinters, and the historic frequency of "T" in historic studs in Europe. I'd conclude that the switch to early short races in TB's caused the selection pressure to favor horses that are either "CC" or "TC".

Northern Dancer may just have happened to be the right horse at the right time with the right genes.

I'd be willing to bet that Zenyatta is "TT" based on her runnings style, and late maturity.

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Postby Pan Zareta » Sat Feb 09, 2013 10:40 am

vineyridge wrote:University of Minnesota is, indeed, doing research on the origins of the c and t alleles in the QH and other breeds and is within a couple of months of publication


Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

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Postby vineyridge » Sat Feb 16, 2013 1:17 pm

Thanks, PZ. Damn good paper.
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Re: The Official "Speed Gene" thread.

Postby Pan Zareta » Sat Jul 19, 2014 1:15 pm

Add the semi-feral Dülmener and Sorraia to the list of old indigenous horse populations in which the 'C' ('speed') variant has been documented at the MSTN g.66493737 locus on ECA18. The single Sorraia sampled for this study was C/C. The single Dülmener was C/T.

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Re: The Official "Speed Gene" thread.

Postby brogers » Wed Aug 27, 2014 6:59 am

New paper that suggests that a SINE insertion, not the C:T intron 1 SNP, is driving the observed muscle fiber type characteristics and is the variant targeted by selection for short-distance racing.

Haplotype diversity in the equine myostatin gene with focus on variants associated with race distance propensity and muscle fiber type proportions
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Re: The Official "Speed Gene" thread.

Postby Pan Zareta » Fri Aug 29, 2014 9:26 pm

Further to the above, 14 breeds/types were sampled for that study. One or more MSTN (myostatin) haplotypes with the C variant at the intron 1 SNP + the SINE insertion were observed in 5 of them - TB, QH, Missouri Fox Trotter, Mangalarga Paulista, and Florida Cracker. One or more haplotypes with the C variant but without the SINE insertion were found in those five and seven others (Tennessee Walking Horse, Shetland, Puerto Rican Paso Fino, New Forest Pony, Mongolian, Clydesdale, & Belgian). No haplotypes with the C variant, with or without the SINE insertion, were found in the Morgan or Standardbred.

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Re: The Official "Speed Gene" thread.

Postby dublino » Sat Aug 30, 2014 2:15 am

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Pan Zareta
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Re: The Official "Speed Gene" thread.

Postby Pan Zareta » Sat Aug 30, 2014 10:38 am

dublino wrote:http://horsetalk.co.nz/2012/01/25/shetland-pony-behind-thoroughbred-speed/#axzz3BrhWzYrR

That article is based upon the proposal, as set forth in the report that launched this thread, that the most likely source population for the C variant at the Intron 1 SNP in the TB was 17th or 18th cent. stock native to the British Isles. The C variant was also found in a few other geographically diverse breeds/types that were sampled for that study. (The report doesn't mention the SINE insertion other than noting that it's polymorphic in the TB but was not found in a resequencing study of European horse breeds.) While the proposal in the report was and is a plausible scenario, the only justification cited for that conclusion other than frequency of the C variant in the Shetland population was that the TB has been a closed population since 1791, a misconception, and premature conclusions about the geographic makeup of the TB founder mare population as drawn from mtDNA analysis.

The SINE insertion was probably an 'addition' (mutation) to a haplotype in which the C variant was already present. The current study indicates that pre-SINE insertion haplotype is present in geographically diverse breeds/types that are unlikely to all have any one recent source population in common. Thus far the post-SINE insertion haplotype is documented only in breeds/types of recent New World evolution, and in the TB. So it seems premature to point to any particular older population as the probable source of modern short distance speed.

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Re: The Official "Speed Gene" thread.

Postby Patuxet » Mon Sep 01, 2014 7:03 am

Pan Zareta write: [i]"No haplotypes with the C variant, with or without the SINE insertion, were found in the Morgan or Standardbred."[/i]

This really surprises me. In the 1870s and 80s, for example, Leland Stanford, in a major push to create trotters with early speed, mated his Standardbred stallion Electioneer with a wide variety of mares, many of which contained an admixture of Thoroughbred and Morgan blood. Some of the latter were provided by my great-grandfather who, like his father and grandfather before him, developed and raced Morgan-line trotters in Vermont.
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