New MTDNA study on Thoroughbreds

[brogers]

A new paper has been released on Thoroughbred mtDNA in Animal Genetics today. I have written a fuller breakdown on the findings of the paper on our blog http://performancegenetics.com/2012/07/24/new-mtdna-study-reveals-closer-genetic-and-pedigree-links/#more-668. There are some interesting finds within the data provided by Bower, et al pointing to shared haplotypes in the breed and rather larger true mtDNA families. Some of the more interesting finds:

• It has been hypothesized that the #4 family is the same as the #2 family by turf historians, the mtDNA data does not support this claim.
• Family #1 (Tregonwell's Natural Barb) is a bit of a mess. Firstly sub-branches that share the same haplotype to suggest that they are all from the same #1 family are 1-e, 1-k, 1-l, 1-n (part of the n branch), 1-s (part of the s branch), 1-t, the 16 branch of the 16 family and American family #1. However, parts of 1-n (Chelandry), all of 1-p (Hilarity) and 1-u (Maid of the Glen) do not share the #1 haplotype, rather than shared by the mtDNA haplotype conglomerate #2/#8/#16. Therefore 1-n, 1-p and 1-u were founded from Family #2 or vice versa. This has considerable implications for pedigree analysis as 1-n, 1-p and 1-u all trace back to Web (1808) and the authors suggest that the error may have occurred there. If that is the case then the branch of La Troienne (1-s or 1-x depending on what chart you read) may not be from the #1 family, but from the conglomerate of #2/#8/#16. More testing would clarify this.
• The conglomerate of #2/#8/#16 includes the sub-lineages of 1-p, 1-n, 1-u, 2-d, 2-e, -2-f, 2-i, 2-n, 2-o, 2-s, 6-e, 8-a, 8-c, 8-d, 8-h, 16-a, 16-c, 16-g, 16-h, 20 and 52. It is with noting that this is a rather large group of horses that includes some interesting branches including 6-e (Fenella) which is the same family as Selene ( dam of Hyperion).
• Family 3 is sort of split. Branch 3-c has an alternate foundation mare that is shared with #18 and includes 3-c (Whisker mare), 18 (Old Woodcock Mare), 18-a and American family 48.
• The other parts of Family #3 share commonality with some of #15 and #19 and includes 3-b, 3-d, 3-e, 3-g, 3-l, 3-o, 15-a (Venus) and 19-c (The Twinkle)
• Families #4,#11 and #13 share a common founder. This is the same as what was found in Hill's study in 2002. The sub-lineages with this common founder are 4-c, 4-d, 4-j, 4-k, 4-l, 4-r, 11, 11-a, 11-d, 11-f, 11-g, 13-a, 13-b, 13-c.
• Family 5 (The Massey mare) stands alone as a well conserved female family excepting branch 5-e (Belvoirina) which stands alone with a separate mtDNA haplotype.
• Family #6-a is its own mtDNA haplotype, but 6-b,6-d and 6-f form share the same mtDNA as family #20 (Daffodil's Dam), 23 (Piping Peg's dam) and sub branches 23-a and 23-b. However, there are errors within the subbranches 23-a and 23-b with some of 23-b having its own haplotype and some of 23-a sharing the same haplotype as 21-a. 23-b is the family of 2012 KY Derby winner I'll Have Another although it is unclear if his branch is in the larger 6/20/23 group or in the smaller standalone 23-b group.
• Families #7, #17 and #22 share the same mtDNA, specifically 7,7-a, 7-f, 17-b, 22,22-a, 22-b and 22-d. Interestingly in Hill's original study she suggested that 7,17 and 22 were also part of the 2/8/16 conglomerate but further analysis proved this not to be the case.
• Family 8-c, that of the great sire Storm Cat, Royal Academy, Last Tycoon and Be My Guest, stands as a separate mtDNA family from the #8 family (in the 2/8/16 conglomerate).
• Family #9 is rather split. One mtDNA family comprises of 9,9-a, 9-e and 9-f. The other parts including 9-c (Mumtaz Mahal) find themselves in another haplotype #2/#9/#12 which includes 2-f (Gone West's family), 9-b (part of it), 9-c, 12-c, 12-d, 12-f and American family #29.
• Family #10, 14 and 42 share the same haplotype as does part of 9-b. The family is 9-b (part of), 10-a, 10-c, 11-g (Mandane), 14-a, 14-b, 14-c, 14-f and 42.
• 11-f, that of Sweet Solera and Honest Pleasure has its own haplotype separate to the 11 family.
• 12-b, that of the Champion Commando and Stimulus, has its own haplotype separate to the 12 family
• Excepting part of 19-c which jumps in to the #3/#15 family and also part of family #20, Family #19 is quite well conserved.
• Family #20 has some interesting branches to it. Firstly, branch 2-a (Ringbone) is part of it, as is part of 19-c falls into it also as does 20, 20-a, 20-c and 20-d indicating that this is quite a well conserved family.
• British Family #4 is its own haplotype
• British Family #3 is its own haplotype
• Family #26 is its own haplotype
• Family #25 is its own haplotype
• The American families A1 and A4 actually trace themselves back to the #1 family (Tregonwell's Natural Barb). However the A4 branch has a mutation that actually makes it a branch unto itself in terms of identification.

[diomed]

Fascinating, Byron. Thanks for posting this.

[Tappiano]

Oh my horses' family is #5A hope that bodes well for his upcoming racing career.

[vineyridge]

I'm finding quite a few interesting things.

Do we know if the Gallopade branch of 23b is the one which doesn't match?

As to 5-e, if it has its own separate haplotype, that is especially interesting from a sport horse point of view, since 5-e is rather famous for extremely good jumping horses.

Did they figure out 10-e (Queen Mary)?

[Pan Zareta]

I'm finding quite a few interesting things.

Do we know if the Gallopade branch of 23b is the one which doesn't match?

If I'm not mistaken, 23-b is active only via Gallopade. The report indicates at least two distinctly different haplotypes among her descendants by stud book record, evidence for error somewhere in the stud book record.

Did they figure out 10-e (Queen Mary)?

Perhaps you mean 10-a? Family 10, including 8 samples from 10-a, has been consolidated into (mitochondrial) lineage 10-14-42, represented in the report as equivalent to haplotype "D" (Hill et al. 2002). However, in 2002 family 10 was reported as hap. "B" which segregated from "D" at nucleotide position 15827. Functionally, these haplotypes may have no meaningful difference, in which case it would certainly be appropriate to regard them as the same mitochondrial lineage. Whether they represent the same founder 1650-1750 is a whole other question. (Longer TB d-loop sequences in GenBank suggest further segregation outside the d-loop sequence used for this report and the 2002 report).

This report presents a great deal of new & useful evidence. It also seems to have more than its fair share of 'clerical' type errors. Their classification/characterization of some branches of family 6, and sub-family 8c is contradictory of their own published sequences and previously published information.

[xfactor fan]

Barcaldine

Ok, so you don't like nicking programs. You think dosage is a crock. Fine. However calling research into mtDNA pseudoscience is a bit of a stretch.

mtDNA is being used to identify maternal lines in paternity cases, body identification, it is accepted by the legal system as valid science. Physical anthropologists are using mtDNA to track ancient migration patterns. There's a huge body of research on the subject.

The science of mtDNA is not bogus, hype, mystic hocus pocus, snake oil, or pseudoscience.

In horses it is passed down via the maternal line, and changes very slowly. It is an accurate method to determine maternal descent.

Perhaps more importantly work is being done on the exact function of the mitochondria inside the cell, and during early embryonic development. Mitochondria play a huge role in energy usage.


The link below is to a Wiki article which give a good overview.

http://en.wikipedia.org/wiki/Mitochondrial_DNA

[diomed]

EXCELLENT response x factor!!!

[xfactor fan]

The science behind mtDNA which involves a genetic inheritance that us passed down unmodified from the female line is different than the inheritance of genes based on the chromosomes. Which do with two exceptions, recombine and change in each generation. The two exceptions are the Y, which doesn't recombine, and the X which doesn't recombine when passed down from sire to daughter.

If mtDNA is not important, then do you believe that Y chromosomes, which also don't change from generation to generation, are equally inconsequential?

[Barcaldine]

fan,

I didnt use the word 'inconsedquential,' I opined that this information (which is of dubious reliability) is of no practical use to practicing horsemen. Much like Astrology--interesting, based in some fact, certainly available in many commercial forms, but not generally known to be accurate as a predictive tool.

[xfactor fan]

Actually when the first study came out connecting mtDNA to distance preferences, I did a quick check, and looked at what mtDNA types winners of the Jockey Gold Cup had, and compared these to the Quarter Horse families where the damline was TB.

If they were mostly the same, then that would show that there wasn't a connection. What the sample showed is that while there were some types of mtDNA on both lists, there were several types that only showed up in the sprint list, or on the distance list.

Is this proof? Probably not, as the sample size wasn't large, but it was enough for spot check the larger study.

I also found it interesting that the mtDNA study showed 5 different aptitudes. Which is the same number of categories that have been used by both Bill from WA in his Conduit Mare work, and older classifications systems.

Do you also believe that Bill's work on Conduit Mares is snake oil?

[Barcaldine]

fan,

I am not familiar with the details of Bill's conduit mares theory. If he were shamelessly pawning it off for profit I would take a stronger look at it. But clearly his is a work of passion, not racketeering.

[vineyridge]

Where can I get a copy of the article without going through Wiley's pay service?

Reason I am interested in 10-e is that it also has produced superlative jumping horses in the past. It descends from the Queen Mary daughter, Blooming Heather.

If 23-b is split and Gallopade is the only living line, then the split had to occur fairly recently and most probably in the US.

[xfactor fan]

A quick overview of Bill's work:

He picked mares from the turn of the century, then traced the aptitudes of their maternal descendents. The only thing a maternal descendent of a mare born in the 1900's will have in common is the same strain of mtDNA. All of the chromosomes will recombine, the X's will recombine.

By selecting the mares at a fixed more modern date, he's able to avoide most of the historical errors that have crept into the stud book.

And yes, he's finding that there are distance aptitudes that follow his conduit mare families.

[Barcaldine]

I just don't put much faith into breeding theories, or systems, or beliefs, or whatever you wish to call them, which tie single distant relatives to present day performance.

For example, nicking products focus on a single relationship (male ancestor to male ancestor), irrespective of any female contribution whatsoever. Thus, the VAST number of other potentially causal relationships are utterly ignored. In addition, the male ancestors in question may well be three or four generations removed, so the reliability of the so-called "nick" must be circumspect, at the very least.

Dosage, too, ignores female contributions. Also, IMO many chefs are unwarranted and misplaced. And, most importantly, Dosage's sacred quotient, the Dosage Index (DI), is most unreliable in predicting or producing racehorses which exhibit the sought-after attributes. They're hit or miss, just like nicking.

So, while I respect Bill for his efforts and am positive he is sincere in his work, I just can't buy into any notion that ancient mares--no matter how strong their families have developed--predispose their great-great-great-great-great-great-great-great-great-great grand offspring to a certain phenotype.

The *LA TROIENNE family has produced champion sprinters, routers, dirt, turf and steeplechase winners; the MYRTLEWOOD and ESCUTCHEON families have done similar feats. From LADY JOSEPHINE have sprung brilliant racehorses like MUMTAZ MAHAL, *NASRULLAH, FAIR TRIAL and *TUDOR MINSTREL, as well as ST. LEGER and English Derby winners. The examples are endless.

It's very tempting for pedigree buffs to develop a calculus for success. While I have no objection to this I do abhor the charlatans--like Dr. Dosage and the Nicksters--who prey on the wanna-believers by peddling their home-brewed bullshit to them.

As a final note, I hope you and others remember that Byron Rogers never responded to either my or Don Engel's criticisms of nicking products. Not a man of few words he could sling the s**t with the best of them, yet he was unwilling to address the straight forward issues we brought to his attention.

His unwillingness, I think, speaks volumes about the integrity of Nicksters products and the ability of their creators to stand behind them.

[xfactor fan]

Apples and Oranges. Genes and Chromosomes are not mtDNA, and shouldn't be confused. They also don't follow the same rules of inheritance.

mtDNA governs energy usage. And does not change. The only thing in a pedigree that doesn't change in fact.

A good way to think of the effect of mtDNA is that it is a type of fuel. Some have diesel, others regular gas, and still others jet fuel. And no one is claiming that this is the only factor to be considered in breeding a racehorse.

One of the research areas that brogers is looking into is how other genes interact with mtDNA. This in my opinion is a very valuable area of research.

Before you dismiss mtDNA as " I just can't buy into any notion that ancient mares--no matter how strong their families have developed--predispose their great-great-great-great-great-great-great-great-great-great grand offspring to a certain phenotype. " A direct quote from your last post, you might take a moment an read that wiki article on mtDNA and how it is transmitted.

And as a side note phenotype is usually used to describe how genes express--genes on chromosomes, not mtDNA. Which is not related, not on the chromosomes, and doesn't recombine. And is passed down unchanged via the maternal line.

For example, take any of the historic dams- and all their true female offspring (discounting errors ) and all the sons of the female offspring will have the same mtDNA. Sons don't transmit mtDNA, so all the foals from a stallion will have the mtDNA from the mare.

So a stallion's racing success is based on his genotype, how the genes are expressed in the phenotype, and how both interact with the mtDNA. When sent to stud, he passes on the genes, but not the mtDNA.

One breeding theory suggests that "Return the stallion to the best blood of the dam" Which has been around for quite a long time. Pre-genetic science. This particular observation fits the idea of breeding the stallion back to the same mtDNA type.

As to the female families that produce a range of runners, I'd guess that the mtDNA type comes from type 3 or 4.

1 Short Sprinter 2 Medium Sprinter 3 Long Sprinter 4 Distance 5 Long Distance.

I don't know if Bill's website is still up, but looking at his research would be a good place to start educating your self about mtDNA.