Dr. Binns and Mr. Morris

Just finished reading Matt Binns's and Tony Morris's Thoroughbbred Breeding: Pedigree theories and the science of genetics, and for all my friends who asked, yes, it is worth the time and money. (You can order it at http://www.amazon.com/Thoroughbred-Breeding-Pedigree-Theories-Genetics/dp/0851319351/ref=sr_1_1?ie=UTF8&s=books&qid=1287774548&sr=8-1)

The first half of the book is Tony's and serves as a brief history of the development of the Thoroughbred and the concomitant development of documentation and commentary on the breed. I've tried to cover some of this same ground in various articles and, to a lesser extent, my book Foundation Mares, but Tony has a better library and better sources available and does a much better job than I ever could. Tony has never had much time for pedigree theories that are not backed by science--appropriately so--so his dismissal of such things as Bruce Lowe and dosage are no surprise.

One of the surprising revelations of Tony's exposition, though is how little development there was--at least in print--of anything that could reasonably be called a breeding theory before the appearance of the work of Bruce Lowe in Australia and England (via William Allison) and Hermann Goos and J.P. Frentzel in Germany in the 1890s. It certainly appears that Allison was really the first commentator to push a particular mating method in print (Lowe's crackpot theories) and, since he was a bloodstock agent, doubtless advise breeders on matings (He was also part owner of a stud). Parenthetically, Allison was the man who helped choose the English broodmares bought as the basis for the studs of seminal American breeders James R. Keene, August Belmont II and Samuel D. Riddle/Walter Jeffords. It is pretty clear, however, from looking at Keene's pedigrees that his manager/brother-in-law Maj. Foxhall Daingerfield, paid no attention to Allison's/Lowe's breeding theories. Furthermore, the success of Belmont and Riddle/Jeffords was dependent almost entirely on Fair Play and his son Man o' War.

The most interesting bit of new knowledge for me in Tony's chapters is the fact that research on coat color through the pages of the General Stud Book actually played an important role in the early 1900s in verifying and popularizing Mendel's work.

Tony's repeated theme, though, is that, up until very recently indeed, none of the theories promoted to aid breeders in producing better racehorses had any real scientific basis, and precious few even attempted to establish some kind of statistical validity.

Professor Binns, a molecular biologist by training who has since started his own equine genetic testing service in partnership with David Lambert, DVM, takes over for the second half of the book. Necessarily, he begins by covering the much-trod ground of basic Mendelian genetics, but his chapters get much more interesting when he moves on to more complex variations on the basic Mendelian themes.

Matt is actually quite gentle in deconstructing theories such as the X-factor and the broodmare sire effect. In addition to pointing out that there is no basis in current scientific knowledge for such simplistic theories, he allows the possibility that future research might salvage some vestige of those and other ideas. That's what a true scientist does--lay out what is known about a subject and point out the probable verdict on a current theory, according to that research, but acknowledge that not enough is known to say precisely what the truth might be (unless, of course, there is sufficient knowledge!).

Matt's half of the book raises several questions in my mind that I plan to discuss with him, once I've followed those loose ends as far as my limited knowledge allows, but I learned a lot from his chapters, and was reminded of other bits of genetic fact that had slipped away over the years.

Matt's half does suffer somewhat from what has become the bane of the equine author--the almost two-year gap between the time he finished writing and the actual appearance of the book in the shop window. (The same thing happened with the publication of Foundation Mares.) On the last page of the book, obviously at the last possible second before publication, he inserted a brief reference to Emmeline Hill, et.al.'s publication of their work on the Myostatin gene related to distance preferences in racehorses. Much else, including Matt's own research and the launching of his testing service, has happened in equine genetics since he wrote his chapters. There are now at least five different companies offering genetic tests of various descriptions, and other than the reference to Hill's paper, none of that appears in Thoroughbred Breeding: Pedigree theories and the science of genetics.

I know that many pedigree pundits and advisors have been anxious that Tony's and Matt's book would be essentially a dismissal of all pedigree theories and research except genetics. Though some may read it that way, that clearly is not the purpose. Matt in particular clearly sees his science as an adjunct to knowledge of pedigree and conformation, not a replacement.

Read it for yourself and let me know what you think.

Best ever racemares

Frank Mitchell has started an interesting debate over on his Bloodstock in the Bluegrass blog at http://fmitchell07.wordpress.com/ by asking his readers who were the greatest racemares of the last 100 years. Naturally most of the responses suffer from the recency effect. Only curmudgeons seem to remember, or be very much interested in, the achievements of what to others is the distant past.

It's an interesting question, though, worth some thought, and a quick look back through the records to remind even this old head of the glories of the past. In truth though, it is almost certainly entirely just to discount the achievements of virtually all of the fillies and mares that raced before World War II. American racehorses were quite simply better after the importation of European stallions and mares reached critical mass in the aftermath of the war. It seems pretty clear that the American racehorse reached something of an apotheosis in the 1960s and '70s, and everything since then must be compared to those horses. The fact that those decades happen to coincide with this old curmudgeon's impressionable teens and 20s has absolutely nothing to do with it.

So what does your list look like? Here's mine, with some semi-credible attempts at justification.

1. Ruffian....Ran too fast too many times not to be at or near the top.

2. Zenyatta....19 for 19....What else is there to say? (Yeah I know, there are plenty who quibble)

3. Dark Mirage...800 pound monster won 10 straight @3 and 4, many by huge margins

4. Gallant Bloom....Beat Shuvee 5 out of 6, 11 straight wins, vastly underrated even in her era

5. Allez France...Raced only once in U.S. when past her best, but beat Dahlia 5 for 5, beat colts 8 times in Europe

6. Personal Ensign...13 for 13, but had to be carefully handled because of soundness and thus difficult to evaluate fairly

7. Dahlia....only 15 for 48, but raced on when well past her best...Beat top colts silly in Europe 5 times, and 4 times in America.

8. Desert Vixen....9 for 11 at 3 in '73...admittedly a sentimental favorite. Led Dahlia a merry chase in D.C. International over distance way too far and almost held on. Great filly.

9. Rachel Alexandra....Sorry folks, generally overrated. Beat a bad bunch of colts, just like any of the fillies rated above her here would have.

10. Tosmah...17 for 22 at 2 and 3, beat colts in Arlington Classic

11. (why stop at 10?) Go for Wand...Another sentimental choice, but 10 for 12 before dying on the lead is pretty damned good.

12. Shuvee...Couldn't beat Gallant Bloom, but beat everything else after GB retired.

13. Bayakoa...16 for 21 and absolutely lethal at 5 and 6 when at her best.

That's my lucky 13. Have at it.

Natural beauty

Nature, in her carefree way, has cast aside her most colorful autumnal cloak over the hills of north central Tennessee and south central Kentucky. That made the drive north from my haven on the banks of the Caney Fork to Lexington last Sunday for the Pedigree and Genetics Symposium on Monday more pleasurable than usual.

I prefer to drive early in the morning, so a gorgeous Sunday afternoon was free for first looks at some new stallions.

Desert Party is the standout on conformation among the three young horses I saw at Darley. He has grown into exactly the perfectly balanced, handsome, miler type one would have hoped when he topped the Fasig-Tipton Calder sale three years ago. There were times during his 10-6-1-0 racing career when the Street Cry colt looked like a G1 caliber horse, but he never stayed good enough or sound enough long enough to prove it. But he looks the part.

Street Boss looks exactly like what he was, a high-class sprinter. He's more heavily muscled than Desert Party, which he should be, and, aside from his chestnut coat, looks more like his sire. Thankfully he's more correct than Street Cry, but most of his sire's good ones are, of course. That's the way it works.

Midshipman is still in the process of letting down. He's a big, attractive horse, with the size and shoulder that Unbridled's Song passes on so consistently, but also managed only the brief racing career that has become all too frequent with sons of his sire. I loved Unbridled's Song from the time I saw him stroll from his stall in the Derry Meeting barn at the Fasig-Tipton Saratoga sale, but too many of his good offspring do not last past the spring of their three-year-old year. Midshipman might be a little light boned for his size, but otherwise has no obvious flaws. He just needs to fill out into a stallion.

From Darley I motored down to Nicholasville to Taylor Made.

I had discovered I didn't have a good picture of Unbridled's Song, so I snapped him, as well as his son Old Fashioned. The latter is probably the best-looking son of Unbridled's Song I've seen. Pretty correct, luckily not as big as his sire, and beautifully balanced. He was better than I expected. Old Fashioned raced even fewer times than Midshipman, but he is pretty clearly a Grade 1 talent for a Grade 2 price.

Eskendereya has a similar 6-4-1-0 record to Old Fashioned, and has a terrific body. Big shoulder, long barrel, nice long hip, but he's nowhere near as correct. He's offset and rotates both front legs, and it's easy to see why he had tendon problems. He's a very attractive horse, but you'd have to be careful what you breed to him.

Which, come to think of it, is true for just about any stallion you look at.

Afternoon session Pedigree and Genetics Symposium

2:50 pm

Matthew Binns will finish off the presentations

Begins by saying pedigree is genetics. Matthew theme is going to be very similar to his recent book with Tony Morris, which attempts to debunk most pedigree theories.

Matthew veered more toward his own research that the Genetic Edge sells...here's a brief summary:

Whole genome study looked at racing performance, distance, surface and height. Developed a scoring system of grades ABCD for racing performance and established the incidence of the grades at sales. Markers include a female-specific SNP. They also found a marker that is specific to Mr. Prospector horses, a SNP that's only present in the good Mr. P horses, and not in the non elite horses.

Data predicts that you can eliminate 50% of individuals on a short list at sales and retain 75% of the GSWs. Blind test found the 6 GSWs hidden among 55 moderate horses. Population is10% As, 40% Bs 40% Cs 10% Ds

Tested 27 G1 sprinters and all were homozygous for sprint genotype. But several horses who won the Kentucky Derby were homozygous sprinters. Race pace is crucial in American racing.

There are multiple SNPs strongly associated with different surfaces, some associated with muscle enzymes.

Matthew ends with perhaps the most appropriate comment of the day:

This is real and it's coming, and we hope that you will embrace it.

1:50 pm

Emmeline Hill of Equinome up next.

Heritability of racing ability is somewhere between 35% and 55%, but heritability of best racing distance is much more heritable, according to an Australian study, about 94%.

Myostatin is a negative regulator of muscle mass....it controls the development of muscles. Mutation in myostatin leads to massive muscling. Knowledge of that fact led to looking for polymorphisms in the horse myostatin gene. Found a polymorphism represented by the base pairs C and T. Found no differences in class of horses carrying the three possible combinations (CT, CC, TT), but differences in best winning distance were found.

Basically Emmeline is going over her original study that was published in January.

Almost all quarter horses are CCs, almost all Egyptian Arabians are TTs. Thoroughbreds, elite graded stakes winning horses, show what you would expect, more CTs than anything else, your basic normal distribution, slightly skewed in favor of CCs. National hunt (steeplechase) winners on the other hand are heavily skewed toward TTs, but no CCs at all.

New Equinome research published today, new study indicates that the myostatin gene is the most powerful indicator of best race distance. Says Equinome's marker performs 15 times better than any other marker in predicting best racing distance.

What genes are responding to exercise. Certain genes activity are significantly enhanced after exercise. The response increases over time as a result of training. It prepares the system to be able to be better able to respond to exercise.

Over 5k genes present in skeletal muscle. After year of training 16 genes increased activity and 58 decreased, The gene that changed the most was myostatin. Decreased its activity over 4 times.

1:10 pm

Bob Fierro of Datatrack International up next. Bob is threatening to use me as an illustration of one of his points. I dread to think what it might be. Should I run? Knowing Bob, yes.

I got to be Alydar (a long legged stride horse), Jay Kilgore was Danzig (power), Alan Porter (light weight long distance runner), and Byron Rogers (the balanced athlete, in his case a triathlete). Who knew.

Bob shows that the distribution of phenotypes of classic winners and leading sires has changed drastically since 1970s. Breed has gotten larger, lighter, more powerful, and not as balanced as they used to be and much less consistent. 2000s starting to be a little more consistent.

Secretariat turns out to be a critical horse in terms of biomechanics....His phenotype helps pull the breed back toward balance, through horses like A.P. Indy, Storm Cat, and Gone West.

Live blogging the Pedigree and Genetics Symposium

Lunch Break....I'll start a new blog entry for the afternoon.

11:40 a.m.

Tamariello discusses epistasis and epigenetics, both of which complicate the simple DNA approach. Just because you have a particular gene, it doesn't necessarily drive the phenotype. The control of the expression of genes into proteins that actually govern the body. Just by looking at the gene sequence alone, you can't predict everything.

Tamariello's company screens for:

Two muscle-related genes

Two behavior genes

Two bone development genes and

One energy-related gene

plus Whole genome screening and other higher-level screening.

11:20 a.m.

Tamariello is going over basic genetic biology that everybody in the crowd should already know. Apologetic for perhaps talking down to the audience, but still that's what he's doing. Good refresher course for those too far removed from Biology 101 I suppose.

Once through with the basics, he moves on to more specific stuff related to the Thoroughbred.

Muscle Gene 1, a gene linked to muscle function. Two alleles, racing and non-racing. Thoroughbred breeders have bred over centuries to have 2 copies of the racing allele, but there is a sub-population that is not homozygous. Heterozygous can be successful, but homozygous recessive (non-racing) are too slow to even make it to the track. This is the genotype found in most draft horses. Having 2 copies of the racing alleles, however, does not make it a fast horse.

11:00 a.m.

Prof. Steve Tamariello up next, hopefully will relate Jamie MacLeod's work more directly to the Thoroughbreds.

10:40 a.m.

Jamie's final comments may ease the worries of certain individuals in the industry:

"Equine genomics will enhance and enable good horsemanship, not compete with it Genomics in no way threatens the importance and artistry of horsemanship."

10:30 a.m.

Jamie gave a detailed explanation of how SNPs (Single Nucelotide Polymorphisms) work, which is much too complicated to try to explain on the fly. Look it up. But here's a summary of how they're used.

"What we're tyring to do is localize what region in the genome has an association with the trait you're studying. We know where in the genome where each SNP is located, know the frequency of each allele in the population. Then we compare the frequency of alleles in the population as a whole to the population with the trait you're studying.

When you find differences, that shows theres' something of interest on that particular chromosome at that particular position. Then look back at the genome map and see what genes are in that region.

10:00 a.m.

Dr. Jamie MacLeod of UK and the Gluck up next on the Equine Genome project. His brief is to give context and background for the geneticists coming up later.

Highlights of the development of the current technology for genetic research include:

The horse was added to the USDA Animal Genome Mapping project in 1996. The Human Genome project extended from 1990—2003. That gave all of animal sciences a blueprint for the genome but also provided new technology for the sequencing of other genomes, including the horse.

NIH decided they could learn additional information by sequincing the genomes of other species to compare the human genome to that of other species. The horse community convinced the NIH to select the horse to sequence among equids, because of the community of scientists working on horse genetics, there were already several well-developed genome maps; there are many biomedical aspects of horse that relate to human health, for example at the elite athlete level; veterinary medical applications; and the existence of deep pedigrees to study the inheritance of traits.

The proposal was submited to NHGRI in 2005. Sent samples to the Broad Institute in November 2005. NIH looked for a highly inbred horse, because of the way DNA is sequenced. With a highly inbred individual, the two halves are more similar, so easier for the computer program to put it together. A Thoroughbred mare named Twilight was chosen. Sequencing started in 2006 and completed fall 2007.

9:40 a.m.

Alan concludes with a look forward:

"We're anticipating that genetic research will reinforce and validate much of the analysis that we see in Thoroughbred pedigrees."

"Relying solely on pedigree is foolhardy, but likewise so is dismissal of pedigree as unimportant. Pedigree will continue to be an important eliminating criteria.Maybe 5-10 years away we're going to see a change in what pedigree actually means. What we're seeing with genetics is that though a mare might be an Easy Goer mare, she has very little of Easy Goer's good genes. Genetics can tell us what has actually been passed on instead of just a theoretical assumption and we might breed two mares by the same sire entirely differently."

Question time!

9:30 a.m.

Alan is basically attempting to cover both the historical background of Thoroughbred research and provide a frame for the other speakers later in the day. Very appropriate way to begin the symposium.

In relating his own personal history, Alan had the good grace to acknowledge the contributions of his late rival Jack Werk, though he noted that they had "philosophical differences." That was something of an understatement!

The heart of his talk can be summed up by this approximate quote (hey I can only type so fast!):

"In terms of pedigree research in my time in the industry we've gone from split pedigree books and doing everything by hand to computer programs that access every horse in the population. Now everybody can have access to the data. What is now important is how to interpret the data."

Of course what came next was basically a sales pitch for Alan's and Byron's True Nicks program, but hey, that's why all the speakers are here. It's a capitalist country!

9:05 a.m.

Alan Porter will frame the day with a talk on the history of technology use in the Thoroughbred industry. Alan has been recommending matings for many prominent breeders for more than 25 years.

_______________

I will be live-blogging (more or less) the Pedigree and Genetics Symposium in Lexington today, so if you want to check in occasionally to see what's going on, this is the place. Don't know what my frequency will be, but it should be an interesting day with dueling geneticists!

Byron Rogers and Alan Porter at Pedigree Consultants expect a full room of 175 people. The scheduled speakers, in order, will be:

Alan Porter, Pedigree Consultants

Dr. James MacCleod, University of Kentucky, discussing the Equine Genome Project

Steve Tammariello, Thoroughgen LLC, SUNY Binghampton geneticist

Gary Falter, Jockey Club Informations Systems

Bob Fierro, Datatrack International, on the intersection of pedigree, biomechanics, and genetics

Prof. Emmeline Hill, Equinome, University College Dublin, on the Myostatin gene

Dr. Matthew Binns, Equigen LLC, the Genetic Edge, on breeding theories and modern genetics

See ya later!

Flood of Books

I have been inundated by horse books lately....horse books I actually want to read. But I haven't had time to read any of them. Tony Morris's and Matt Binns's Thoroughbred Breeding: Pedigree Theories and the Science of Genetics arrived this week. I have shelved it neatly on my (wholly metaphorical) bookshelf, right next to Edwin Anthony's The American Thoroughbred and Maryjean Wall's How Kentucky Became Southern.

There is so much to read these days. I read dozens of websites every day, some several times a day, just like everyone else--but I have this blog thingy, so I get to bitch about it. And then there's always a novel or two on my nightstand.

All that takes a rumble seat to writing three days a week, since that's what pays the bills....sorta. But Mim Bower et.al.'s recent paper on the ethnicity, as it were, of the female foundation stock of the Thoroughbred has taken precedence the last couple of days.

The subject has long been one of my pet historical questions. Everybody from Lady Beaverbrook to C.M. Prior has argued that most if not all of the original foundation mares--the mares at the head of modern tail-female lines, were mostly if not all Arabians. That there has been practically no documentary evidence to support that contention seemed to matter not at all.

Bower et.al.'s study uses mtDNA haplotyping to answer the question, at least as accurately as it can at a span of time of roughly 300 years. And, no, most of the 75 or so original mares in the GSB were NOT Arabians. Roughly 8% probably were. The rest were native English and Irish breeds, and a much larger portion were Barbs than previously imagined. That makes sense if one takes into account the Moorish conquest of Spain. Their Barb stock mixed heavily with native Spanish stock, and then spread throughout the continent. And I seem to recall that there are documented importations of mares from Spain and Italy in the records of the Royal Studs, but few if any directly from the Middle East, and much of the assertions about Arabian origin of female lines were based on assumptions that the "Royal mares" at the head of several families were Arabians. Nope, not according to modern genetics.

The publication of the study provides a wonderful lead-in to Monday's Pedigree and Genetics Symposium in Lexington. I'll be there. Will you?

I promise I'll put down my sci-fi novel.