Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

Edward — Sat, 19 Sep 2009 01:41:57 GMT

I would be interested to see how the geneticist who say there has been no gain in the thoroughbred explain the huge difference in winning times for, say, the Triple Crown series. I know they would try to make a case about track difference, training, timing methods, and on and on and on until you realize that a subject that has that many variables is not open to a neat and tidy root cause. And breeding is not open to any type of predictability.I do agree with Don that it gets silly sometimes and I would use your claim about Spec. Bid being a great 2nd sire. You are aware that when you flip a coin it doesn't come out heads or tails every other time? So perhaps when you see a pattern like Spec. Bids, it's just part of the random distribution. It does seem that TB breeders have a little of the Bible/Torah Code syndrome even though its been proven that Moby-Dick can also "predict" events as well as the Kabbala, prepotently when the prediction comes after the actual event. However, Mr. Knockles sums it up the best when he says that breeding is a romantic pursuit at heart even if science can add a thing or two to give breeders a leg up. Also, in regard to training, I agree that it is the place where a lot more progress could be made. Trainers should be studying the results of human athletic training methods because it has advanced so far and so fast if for no other reason than the human athlete is able to communicate way more information in the way of feedback and implementation.

Top 6 Sires-of-Sires at Keeneland September

The Five-Cross Files — Tue, 01 Sep 2009 18:48:51 GMT

Only six stallions have at least eight sons represented by hips at Keeneland's yearling sale later this month. We look at the sale's count by sire-of-sire as well as by larger sire lines.

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

sceptre — Wed, 18 Mar 2009 02:53:52 GMT

To vineyridge-

It's a bit difficult to respond to your querry (or is it merely a statement?), since your premise(s) and, perhaps, line of reasoning appears faulty. Also, DonW is the geneticist, not I. That said, I'll try-

Firstly, I read a portion of the dissertation you offered, and it does not appear that he's suggesting that the Y chromosome of all horses is identical, but for one position. I suggest you read more carefully what you had offered us. Had, however, this been the case, your conclusion (last three lines of your note) does not necessarily follow. For one, and while I may not agree that his rationale is persuasive, Scott in his answer (see paragraph which begins-"A few factors blur the picture) suggests some factors which might cause the male-line to exert more relative influence...The (top) male-line on average contributes the same number of chromosomes to the offspring as any other line within the pedigree. While it is true that the Y chromosome (passed only via the (top) male line) contains far less dna than the other chromosomes it (the male) still offers 32 (31 autosomes and 1 sex chromosome-in this case Y) haploid chromosomes to the offspring as does the female, 32 (31 autosomes and 1 sex chromosome-in her case, X) haploid chromosomes. If some are confused, as one can see the male offers much more than merely a Y chromosome. Take a look at any pedigree and you'll quickly notice that the (top) male line is but a small fraction of the entire pedigree (it is, however, the sole source of the Y chromosome)... You will also grant that it is the stallion, rather than the dam, who more likely possesses the better genetic material. I said more likely, not absolutely. The simple reason for this is that the selection process for stallions is far more stringent than for dams (because far fewer stallions are required than dams). On average, therefore, all male lines in a pedigree should be "stronger" than the female lines. (yes, I realize there are exceptions). With this in mind one can conclude that the very (top) male line is, on average, the source of the finest genetic meterial. This can be deduced by simply realizing that the sire (1st generation) was, on average, "permitted" to be a sire through a process of selection far more stringent than was the case for the 1st dam. Yes, the names in the pedigree may appear to be relatively equal throughout, but they are names, not actual genes. The best genes from those names are more likely to be passed down through the males. To confuse you a bit more allow me to add that it is rather likely that some females through time possessed the best genes of all. Our inability to easily identify them has weakened our ability to have them proliferate...So, I wouldn't suggest that the sire has more "influence" than the dam, but that, on average, he exerts a more positive influence. By what I've offered above, one could more easily conclude that it is the dam who exerts more relative influence, since, on average, her genetic material is more qualitatively variable than that of the stallion.-far more females are "accepted" into the breeding population than males...Lastly, while the Y chromosome is involved in the stallion's fertility this has no relationship to the quality/quantity of genes he transmits to the next generation (I hope that's all you meant by the term "breeding aspects").

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

vineyridge — Tue, 17 Mar 2009 16:28:36 GMT

Okay, all you geneticists and scientists, here is an unpublished doctoral dissertation for your edification:

http://tinyurl.com/clotz2

If the Y chromosome controls the breeding aspects of the male, and if all horse Y chromosomes in the non-recombinant portions are the same except at MS30, where two variations have been found in TB males, how can the top line be any more influential in Phenotype and Performance characteristics than the dam sire line or the sire's dam sire line?

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

Alfred Nuckols, Jr. — Mon, 16 Mar 2009 02:28:40 GMT

Sceptre,

I would love to know who I've been discoursing with. Please e-mail me and let me know. If you are interested, I would like to use you as a sounding board about a lot of my other feelings about this industry and where it is going

Thank you for your enlightening comments.

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

sceptre — Sun, 15 Mar 2009 18:59:59 GMT

Dear Mr. Nuckols:

Appreciate your relevant input which at times appears to reflect agreement with DonW's position, while at others with my own. One can infer from your remarks that environment influences greatly the outcome-suggesting, perhaps, that performance heritability is rather low (what appears to be DonW's contention, not mine). You also, however, seem to embrace one of my positions-that one (scientists, statisticians, etc.) may not adequately appreciate the variables and nuances associated with performance evaluation, etc... Further, you suggest that lack of progress in training techniques (and, perhaps, husbandry), and an inherently small sample for study has deterred the "progress" of the breed. While I see some truth to this, I feel the breed's history "database" is sufficently large (larger than any performance database) that if "programmed" properly (very difficult task) would yield results such to enable us to better "improve" the breed. Within this program would be also what science/genetics has to offer. Absent such a project, I believe we have demonstrated some degree of ability in identifying the better genetic material. Yes, many savvy breeders through the years have managed to succeed in this area without possessing much background in genetics. But this is not to suggest that a better understanding of "genetics", or other disciplines (bloodlines, etc.) would not have caused them greater success. For example, Mr. Nuckols, isn't it possible that what you've concluded about Street Cry is incorrect-that had you greater familiarity with "genetics" you might conclude differently despite your one example on the ground? Also, the fact that one ( through science, study) cannot replicate a Secretariat should in no way minimize the value of science, study, etc. as it relates to thoroughbred breeding... It is also not an either, or situation, in that if one isn't hands-on in a day to day basis their opinions have no merit (or, for that matter, the reverse). And, why do you assume that I haven't hands-on experience? Must we be one or the other? While I may not be the owner, or heir, to a large Bluegrass farm steeped in tradition, I've still been in this for nearly 50 years as a breeder, owner, stallion owner, advisor, and mating consultant. I have also been "hands-on", perhaps not day to day, but week to week. I've countless times seen or done everything you've mentioned-not just read about it. I doubt that you're privy to any nuances related to this topic that I am not... I do absolutely agree with you that we may be better to simply appreciate the romance of this, to admire what they are, and to revel in our association with these admirable creatures. Rather than focusing on the breed's improvement, better that we offer our efforts toward their welfare (safety, care, freedom from injury, right to life, etc.). At this point I see little justification for this sport, but for that less thoroughbreds would exist without it.

You and I have crossed paths. Many choose not to use their names on these blogs due to privacy concerns. Not all of us merely preach to the choir. If you do wish my name I'll be happy to email you at the farm. Just let me know.

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

Alfred Nuckols, Jr. — Sun, 15 Mar 2009 02:00:52 GMT

To both DonW and Sceptre:

While I have to concede that both of you are extremely knowledgeable geneticists and doctors, I think that one reason you may not have seen that much improvement in the breed is "environment". Most trainers still train thoroughbreds like they were trained years ago and there have been no fundamental breakthroughs in this area other than the introduction of "interval training", which may have been used in training over the years, but not labeled as such.

Also, due to the number of possible genetic combinations and the relative small number of thoroughbreds foaled each year (roughly 40,000), is there really a large enough genetic sample for each sire, given the number of sires in the gene pool? The gene pool for significant broodmare families is much smaller, given a mare's relatively low reproductive capacity.

You can beat this horse as hard as you like, but the people that breed, foal, raise and race these animals on a full time basis see a lot that you both will never see or read in a textbook. The eye of a knowledgeable horseman interprets a lot of data that doesn't show up on a printed page. That is part of what makes this business more of a labor of love and an avocation rather than something one can easily pick up reading tomes about it. I have learned a lot by reading and studying pedigrees over the years and I was in preveterinary medicine before going to law school. So, while my educational background can't compete with yours, this is what I have chosen to do for the past thirty some-odd years.

I would invite you to get on the end of a shank with a teaser on the other end and study a mares estrus cycle from that standpoint, or handle a stallion in the breeding shed and watch how he breeds a mare. Then, there are the nights in the foaling barn when you are assisting one of your favorite mares in delivering her foal to finally see if your ideas about the mating had merit. Also, try working with the resulting foal and teaching him to lead and walk and hoping that he will not get hurt or killed in a freak paddock accident. Bring that foal along until a year later you have a yearling that you have tried to feed correctly and raise properly in a social atmosphere where you allow their ingrained herd mentality to blossom. Finally, comes the day you ship him/her to a horse sale or to a training center to watch him/her learn his/her next lessons, again hoping that there will be no catastrophic event that will now undo three years of your work. With all that work done, if you are lucky, you may see that thoroughbred run at two (although I prefer not to)or maybe early in his/her three year-old year year. That is where the true genetic mating takes over, subject to all the aforementioned environmental input.

Only then can you determine what kind of job you did. This is three to four years into the process with just one horse.

So, genetically, you have a very lengthly experiment to test your initial hypothesis. And, like Secretariat, I'll bet you will never replicate that individual, whether he prove to be a champion or a lowly plater.

Therefore, when I say a Street Sense foal looks more like Street Cry, this physical example will help me determine the phenotype that I will next send to that stallion based on what I see with my own,now aided,

eye and what I have observed in this mating. It will also have to match up with pedigree ideas that I have studied and observed.

Therefore, I would beseech you both to enjoy this business for what it is: man's romantic attempt to play God with a truly wonderful and beautiful creature. I do this for a living, so I have to be a romantic optimist!

Also, something that I have never understood about this email business is why people can't use their real names. Who are you gentlemen?

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

sceptre — Sat, 14 Mar 2009 16:53:12 GMT

DonW:

Appreciate the references you offered. Had read Cunningham's some time ago and recall having dismissed it. Will attempt to locate it again. Just now read abstract on AJ Wilson et al study. Theirs' is a prime example of my remark to you (last sentence of my last post). He basically concludes that there is no correlation between stud fees and progeny earnings. He also ackowledges there is heritability with respect to earnings, albeit quite low. Once again, here, we have educated "scientists", using sophisticated formula, adhering to scientific method, but with little understanding or regard for the variables involved in their undertaking. They would no doubt have one conclude from their work that breeders have (practice) no insight relative to identification of better genetic material. You, yourself, imply as much in your post, and I assume offer (to me) this study in support. For years the sport has struggled to arrive at a single parameter/formula (simplified means) to indicate racing class (there is even some lack of consensus regarding this term). Yet, Wilson readily assumes that lifetime earnings is the appropriate parameter.-I offer this only as example of my point-(One might argue that earnings/start is a better "gauge"-but, likely far from accurate). My point is, that in all their precision, these "researchers" are remarkably sloppy in their premises. They simply don't possess sufficient perspective (in this area) to understand that they are incapable of making the proper assumptions. -As an aside, they are almost certainly wrong in their low heritability assessment...The limitations inherent to this forum make it impossible for one to adequately address this issue, or to respond to you, but I hope it will cause some reflection.

re: Do Thoroughbred Sire Lines Carry More Weight Than Other Pedigree Influences?

DonW — Sat, 14 Mar 2009 05:47:38 GMT

Sceptre:

To get an idea of some good geneticists looking at thoroughbred breeding, you might start with:

B Gaffey and EP Cunningham: Nature. 332: 722 (1988) -- Although there is heritability of racing performance, it has not improved in the past century and so the breeders are not properly tapping into genetic traits.

AJ Wilson: Biology Letters. 4: 173 (2008): There is no correlation between stud fees and racing performance as measured by modern statistical genetics. Therefore, stud fees probably do not reflect genetics.

T. Tozaki: Gene. 346: 127 (2005). DNA studies by a method called linkage disequilibrium to relate genes to racing performance are possible in race horses but not being used.

I have been involved with thoroughbreds for 35 years.

re: Do Thoroughbred Sire Lines Carry More Influence Than Other Pedigree Influences?

sceptre — Fri, 13 Mar 2009 20:57:03 GMT

To DonW:

While I agree (see my previous posting) that many breeders may have little understanding of basic genetics, let alone its breadth (which I doubt also you possess), I question your certainty that application of such knowledge, then or now, would have appreciably "improved" the thoroughbred racehorse. As you likely realize, it is one thing to apply genetic knowledge to great advantage in creating a cow with better/more milk production, a sheep with more wool, etc., and another to enable one to produce a better, faster, more efficient, sounder, etc. racing athlete. If this were the case, I can assure you that, owing to the economics of the industry, there would already be evidence of such accomplishment. What I find more objectionable are those who exaggerate the relevance of each new(er) genetic "discovery" in relationship to thoroughbred breeding practices. An example of this is found in this very blog-the person who cited mDNA=the "run genes". Another example would be "genetic imprinting" as the cause for certain perceived exceptional broodmare sires not themselves being good sires, etc. You know the saying-a little bit of knowledge can be dangerous. DonW; notwithstanding your title, molecular geneticist, it appears you are also guilty in this regard...While I may not be a molecular geneticist, I am a physician with a longstanding interest in genetics, particularly in its application to racehorse breeding. What I may (or may not) lack in knowledge of molecular genetics vs you, is likely more than compensated by my nearly 50 years (as a breeder/owner) in the study of thoroughbred bloodlines and racing history. It is evident from your post that you are a relative novice in these areas-to suggest that there has been no improvement in racing performance over the past century is absurd. An argument for the past 30-40 yrs might have some validity, but not 100 yrs. The basis for your uninformed opinions are not unlike those heard from some statisticians. They too are often quick with their conclusions while lacking sufficient perspective of the variables.

re: Do Thoroughbred Sire Lines Carry More Influence Than Other Pedigree Influences?

DonW — Fri, 13 Mar 2009 15:54:54 GMT

I am a molecular geneticist with over 30 years' research experience, as well as a teacher and textbook author at the university level. With that introduction, I can say that throroughbred breeding is in the scientific dark ages. Just looking at the blog and responses so far, I see the following phrases: "prepotent", "energy producing cells", "nicks", "relative homozygosity", and "stallion passing traits of his own sire". All of these have no scientific basis and essentially deny the great progress we have made in our understanding of the principles of genetics since Mendel published his studies on pea plants over 140 years ago. Take a look at other animal breeding and you will see such terms as "QTL breeding", "DNA markers", "back crossing", "multiplication herds", "F1 hybridization" and, (horrors) "artificial insemination" and "embryo transfer". Scientific approaches to breeding of cows, sheep, pigs, etc. have led to significant improvements in agriculturally important traits. This is in contrast to thoroughbreds, where data from Europe indicate no improvement in the past century in racing performance. I fully understand why thoroughbred breeders continue to deny genetic science and use the "hay, oats and water" approach: It's all about the economics of mystery, prestige and restricting supply. The amusing paradox to me is that, as I tell students, horses were apparently the first animal deliberately bred by humans for desirable traits, as far back as about 5000 BC. Yet the breeders act as if there has been not much scientific progress since then.

re: Do Thoroughbred Sire Lines Carry More Influence Than Other Stallion Sources?

Harp — Fri, 13 Mar 2009 11:58:41 GMT

Scot,

The mare is the exclusive source of mitochondrial DNA(energy producing cells) in a pedigree, and I find it interesting that most of the focus (when discussing successful nicks and crosses)seems to be on the stallion's contribution instead. If the differentiated "run" genes come solely from the dam, shouldn't commercial breeders be looking much more closely at that factor, (i.e., not only whether a mare raced, placed or was unraced, but also whether her siblings raced and won, and if the immediate family members ran and threw runners themselves) when planning matings?

re: Do Thoroughbred Sire Lines Carry More Influence Than Other Stallion Sources?

blackmamba — Fri, 13 Mar 2009 03:05:13 GMT

Well, let's see. If you're paying attention to the triple crown trail. You'll notice the influence of unbrideled. He produced the likes of empire maker and unbridled song. Now those sires have pioneerof the nile, old fashioned, dunkirk and so forth. Those horses are carrying unbridled's legacy.

re: Do Thoroughbred Sire Lines Carry More Influence Than Other Stallion Sources?

sceptre — Fri, 13 Mar 2009 03:01:45 GMT

Dear Scot,

With regards a portion of your answer:

It is generally assumed that prepotency is merely a function of relative homozygosity. If you view this otherwise, please comment. If, however, you agree, please offer your genetic dynamic on how sire LINES can tend to REMAIN prepotent, and prepotent for what traits? There is still much not yet resolved in genetics and, perhaps, a truly thorough study of the breed's history (database) may yield (correct) conclusions that differ from accepted genetic theory. That said, mere anecdotal obserations are insufficient evidence to refute present genetic knowledge...As to your observation that Spectacular Bid is a better 2nd damsire than 1st- Should this be correct (statistically), without more explanation this might lead one down the wrong path. Spectacular Bid initally stood at Claiborne to a high quality book of mares. Later, after he essentially failed, he stood in NY to a far lesser quality book of mares. At this point in time one would expect the quality of 2nd dam Spectacular Bid mares to be far superior to present (1st) Spectacular Bid broodmares. As the years pass, 2nd dam S. Bid mares will likely prove equally inferior (to those now 1st). Lastly, regarding Mr. Nuckols' observation about his Street Sense foal resembling much more Street Cry-certainly this can happen (much like many of the Stop The Musics (who was much smaller) resembling more Hail To Reason-would happen on occasion, but shouldn't consistently (just a result of the spin of the genetic wheel). But, one should also realize that those "looks" may be nothing more than skin deep. What is also inherited are many traits far less seen-pulmonary, cardiovascular, neurological, etc. Even should it inherit more of Street Cry's looks, shouldn't lead one to assume that it more likely inherited more of Street Cry's other traits...We breeders like to believe that we have far greater control and insight than is, perhaps, the case. We then broadcast these "truths" to others and to some extent they become set in stone-to the detriment of all.

Scot's reply: I will admit that it's been about a dozen years since my most recent genetics course; however, I do keep up with at least the largest breakthroughs in genetic theory and I know that our understanding of genetic inheritance is still rudimentary. Why do certain sires "stamp" the vast majority of their foals, while other sires' offspring bear no resemblance? Why has the simple, almost infantile "male line / female line" or "sire / damsire" mentality worked so well over the years, with repeatable results? Yes, I agree that Thoroughbred breeding is considerably more scientifically underdeveloped than most livestock industries – but I also do not summarily dismiss several centuries of observation simply because we do not yet have studies to support or disprove the data. It's impossible to bring truly "hard" science into Thoroughbred breeding – but we sure can apply scientific principles with a little more enthusiasm than has been done in the past. We can and should identify genetic influences on the breed and make sure to separate fact from bias or emotion. But, with all that said… the sample sizes are too small and the ethical/financial costs too large to resolve every detail to the satisfaction of the pure scientist. At some point you reach the nirvana / "perfect solution" fallacy stage and you have to decide whether you want a series of good theories and likelihoods… or if you'd prefer to lament the insufficiencies and imperfections of today's knowledge.

re: Do Thoroughbred Sire Lines Carry More Influence Than Other Stallion Sources?

Alfred Nuckols, Jr. — Thu, 12 Mar 2009 23:53:17 GMT

I enjoyed reading your reply to the reader question. I just wanted to mention a 1st year sire that appears to be throwing back to his sire, instead of himself, based on the one foal I have had here this year. That sire is Street Sense whose filly that I had out of a Dynaformer mare (who tends to throw to the sire) bears a strong resemblance to what I would have expected from Street Cry. The filly bears a striking resemblance to the Street Cry foals that I have had or seen. I don't know what other breeders have had or what they look like, so I would love to hear who other Street Sense foals resemble.