The Genetics of Nicking

re: The Genetics of Nicking

sceptre — Tue, 07 Dec 2010 16:44:50 GMT

Dave York-

The closing paragraph to which I referred is the one contained in Byron's (brogers) 05 Dec 2010 reply to Vineyridge. Sorry for my lack of clarity.

re: The Genetics of Nicking

sceptre — Tue, 07 Dec 2010 04:50:12 GMT

Dave York,

If you're looking for consensus- I, for one, agree with the basic science and conclusions offered in Byron's closing paragraph. It's really stated quite well, and sums up the likely near-complete "mechanism" for end result (phenotypic) variation. Too often, mating decisions are derived from false mechanistic assumptions. If nothing else, one should attempt to understand what was offered here, and adjust their thinking acordingly. There are many additional nuances to all this (both quantitatively and qualitatively), some known, some yet unknown, but as an overview it's likely very near to reality.

re: The Genetics of Nicking

dave york — Mon, 06 Dec 2010 20:42:49 GMT

I read the entire give and take twice. WOW!!! I admit I comprehend so little of the science and specifics of genetics that this question may be foolish but here goes. Is there much that can be agreed upon or is there little than can be agreed upon with respect to predicting outcomes of mating thoroughbreds? As a retired Marine fighter pilot, top gun graduate, and as an owner of a business that is somewhat successful I believe that I have some skills in making decisions. I have not been successful in my thoroughbred mating endeavor as yet but I have one decent looking yearling and my two weanlings have the best conformation of any I have produced in my 11 years in this game [that does not mean they have the intelligence or aptitude to endure the training regimen]. My favorite line is good at business- horrible at horses. I have read the TrueNicks blogs with great interest for a good while. I enjoy the challenge of trying to breed, raise, train and race a stakes caliber thoroughbred. The variables after birth are so many that it is frightening to consider how the odds are stacked against getting to the point of having a stakes caliber thoroughbred even if you have bred a physically and mentally talented thoroughbred. Never the less, I will continue this endeavor until my wife makes me stop. I would like to believe that there are likely outcomes when mating thoroughbreds. Is there any common ground for those of you who have spent a life time studying this or is there so little that can be agreed upon that I should consult the mystics for my breeding advice?

re: The Genetics of Nicking

Byron Rogers — Mon, 06 Dec 2010 00:45:46 GMT

Vineyridge,

Sorry for the delay in replying. Sceptre has indeed answered some of the questions that you have stated but there one statement that you made that don't quite hold true.

"The x chromosome is by far the largest one there is." In terms of the # of genes per chromosome, that isn't quite right. Chromosome #1 of the Equine genome assembly (EquCab2.0) has almost 2200 genes on it while Chromosome #7 has over 1400. The x Chromosome has a little under 1400, so in terms of being "the largest one there is", I would suggest that chromosome #1 gets the prize.

This of course doesn't mean that Chromosome #1 is where all the action is, as it relates to thoroughbred performance. Indeed there was a study released last week (www.ncbi.nlm.nih.gov/.../21115378) whereby they looked at the candidate genes for elite performance in the human field and applied these genes to the equine genome. They found that if, and that is a big if, the same genes that separate out elite performance in humans, apply to horses (specifically thoroughbreds) then chromosomes #4 and #12 in the equine genome are over-represented with candidate genes for performance. Of course they are presuming that the genes for performance in humans is the same in horses which it will probably not (completely) be.

Truth be known, elite performance in thoroughbreds will most likely be polygenic with the combined effect of literally hundreds of genetic variants. These variants could form part of a total genotypic score in thoroughbreds where a horse with elite potential may get a score of say 75 out of 100, but the construction of that 75 could be made in any number of ways. Importantly, in humans at least there have already been studies to show that a mean 'total genotype score' is a significantly better indicator of athletic performance than the reflection of one polymorphism from a single candidate gene.

re: The Genetics of Nicking

vineyridge — Sat, 04 Dec 2010 23:44:04 GMT

Just speculation, mind you; I've do no studies of the literature so am talking out of a very large hat.

But think how many fundamental physical differences there are between males and females. I was just reading something today about scientific studies that are suggesting a connection between testosterone which is much reduced in the female and anxiety disorders which are far more common in women. And there are many such differences which I would suggest have to come from the sex chromosome, the number of which *might* be 21, but then I might be remembering wrong. Both sexes have many things in common, like the skeleton, most of the organs, etc. But they don't always end up the same or functioning the same in the male and female. Something has to control the differentiation, and the logical place is in the XX or XY chromosome.

re: The Genetics of Nicking

sceptre — Thu, 02 Dec 2010 23:19:55 GMT

Vineyridge,

I now understand better your point-I had interpreted differently your 2nd paragraph's phrase "...reduced in the first generation from the daughter."-Since, unlike autosomes that might be inherited from Darshaan to a Sadler's Wells-Darshaan daughter offspring, a Darshaan "x" if inherited by same offspring could be "deactivated", thus in some cells (of that offsping) a loss of that potential Darshaan "positivity". So, let's forget about the Barr Body issue and, instead, focus upon the rest:

Yes, a Darshaan daughter will receive an intact ("unmodified"/non-recombined) Darshaan "x" chromosome. Whereas this same Darshaan daughter will also receive Darshaan autosomes that have undergone recombination (resulting in some being "better" than "average", and some worse than "average")--("average" relating to Darshaan's potentiality to cause a + nick with Sadler's Wells)... So, going back to Byron's schematic, if one assumes that only 50% of these Darshaan daughters inherited the "good variants of (autosomal) genes" ("good" here meaning that they served a + nick with Sadler's Wells), I assume you (Vineyridge) believe that an intact Darshaan "x" chromosome is a given positive as it relates to the Sadler's Wells-Darshaan nick. Said another way-that it is more likely than a 50/50 chance that a Darshaan "x" would yield a relative "positive" (regarding this nick)? I wouldn't presume the Darshaan "x" to be a given +, but in light of crosses' data I'd be inclined that it does have a better than 50/50 chance...But, I see this all as very slight, certainly not "considerable". And while the "x" chromosome may be slightly larger (than the autosomes) I'm not so sure that the genetic material it contains relative to overall performance is any greater than that found in the autosomes. Lastly, why is it more likely that "...some sort of controllers..." are located on the "x" chromosome, rather than on the autosomes?

re: The Genetics of Nicking

vineyridge — Thu, 02 Dec 2010 19:21:29 GMT

Maybe I just don't understand enough.

The x chromosome is by far the largest one there is. It seems to have a lot of genes that function in other ways than just reproduction. Otherwise there wouldn't be sex linked characteristics. The X and Y chromosomes could function as some sort of controllers for the rest of the horse building process. At least that's a possible hypothesis.

Even though one of the two Xs in fillies is rendered inactive in her at the outset, both are used in egg formation through recombination and then meiosis, aren't they? Recombination always seems to involve chance. A colt, on the other hand, never gets anything from the sire's X chromosome, because he doesn't get it at all. So whatever happens in fillies that have that chromosome activated cannot happen in colts from the same sire. The colt only gets his dam's recombined X, which he then passes on in "pure" form to his daughters.

This is all very deep and difficult to comprehend.

re: The Genetics of Nicking

Mark — Thu, 02 Dec 2010 13:26:16 GMT

Ian,

Thanks for your comments. So, since my father and I will be breeding and/or buying at auction, at the lower end of the price spectrum as we do not have several million in disposable funds, I've got to find an effective way to narrow down the sales catalogs to those animals which give us the best chance of producing winners. Since most purses pay 60% to the winner, unless you are competing in a decent stakes races, place and show money will barely pay the training bills for the month.

Therefore, I've been analyzing which sires consistently produce higher percentages of winners from runners, and am also doing the same for broodmare sires. I think this information will help me narrow down the catalogs some as I will focus primarily on these individuals. Then, I will look for progeny by them that also come from the female lines I've recognized are more likely to produce good results. Once I've used that information to narrow down my choices, then I should use your service to further "confirm" the likelihood that this filly or colt will be successful. I realize genetics is a shot in the dark, but I feel with what I'm doing, it at least improves my chances of success, and thus, earning a profit. Let me know if this is a somewhat sound approach, or if I'm wasting my time.

Thanks,

Mark

You don't have to post this if you don't want to.

re: The Genetics of Nicking

sceptre — Thu, 02 Dec 2010 05:53:01 GMT

Vineyridge:

Your question(s) seem to be directed to this topic's author, so I didn't wish to intrude. But unlike me, Byron is probably a busy guy, and I now noticed that Ian, his colleague, has responded to one. For what it's worth, I'll try to answer your questions. Your first paragraph of statements (albeit formed as questions) is, to my knowledge, accurate, while your second paragraph remarks are incorrect. As you no doubt realize the horse has 64 chromosomes-an individual x chromosome being but one of the 64. To modify somewhat your wording, I wouldn't think that 1 out of 64 could be called a considerable proportion even had your basic premise (2nd paragraph) been correct, which it isn't. At the embryo stage, if there are two x chromosomes one becomes a Barr Body which is inactive. There is a 50/50 chance as to which of the two x chromosomes will be rendered inactive (loses it ability to be involved in polypeptide synthesis). So, merely from the standpoint of Byron's example (a hypothesis I don't share), his figures retain their validity.

re: The Genetics of Nicking

Ian Tapp — Thu, 02 Dec 2010 02:41:45 GMT

Mark,

Excellent comment. Yes, the mare is just as important as the sire. In effect, their genetic contribution to the foal is equal.

The difference is a matter of statistics. A sire can have 1000+ foals in his lifetime, while a mare can have only 10-15. While the mare's genetic contribution to her foals is no less significant than the sire's, statistical analysis of her influence is more difficult because of the small sample size.

This is why our nicking calculation references the correlation between sire and broodmare sire. If both sire and dam had large numbers of offspring to study, then it would be simpler to compare their respective influences.

By grouping mares of the same broodmare sire line together, we are able to identify certain trends. Mares sired by the same broodmare sire have a degree of genetic commonality, and therefore we can compare the average to the behavior of specific crosses.

The nick rating goes hand-in-hand with pedigree analysis. The strike rate of a nick helps qualify study of the pedigree and female family. It's not an either-or scenario, but a tool that gives breeders more information to make a decision.

Ian

re: The Genetics of Nicking

Mark — Wed, 01 Dec 2010 20:58:25 GMT

I am new to the horse industry personally, although my father used to train. I am analytical which tends to move me toward nicking in general. That said, it appears to me that the majority of the focus is on sires and their impact on the breed. If the dam provides potentially 50%+ of the genetic material, it would seem logical to me to focus equally on the girls. Yet, when one reads a racing form, they give 4 ancestral names, 3 of which are male.

Therefore, I'm attempting to learn, not only the tail-male side of breeding relationships, but also, tail-female. There are obviously some sires that improve their mares, but there are many who performed well because of the mares they had access to. I'm compiling a list of mares who've produced multiple stakes winners and I find trends in female families regardless of which sires they are bred to. That has led me to think the girls are just as important as the boys. Am I incorrect, or is all of that logic included in the mathematics of your proprietary formulas?

re: The Genetics of Nicking

vineyridge — Wed, 01 Dec 2010 15:22:57 GMT

Is it true that the sire will pass on his X chromosome unmodified to his daughters? While the X chromosome from the dam is always subject to recombination?

If that is the case, then the genetic lottery probability would be considerably reduced in the first generation from the daughter.

re: The Genetics of Nicking

Byron Rogers — Tue, 30 Nov 2010 21:13:20 GMT

Sceptre,

I would indeed require Sadler's Wells to possess total or near total homozygosity to the complementary genes. While one is pensioned and the other dead, I would suggest that with enough horses bred on the cross and enough sons of Sadler's Wells out there and enough daughters of Darshaan that a geneticist could indeed rebuild the genotype for both to see if this held true, but that is something that I will leave to the geneticists.

The intention was not to make the numbers absolute, rather show how in a practical sense it all may work. No doubt environment plays a part, even within those horses that were stakes winners that were bred on the nick. i.e not all of the horses bred on the cross that presumably got the good variants of genes (and this is a presumption) ended up as Gr 1 stakes winners - there are some that are Gr. 1 winners and some that are listed winners. Environment (the way the horse was raised, the trainer, jockey, race conditions, etc) may well have eroded the latter's ability to get to the top where others made it.

re: The Genetics of Nicking

sceptre — Tue, 30 Nov 2010 20:08:23 GMT

Byron,

As to your "real life example"-"work our way back" (Darshaan mares bred to Sadler's Wells): your stated schematic would require Sadler's Wells to possess total homozygosity to the complementary "good variants of genes" (from Darshaan) to support the percentages offered in your conclusion. While not discussed, the spectre of variable homozygosity from one stallion to another could factor into potential genetic explanations for nicking. Lastly, if one is presumming that an all or nothing scenario exists relative to the achievements of these end product nicks (which seems to follow from your example), then wastage (due to all environmental factors) should further erode your figures.