Genetics gurus, the X Chromosome

[vineyridge]

Would someone please explain in basic terms how it works in a foal. A mare always has two from different sources which have to be merged with a third from the sire. Are there any non recombinant parts of the X?

So in the mare, her two Xs would combine for the egg, wouldn't they, but then how does the sire's X fit into the picture? Would it even matter until the eggs were produced in a female during the fetal stage?

Sorry to ask, but I simply cannot get my head around this. I keep thinking that the tail female line is the most important in production, but if it isn't consistently from the female why do so many mare lines produce for generations?

[Pan Zareta]

Would someone please explain in basic terms how it works in a foal. A mare always has two from different sources which have to be merged with a third from the sire. Are there any non recombinant parts of the X?

So in the mare, her two Xs would combine for the egg, wouldn't they, but then how does the sire's X fit into the picture? Would it even matter until the eggs were produced in a female during the fetal stage?

Sorry to ask, but I simply cannot get my head around this. I keep thinking that the tail female line is the most important in production, but if it isn't consistently from the female why do so many mare lines produce for generations?

There's no merging. During meiosis sperm and egg are reduced to the haploid state (single copy of each autosome and sex chromosome). All foals receive one X from the dam & either an X or Y from the sire, who essentially passes along intact the X rec'd. from his dam. In a female the entire X is recombinant. In a male, only a small pseudo-autosomal region of the X which has a complement on the Y chrom. undergoes recombination. The only unique aspect of tail female lines is their maternally-inherited mitochondrial DNA, but the fact that certain tf's, more accurately certain tf branches, consistently produce more talented foals can in no way be attributed to that alone.

[vineyridge]

To put my question again in a simpler form that MAYBE I can understand:
The nuclear material of all of a female's eggs are determined during the fetal stages, isn't it? So each egg would contain some of the X genes from the sire and some from the dam's own dam and sire's dam. The egg is already scrambled before any male comes into the resulting mare's life. Which egg matures and which genetic material is in that egg is a sort of lottery in breeding, isn't it?

Then, in fertilization, the sperm brings either an X or Y to the fetus. In the creation of a female offspring from that mating, all of the X chromosome material from a particular egg and sperm would be scrambled again to produce her and HER eggs. In the case of a male, the offspring gets the sire's Y plus one of the millions of possible combinations of the genetic material from the dam's eggs, depending on which one matured and got fertilized.

Is that right? Or are we still limited by the number of "parents" involved. All of the Mendelian charts go by combining 2 parents each with 2 genes and come out in quarters, not millions of possibilities. I think I read somewhere that inactive genetic material from ancestors can be passed along by a sperm or egg and activated in a descendant. Am I misunderstanding what I read?

Where do sex linked characteristics come into this? Have any sex linked characteristics actually been found in horses, and if so, where would they be on the gene map? I'm assuming that all of the other things that we talk about like color or some diseases or genetic abnormalities (Fetal White Syndrome, etc) that have to come from one or both sides have nothing to do with sex, but are the result of genes on other chromosomes.

[Pan Zareta]

To put my question again in a simpler form that MAYBE I can understand:
The nuclear material of all of a female's eggs are determined during the fetal stages, isn't it?

Yes. During embryonic development the 'eggs' arrest in early meiosis and don't resume development until the organism reaches sexual maturity, at which point one (usually..hopefully ) egg is targeted to resume meiosis and produce a mature ovum (egg ready for fertilization) during each cycle.

So each egg would contain some of the X genes from the sire and some from the dam's own dam and sire's dam. The egg is already scrambled before any male comes into the resulting mare's life. Which egg matures and which genetic material is in that egg is a sort of lottery in breeding, isn't it?

In simplest terms, each ovum contains ONE X chromosome which due to 'scrambling' (recombination) is a composite of ~50% DNA rec'd. from the female parent's X and 50% from the male parent's X.

Then, in fertilization, the sperm brings either an X or Y to the fetus. In the creation of a female offspring from that mating, all of the X chromosome material from a particular egg and sperm would be scrambled again to produce her and HER eggs.

Only her eggs undergo recombination. In all other cells one of the X chromosomes is 'turned off' (X inactivation), but there's no 'scrambling'.

In the case of a male, the offspring gets the sire's Y plus one of the millions of possible combinations of the genetic material from the dam's eggs, depending on which one matured and got fertilized.

Yes, but the male passes his one X chromosome pretty much 'unscrambled' along to his daus. b/c other than a tiny pseudoautosomal region the X and Y don't recombine.

Is that right? Or are we still limited by the number of "parents" involved. All of the Mendelian charts go by combining 2 parents each with 2 genes and come out in quarters, not millions of possibilities. I think I read somewhere that inactive genetic material from ancestors can be passed along by a sperm or egg and activated in a descendant. Am I misunderstanding what I read?

I may be wrong, but I think you're referring to the fact that some genes are activated or not depending upon the gender of the parent that contributed the chromosome on which they reside. What I've read dealt with autosomal genes, but perhaps this is possible with X chromosome traits in females.

Where do sex linked characteristics come into this? Have any sex linked characteristics actually been found in horses, and if so, where would they be on the gene map?

Any characteristic governed by genes on the X or Y chromosome is sex-linked. The term is often synonymous w/ X-linked b/c the tiny Y contains only the 'instructions' necessary to make the male a male, whereas the X carries genes for traits other than secondary sex characteristics. To find out what traits have been mapped to the equine X, try the Horsemap database

I'm assuming that all of the other things that we talk about like color or some diseases or genetic abnormalities (Fetal White Syndrome, etc) that have to come from one or both sides have nothing to do with sex, but are the result of genes on other chromosomes.

I don't know about 'all the other things' but Dominant White is an autosomal (all chromosomes other than the X & Y are autosomes) trait.

[vineyridge]

PZ, thank you so much for being so tolerant of my ignorance and trying to enlighten me. So far you've done a wonderful job.

Let's get down to a specific case. Because it would seem that there could be a huge difference between the effect of the X on performance aspects of a mare, if there are any performance aspects , as opposed to breeding (eggs) and being a good broodmare.

Buckpasser is out of Busanda, FF 1x. So he will be passing his Busanda X chromosome pretty much intact to all his daughters. It as a whole either will or will not be turned on in a filly. Is that right? Or, in the process of filly creation will his be mixed up with the dam's for whatever processes the X controls?

He was bred to Intriguing, also FF 1x, but several more generations removed from La Troienne. The X that she contributes will be more of a Mish Mash than his, because it contains material from both Swaps' dam Iron Reward and Glamour. Intriguing's X, though, might be the one that is inactivated except in the production of a filly's eggs. Or the filly could inherit the mixture talked about in the previous paragraph.

Their daughter was Numbered Account, who was both a great race mare and a great broodmare. Here's where my confusion lies.
a) she could inherit Buckpasser's X intact and it would be the one that is either turned on or turned off. If that's the case, and the X has any performance effects, that could be huge, because she would be living with 100% Busanda.
b) she could inherit an X from Intriguing that is a mishmash of Glamour and Iron Reward, but it would stay whole on one side of the chromosome and be turned on or off. Also could have a huge effect on her life, as she would live with 100% the dam side.
c) Her X for her own life could be a mixture of Busanda and Glamour at 50% each but all scrambled. One strand of the chromosome would be turned off, but the turned off side would be as much of a mixture as the side that is active.
d) For breeding purposes, the X in her eggs would be a scramble of Busanda's and Iron Reward's and Glamour's.

No wonder Numbered Account was such a great performer and broodmare, if the X has control over what gets turned on and off in foals. Since she is 1x and has so much linebreeding to super horses top and bottom, there would be far less diversity among the possible combinations that could be turned on and off. That would mean, wouldn't it, that the probability of her being great would be greater than if there were no top and bottom linebreeding? (Yes, I know that technically in TB land linebreeding HAS to be top and bottom, but that's not the case in the rest of breeder land. )

It's possible for humans to "skip a generation" on many heritable traits. How does this "skipping a generation" work? Sometimes it's more than one generation. Is that just simply recessive versus dominant? I'm thinking things like height and proportion and shape of jaws and ears, etc. Those things aren't just limited to what showed up in grandparents, are they? Didn't I read somewhere that in the "dead" DNA (can't think of the term) that scientists used to think was trash, there might be material that moves to an active spot during recombination? And that that stuff allows for many millions more possible combinations than just the 2x2 from the parents?

BTW, I can't translate the horse map site. Is there a summary in plain English there on what the Horse X controls?

[Pan Zareta]

Buckpasser is out of Busanda, FF 1x. So he will be passing his Busanda X chromosome pretty much intact to all his daughters. It as a whole either will or will not be turned on in a filly. Is that right? Or, in the process of filly creation will his be mixed up with the dam's for whatever processes the X controls?

In somatic cells (all body cells other than reproductive cells in the ovary & testes) there's no "mixing up", but within this hypothetical filly the inactivated X is not always the same one. X inactivation occurs early in embryonic development, but at a multi-cell stage, and in placental mammals which X is inactivated is random. In some cell lines it's the mothers, in others it's the father's. After inactivation all descendants of those cells will have the same X inactivated. In other words, the X that's inactive in bone cells may not be the same X that's inactive in muscle cells. Muddying the water further is the fact that inactivation does not seem to apply to a few genes on the X, although how they can 'send instructions' from the Barr body (the inactivated X) is unclear.

It's possible for humans to "skip a generation" on many heritable traits.

No, it's not, but there are a number of reasons why that might seem to be true. Single gene traits with a simple recessive mode of inheritance can easily appear to skip a generation.

Sometimes it's more than one generation. Is that just simply recessive versus dominant? I'm thinking things like height and proportion and shape of jaws and ears, etc. Those things aren't just limited to what showed up in grandparents, are they?

It's seldom as simple as recessive v. dominant. Many traits, like height, are multi-factorial, dependent upon more than one gene. The degree to which some traits are expressed is dependent upon the number of times a particular DNA sequence is repeated. As mentioned in a previous post, expression (or not) of some genes is dependent upon the gender of the parent from whom they were rec'd. Etc.

Didn't I read somewhere that in the "dead" DNA (can't think of the term) that scientists used to think was trash, there might be material that moves to an active spot during recombination? And that that stuff allows for many millions more possible combinations than just the 2x2 from the parents?

I'm guessing you mean the DNA that does not code for protein, often referred to in the fairly recent past as "junk". Yeah, it appears to be more important than was once believed, but I'm not clear on what you're asking in the last sentence.

BTW, I can't translate the horse map site. Is there a summary in plain English there on what the Horse X controls?

Try this one.

[vineyridge]

Thanks, PZ

You've explained this so well, even I can understand.

From the map, it would appear that the X chromosome is by far the largest in the horse in terms of size and is composed of two different segments, one smaller than the other.

[Pan Zareta]

From the map, it would appear that the X chromosome is by far the largest in the horse in terms of size

You might want to have another look at chromosome #1

and is composed of two different segments, one smaller than the other.

aka: the long arm and the short arm

[vineyridge]

I've saved a link to a free MIT genetics course. Looks like I need to be trying to wade through it. At my age and lack of education, it's going to be very tough going.

Do you think the fact that Summer Bird was carrying Pocahontas's MtDNA might have had something to do with his closing kick in the Belmont?

[Pan Zareta]

Do you think the fact that Summer Bird was carrying Pocahontas's MtDNA might have had something to do with his closing kick in the Belmont?

Summer Bird *may* have the same mtDNA haplotype Pocahontas did. It appears (from Genbank accession definitions) that at least two haplotypes have been identified in family 3, but no specifics are publicly available as to lineage for either. Even if he does, I'd say that as far as genetic factors go SB's performance yesterday had far more to do with the fact that 50% of his DNA came from a sire who did pretty much the same thing in the same race.

[vineyridge]

Oops. He goes back to Black Duchess and the Wild Dayrell Mare, not Pocahontas in the direct line. The Black Duchess line is really nice for sport. You have to go all the way back to Fractious for a common ancestress.

There are a really large number of super mares and producers in Summer Bird's direct lineage (3-o) for many generations, all the way back.

I love to see Spotted Beauty and Beadah and Foggy Note and Ruby Slippers in pedigrees.

Mine That Bird is 23-b, and that's the FF of Cotillion and Gallopade. Their progeny were superlative at the 4 heat, 4 miles races that were common in the USA in the 19th century. He goes back to them.

If the mitochrondia are the engines that fuel cell performance, wouldn't very efficient mitochrondia affect stamina?

[Pan Zareta]

You have to go all the way back to Fractious for a common ancestress.

Actually, her dau. Amazon is the most recent common ancestress in tail-female of Pocahontas & Summer Bird. She tails to Amazon's dau. Harpalice 1814 x Gohanna, he to Antiope 1817 x Whalebone. In theory (and absent de novo mutations) they should still share the same mtDNA haplotype, as should all branches of fam. 3, but apparently there's at least one misplaced lineage in there, somewhere.

Mine That Bird is 23-b, and that's the FF of Cotillion and Gallopade. Their progeny were superlative at the 4 heat, 4 miles races that were common in the USA in the 19th century. He goes back to them.

So does one of the most brilliant speedballs ever, the great Domino.
That's another family (23) in which two mtDNA haplotypes have been identified, specific lineages undisclosed.

If the mitochrondia are the engines that fuel cell performance, wouldn't very efficient mitochrondia affect stamina?

Sure, but it's just one of soooooo many factors that do. Look at all the G1 winners w/ full siblings that can't run fast enough or long enough to get out of their own way. Same mitochondria, 50% +/-15% shared recombinant DNA -- radically different results.

[vineyridge]

23-b is one of the strongest female families in North America, probably because of Gallopade lines.

Is it equally strong in GB/Ire and Europe? From the lineages on Bloodlines.net, it looks to be almost exclusively North American sourced at this point and based on Gallopade and her daughters.

Speaking of Domino, Mannie Gray didn't hurt. His full sister, Correction, according to the DB, had 122 starts, and won over 45k in the early 1890's which would have been a huge amount of money. Her line still lives. She too was a brilliant sprinter, but what was considered a sprint at the time? NA had only recently gone from heats racing, and any single race of less than a mile and a half was called a sprint at the time of the changeover, IIRC. TB Heritage says Domino was best at sprint distances of a mile and an eighth or less. He seems to have been what we'd call a miler after his two year old year from what I can discover to this point.

Domino's story and how he was misused at the beginning of his career is very sad.

[xfactor fan]

Don't know if this should be another thread, but here goes.

Let's simplify the parts that make up a race horse.

Conformation
Muscle type
mtDNA

And yes the list could be lots longer.

We know there is a connection between mtDNA and energy usage.

How does that affect/interact with different body types.

Lets say the typical distance horse, tall, lean, with lots of distance muscle.
How do the assorted mtDNA types impact performance.

Or the sprinter? Short stocky bulky muscle?

[Matchemforever]

Conformation
Muscle type
mtDNA

And yes the list could be lots longer.

We know there is a connection between mtDNA and energy usage.

How does that affect/interact with different body types.

Lets say the typical distance horse, tall, lean, with lots of distance muscle.
How do the assorted mtDNA types impact performance.

OK, I think the one that always puzzled me was Secretariat. He looked like a Quarter Horse in a lot of ways, big, bulky horse. Ran either way and certainly could stay the distance. I'd have thought he had lots of fast twitch muscles with all that bulk and couldn't go the distance, but yet he did.

And the Bold Ruler's were not known as exactly distance specialists although there is the Princequillo on the dam's side.

Still, just by looks, I would not have thought he'd go much over a mile.

Is it the mtDNA in this case?