Y chromosomes

[xfactor fan]

What's the current thinking about the Y chromosome? Last study that I saw claimed that all TB's carry the same Y, no matter what the sire line. This was followed by some outcry about what part of the Y was really being studied. Has this settled down? Has more research been done?

Are sire lines meaningless?

Was thinking about this in regard to the Galopin thread. And the Eclipse, and all the other presumed mistakes in paternal lines that could be out there.
mtDNA is certainly finding errors in the maternal lines.


Thanks

[diomed]

What's the current thinking about the Y chromosome? Last study that I saw claimed that all TB's carry the same Y, no matter what the sire line. This was followed by some outcry about what part of the Y was really being studied. Has this settled down? Has more research been done?

Are sire lines meaningless?

Was thinking about this in regard to the Galopin thread. And the Eclipse, and all the other presumed mistakes in paternal lines that could be out there.
mtDNA is certainly finding errors in the maternal lines.


Thanks

I wasn't aware of a Y chromosome study. Cool. Is there a link you can provide?

I have always had my suspicions about the Y chromosome being genetically weak.
The amount of material contained has already been proven to be WAY less(both good and bad genes too).
In humans, they have found the same thing. That all humans come from 3 different Y Chromosomes. It was a documentary on PBS that I watched and they were able to trace the "journey" of man based on different Y chromosomes. They are now just starting with the mtDNA story, that is very much more diverse.

The problem with the "sire line" mentality is that under that Y chromosome line are many other lines and families that often get ignored and play a much larger factor in the gene pool.

The latest thread on Hyperion(in another section of this board) is a perfect example of that.
People seem to think that when the Y line disappears then so does the said horse's influence. Nothing could be farther from the truth.
Think of how many horses are inbred/linebred to the individual but are not necessarily from that Y line.
They still carry those genes!
Nearctic is from a Hyperion mare. Look how much Nearctic is out there!

I try to explain this to people but the 'sire line obsessed' just don't want to hear it.
I think it is a MALE bias myself. LOL!!

[Bill from WA]

Here is a discussion re: that subject.
http://daughterofthewind.org/the-y-chro ... ing-stock/

Bill

[diomed]

Thanks for that link Bill.
It just furthers my beliefs that: (A) The Y often does this very thing in nature (B) People are still obsessed with the MALE line (C) Arabian people are still elitist snobs(LOL).

I believe that the influences of the Godolphin Barb and Byerely Turk still have more overall influence in the TB's overall genetic profile than the Darley Arabian.
But as everyone else points out the 'King' has to be the Y ancestor. (rolls eyes).
Bah!!!!!!
People need to look at the deep ancestry of the TB.
There is much more Turk and Barb influence than Arabian.

[xfactor fan]

Diomed,

I think your documentary was out of date. There's more than three versions of the human Y out there. And in fact the Y chromosome data is reinforcing the mtDNA data on human migrations.

There was a great article in Discover magazine about the Y chromosome of Ghengis Khan. It sure looks like every other male in Mongolia is a direct male line descendant of the great Khan. Or his father, or brothers.

There's a theory floating around out there that ALL domestic horses are descended from one stallion.

Wild horses (true wild horses, not feral horses) have 66 chromosomes. Domestic horses 64. At some time there was a mutation that fused two chromosomes together. Because all the genetic data was present on the fused chromosome, this mutation was not fatal, and resulted in a breeding population that had horses with 66, 65, and 64 chromosomes.

This over time resulted in two herds, one with 66 chromosomes, and one with 64 chromosomes. All domestic horses spring from a stallion, or stallions from the herd of 64 chromosomes.

Given how unenthusiastic wild horses are about being "tamed" I've always wondered if something did get left out when the original two chromosomes fused.

As for the fixation on the male line, in part it comes from the bible--just think of the begats. And John begat, Saul, who begat Ralph, who begat....

Also the economic realities of the horse business. It pays to advertise your stallion once he has retired to stud. Lots of folks advertising lots of stallions over many years, coupled with the western view that females were only vessels for male energy, has contributed to the fixation on male lines.

Bill,

Great site. I'd love to hear the Arab side of the history of any of the original imported Eastern stallions that were the foundation of the TB.

[Pan Zareta]

A doctoral dissertaion submitted 12/2004 at TAMU sampled a variety of domestic horse breeds, including the TB, and found one point of segregation on the Y chromosome, MS(microsatellite)30 at which 3 y-specific (MS30 has an analogue on the X chrom.) alleles were found. Full text in pdf for can be found here. Implications for pedigree research - and sire line mythology - are unknown. Meaningless or not, sire line reverence lives on. The AQHA will probably approve registration of clones soon, regardless of the fact that it isn't a true clone unless the mtDNA of the host ovum is identical to that of the cloned individual. But clones would never be registered if that was the y chromosome being changed out. Why....it wouldn't be an Own Son of Old So 'n So!!

Diomed, most sources agree that Herod exerts the single greatest genetic influence on the contemporary TB.

Xfactor fan, I enjoyed that article about GK too. Wasn't there a map in which you could pretty much track his path across Asia by presence of a certain yDNA haplotype in the contemporary population?

[vineyridge]

PZ, as you know, Gem Twist was cloned.

At the time the Chapots owned his full sister and some of her daughters. If she donated the egg and also served as the recipient mare, wouldn't that be a "better" clone than otherwise?

Thanks for the article on the equid Y chromosome. It's long but well worth reading.

[Pan Zareta]

PZ, as you know, Gem Twist was cloned.

At the time the Chapots owned his full sister and some of her daughters. If she donated the egg and also served as the recipient mare, wouldn't that be a "better" clone than otherwise?

It would probably be as close as possible to a true clone. I don't have a problem with cloning, per se. My issues are the registration of clones as breeding stock and, to borrow Diomed's term, the "sire line mentality", esp. as it applies to some QH breeders of my acquaintance. If matrilineage = mtDNA and patrilineage = yDNA, all evidence indicates that the former is far more influential to performance, but some of the good ol' boys around here haven't gotten that memo yet. It's just a personal peeve, and I'm off the soapbox now.

[xfactor fan]

Yes, the Discover magazine had a map with the whole cluster/clade thing. And while they were being very openminded about it, and suggested that this simply could be a Y common to GK's paternal family, it sure looked like the Y concentrations matched the conquests.

I've always thought cloning without matching the mtDNA families would be a great way to look at and test the influence of mtDNA on racing ability.

Also since in a regular foal the maternal X is always the active X in placental tissue, what happens if neither of the X's is a match to the surogate mare's X's?

[vineyridge]

In the paper that PZ cited, there is a finding that the equid Y seems to be far less variable than some other mammalian Ys. If I'm reading it correctly, there ARE a very few microsites of difference, in some of the genes that regulate fertility.

Question for the genetics experts: The gene map that was done was only of the parts of the Y that are not subject to the recombining (is that the correct term) process during the creation of the Y chromosome. Do we know what those genes control? Sire lines could still be important, but just not in the non recombining Y part.

Good question, x factor.

[Pan Zareta]

The gene map that was done was only of the parts of the Y that are not subject to the recombining (is that the correct term) process during the creation of the Y chromosome. Do we know what those genes control? Sire lines could still be important, but just not in the non recombining Y part.

The only part of the Y that's recombinant is a small pseudo-autosomal region which recombines w/ its analogue on the X. Since it does recombine, it isn't unique to a sire line and so is meaningless in that regard.

Also since in a regular foal the maternal X is always the active X in placental tissue, what happens if neither of the X's is a match to the surogate mare's X's?

Excellent question, and the answer probably has something to do with why there have been so many placental problems in clones. ViaGen claims they've solved this problem in the horse, but they have a commercial interest in the matter. TAMU says the technology's improving, but I don't think they've claimed this problem's solved yet.

[xfactor fan]

Well, I waded through the Y chromosome paper, and have a couple of questions.


Did the author ever tie the three markers they did find to any breeds?

And does the lack of variation confirm a major bottleneck sometime in the recent past for the domestic horse?

[Pan Zareta]

Did the author ever tie the three markers they did find to any breeds?

See Table 4, p. 97-98. As many as 2 alleles may be present on the TB Y, based on the 4 TBs tested. Three may be present on the QH Y (4 tested). For other breeds see Table 4, p.97-98.

Obviously, meaningful conclusions are impossible by sample size, but it's the only encouragement to date that there might be some yDNA distinction between sire lines.

And does the lack of variation confirm a major bottleneck sometime in the recent past for the domestic horse?

I'm not sure the term bottleneck is used, but that's essentially what's suggested in the discussion of the lack of the diversity in the domestic horse Y. Iirc, the other equids sampled weren't quite as monolithic.

[vineyridge]

If all that the non-recombining parts of the Y chromosome do is control maleness, what difference would a single MS site of variation be likely to make where performance is concerned?

[Pan Zareta]

what difference would a single MS site of variation be likely to make where performance is concerned?

Probably none whatosever.