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Okay, I've spent some time over the past couple years checking my lined horses in my appy lines for these genes and putting their results in their notes. Now I wish I'd checked more of them before they were bred and I couldn't take them into the lab to check anymore, but I think I've pretty well figured out what all these genes do from the ones I've tested.

Varnish

This is what determines how much and how fast an appaloosa varnishes out. Any horse can carry for non-varnish (denoted by - in the lab) but only the Evergreen Boughs herd helper is guaranteed to be homozygous for non-varnish. There's no way to tell if a foundation has it or not, until they either varnish out or don't, except by checking what alleles their offspring carry in the lab and seeing if there's any other option to change it to. Het varnish horses varnish out more slowly than hom varnish horses and leave the spots unvarnished. Homozygous varnish horses eventually lose the spots as well. (I'm not sure yet if my het varnish horses will also lose their spots, just more slowly, or if they'll always keep their spots.) Only homozygous non-varnish horses never varnish at all.

Here's a 16 yo horse with hom varnish:


2G Morel 14306492 DP

This was her before she varnished out, I forget what age exactly, but under 6 yo I'm pretty sure:



Here's a 10 yo horse with hom varnish:


3G Morel 15688091

Here's a 10 yo horse with het varnish. You can see compared to the hom varnish that this horse is varnishing much more slowly:


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Here's a 16 yo horse with het varnish, the spots haven't varnished out. I'm not sure if they will eventually and are just slower to varnish or if they will always stay:


2G Morel14306523 DP BoB

Here's a 12 yo horse with no varnish:


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Here's a 17 yo horse with no varnish:


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I have this 16 yo hom varnish, het LPP2 that still has spots, so I'm wondering if LPP2 can let a horse keep the spots? Or at least keep them longer? Or maybe it's the PATN2? All my completely white 16 yo hom varnish horses don't have LPP2 or PATN2. I would have done more testing to have a larger sample to check if I knew I was going to have this question.


2G Morel 14306505 DP

LP Promoter

This determines spot size and is independent from ASR1 (the paid gene that boosts spot size). The non-carrying form (denoted by - in the lab) and LPP1 seem to have about the same effect. I haven't noticed any difference in spot sizes between these two alleles. Sometimes LPP1 seems slightly larger to me, but it might just be normal variation. However, LPP2 causes distinctly smaller spots. It also appears to be incomplete dominant, as two copies cause even smaller spots than just one copy.

Non-carrier:


2G Morel 14306493 DP

Heterozygous LPP1:


2G Morels Treasure AGAXP

Homozygous LPP1:


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Heterozygous LPP2:


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Homozygous LPP2:


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PATN1 & PATN2

Both of these control blanket size but only PATN1 is testable. Het PATN1 causes a partial blanket and hom PATN1 a full leopard appy. You can tell for sure if a horse has PATN2 if they don't have PATN1 yet still have a blanket (a small patch with a spot or two on the rump doesn't count), or if they have one PATN1 but still have a full leopard coat. It can be hard to tell if a horse is het for each because both of these alleles can have a range of expression, anywhere from a small patch on the rump to almost full body blanket. So it can be hard to judge if a het PATN1 horse with a medium sized blanket has that because of the PATN1 alone or possibly also carries for PATN2. One thing I've noticed is it seems that PATN2 often has a slightly "messier" edge with a more stripy look near the underside of the barrel.

Het PATN1:


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Het PATN2:


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Here's a mare that's het for each and partially varnished out, so you can see her spots extend well beyond the white blanket patch, more than most. I don't have a ton of horses like this that I can check, so I'm not certain yet, but I suspect it's the PATN2 pushing the spots beyond the edge of the white blanket. She definitely carries for PATN2 because she has offspring that don't carry for PATN1 yet have large blankets:


3G Morels Albania

Wow, this is amazing. So how is it that you have old photos of some of your horses?

Digging this post back up because the info was super helpful.

When you're back from vaca Ammit, can you explain a bit more about LP promoter? Your wording makes me think it's like PATN, but in the GMT lab "Secondary LP spot size controller" makes me think it is specific to spot size.

When Ammit said that, I started thinking maybe LPP2 makes the blanket white encroach on the spots, so the spots shrink? So in that way it's making the blanket "bigger"? But I'm not sure if I'm thinking about it right. I have noticed since this original post that getting rid of LPP1 and LPP2 will get rid of a tiny white patch on the rump on non PATN appies.

Somewhere, we were talking about PATN 2, but I think I've got the wrong post. I made this foundy this morning, and noticed it has "spots" visible outside its blanket. Does this seem like a candidate for PATN 2?


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Also, Fiddler, I just find an appy herd helper, make a bunch, and check their genes. It takes a while, but it seems like ~1/4 of what I make at least doesn't have varnish.

I just wish we'd had the option to GMT secondary appy genes on foundations when I was still working on my era 14 studs. I think my snowflake stud is homozygous for varnish... just my luck. :P

@Lecobb8, exactly!