Basics and coat colors

Since there was a request (Hi, Dom!), I'm going to work my way through the other horse color genetics, a few at a time.

Caveat here: I learned all of this a few years ago.  If I get energetic, I might go look up some of the newer stuff, but that's going to depend on how curious I get. It's also going to be the as-layman's-terms-as-I-can-get version of horse color genetics; I am by no means a biologist and I honestly check out when you get into things like "these genes share the same locus."  (Which I think means they're on the same piece of the gene?  Maybe?)  So a) bear with me, and b) bear in mind that I could be wrong in the details.

Let's tackle the basics first.  Every gene we talk about will have an off state and one or more on states.  Every horse has two copies of the gene, one that came from mom and one that came from dad.  And every horse has... well, pretty much all of the genes they've discovered; what's turned on and what's turned off is what determines what color they are.  All the genes together kind of build a chain of information, and if you know how to read the genetic results, you can generally guess what color the horse is without seeing it.

Some genes are dominant.  That means that if one copy is turned on, you see the effects.

Some genes are incompletely dominant.  That means that if one copy is turned on, you see the effects... but if both copies of the gene are turned on, you see a different effect.  (LP is a good example of this.)

Some genes are recessive.  That means to see any effect, you have to have both of them.  I actually don't know that they've spotted any of the color genes that are recessive for sure?  Most of them seem to be dominant or incompletely dominant.  That said - there are genetic diseases that affect horses (HERDA, I'm looking at you) that are recessive, so it's good to know what it does.

When you write down the genetics, you write them in pairs.  So, for instance, Ee means a certain color.  Generally, uppercase means the gene is turned on; lowercase means it's turned off.  And a question mark, which you'd see as E? or e?, means that half the genetic pair is known, but the other half either is unknown or - as will be the case when I use it as I'm explaining - unimportant.

And now... because we have to start somewhere, let's start with chestnut!

From a local show

Chestnut happens when a gene called extension is turned off and nothing else that would affect the red coat is turned on.  (Some genes affect chestnuts only, some affect black-based horses only, and some affect both - so as long as those are off, you've got chestnut.)

Now, if extension is turned on - one or both copies, as it's a dominant gene - you get black.

Gorgeous Morgan at the same local show

Again, as with chestnut, this assumes that nothing else is turned on that would affect the color.  Interesting side note: there was some discussion about whether there were two types of black - either separate genes or Ee vs EE - one of which fades in the sun and one of which doesn't.  I'm not sure where that debate stands at this point, but it is an interesting point that some black horses fade and some don't.

So what affects the color?  Agouti, grey, cream, pearl, silver, dun, and champagne.  With the exception of agouti and grey, they're generally referred to as dilute genes, and considering how freaking long this post is getting, I'll save the dilutes for another day.

Agouti is kind of special.  Why?  It's what gives us bays and browns, the third "basic horse color" everybody learns.

Who, me?

To get a bay horse, you have to have extension turned on and agouti turned on.  So the horse has to be E?A?.  Now, they could be EEAA; they could be EeAa.  They could be some combination of the two.

Brown is... brown depends on who you listen to.  Some people say brown happens when you've got a horse who is E?AA.  Some people say that brown is actually a different version of bay, generally notated as At - and there was a test for that for a while, but it seems to be unavailable these days.  Some people say that brown is actually bay plus some darkening genes (generally referred to as sooty) and a gene that lightens the muzzle and flanks (generally referred to as pangare). 

Theory at the time I was really researching all of this leaned towards the At gene for brown.  It furthermore suggested that there was an additional gene in there called A+ that produced wild bay (a bay where the black only goes up to the pasterns or so).  I haven't seen any recent, reliable research on the subject, though.

And last but not least for today is grey.  (Or gray, if you prefer that spelling.)  Grey is special because grey ruins everything.

One of the BO's mares, sadly deceased.

Well, okay, it doesn't actually ruin anything except color.  :)

Grey basically takes whatever else you've got going on, color-wise, and just... hides it.  And it's dominant - one copy turned on means you've got a grey horse.  There's some theory back and forth about whether two copies mean you grey faster or not, and there's some fascinating discussion among breeders about whether you can tell if a foal will turn grey before their coats start to turn (answer: sometimes, there are certain characteristics that tend to point that way - but not always)... but in the end?  Grey is grey, and it only really matters what's underneath if you're breeding.

Now, I say grey ruins everything... that's not entirely true.  Grey on a horse with LPlp and a PATN gene does something funky.

Like this mare.  Born so dark a brown she was thought to be black, greyed out to this.

The color basically concentrates in the spots, which either don't ever go grey or go grey so slowly that it's hardly noticeable.  The rest of the horse greys out just like any other horse would.  If you google the Friesian/App cross Mystic Warrior, he's another great example of this.  I'm not sure what would happen if you've got LPLP and grey, but I'm going to go out on a limb here and say you'd have a white horse!

Filling in

Not the best photo, between the shadows and the shave lines, but he's been an adventure to photograph.

Another cold weekend, complicated by various things (including a late night, a spousal stomach bug, and assorted other fun), meant I didn't get out to the barn.  Instead, have the above picture of a 10 month old Justice, in what is probably the one full-body photo I have of him from 2016 that isn't thoroughly embarrassing.  (Poor baby boy.  I keep thinking of the rule of thumb from the Chronicle of the Horse breeding subforum: three days, three months, and three years are the ages where you can best see what you've got.  Three days and three months?  Beautiful.  C'mon, three years...)

Instead, I figured I should probably explain what the heck I'm talking about when I talk about Justice's color and genetics.

I'm not going to go into color genetics right now, other than to note that I can make some basic assumptions about Justice's.  His father is a chestnut; his mother is a bay.  So I know his extension gene (the thing that determines if you start from a black or red base) and I know part of his agouti gene (the on/off switch for bay, only visible if your base is black).  He has to be Ee A?, because he's visibly bay!  I also feel pretty confident that he doesn't carry cream, dun, or grey; with all three, if you have one copy of the gene turned on, you're going to show it, no matter what base color you've got.  Neither parent is grey, neither has dun, and dad definitely isn't carrying cream, because he's chestnut and not palomino; while it's possible that mom could be a buckskin, she presents as a pretty classic dark bay.

I'm also not going to talk too much about the non-Appaloosa white patterns.  There are a metric butt-ton of them (from the classic paint tobiano, frame overo, and splash to the roans, rabicanos, and sabinos to the dominant white/white spotting, which depending on which one a horse has, what they look like).  If there's interest, let me know; I don't have a problem talking about them - the Ws are particularly fascinating to me - but for talking about Justice, none of it matters.  His registry says no tobiano, no frame, no dominant white, and no to certain types of splash; dad's been tested and carries none of it, and while it's possible that mom might carry one of the ones that likes to hide (frame, for instance), she wasn't required to test.  So we can assume he has none of them.

These two are great examples of classic tobiano.

Classic frame, with the addition of a bald face and some leg markings.

Pretty sure this guy is either splash+sabino or splash+dominant white.

Instead, I'm going to talk about the two parts of the Appaloosa genetic shenanigans.  Part one is what's referred to as the Leopard Complex gene (or LP).  Part two is the PATN genes, the ones that actually dictate the pattern.

LP is an off-on-REALLY ON switch.  If both copies are off, you've got a solid horse.  It doesn't matter what PATN genes the horse might have; they're never going to show, because the thing that activates them is LP.

Hmm, this example looks familiar...  Cessa is known to carry at least one PATN gene, but has no LP - so nothing shows.

If one copy of the LP gene is turned on, then the PATN genes can start to show.  That's when you can get patterns with lots of spots, big or small.  That's when the mottled skin, white sclera around the eye, and striped hooves show up.

Cessa's 2015 foal, Reign of Stars - one copy of LP, and at least one PATN gene. Also Justice's half-sister!

If both copies of the LP gene are turned on, then three things happen.  The PATN gene will show, of course - but the spots vanish or almost vanish, leaving vast white territory.  And the horse will be night-blind.  Horses with both copies of the LP gene turned on produce what's commonly referred to as fewspots - the fully white Apps and the ones with white blankets with no spots on them.

One of the horses at the barn - LP/LP with a heck of a blanket.

The PATN genes are where most of the research into Appaloosa genetics is concentrated right now.  They know that no PATN genes means a horse that can only display Appaloosa roaning (aka varnish roan).  Varnish roan can look very similar to classic roan, but it has one very specific characteristic aside from the Appaloosa stuff (striped hooves, etc): they tend to retain dark areas over prominent bones.

Like Justice's daddy here

And the roaning isn't just limited to horses with no PATN, although it's only called varnish roan when there aren't any other patterns.  Any horse with LP can roan in the non-patterned areas of the coat.

Some horses roan quickly; some don't.  I know one LP/lp individual who is creeping up on 10 and has a few roan patches - and that's it.  On the other hand, Reign looks like she means to shed out almost pure white this spring - and she's only a couple of months older than Justice.

Research has also shown that PATN1 controls large areas of white patterning that cover 60-100% of the body.  Most leopards will have PATN1.  PATN1 is the first (and at this time the only) pattern gene available for public testing.

All the other patterns seem to be built via multiple different PATN genes, very few of which have been identified. For example, they know that PATN2 is related to the blanket pattern, but it's not a strict 1 to 1 relationship; the size and shape seem to be determined by other PATN genes, so a horse with a spectacular, large blanket may or may not pass it down.

Most of the research about LP and the PATN genes is coming out of The Appaloosa Project, and they're still working to understand it.  Any mangling here is totally my fault.  :)

Now, all that explained... when I natter on about this little face:

And what he's got going on with his LP, I've got some thought processes going on:

1. I know dad was tested as LP/lp.  I know mom is the daughter of a Percheron and an Appaloosa, and I know she shows the characteristics of having LP, so she can only be LP/lp.
2. I know mom doesn't have any PATN; aside from her random traveling spot, she doesn't have any white at all.
3. My best guess at dad's pattern is that he's got a blanket.  He's pretty thoroughly roaned out, but he's got spots in roughly the right area for a blanket and two of his three foals bred at the farm have blankets.
4. I know Justice has at least one copy of LP, from one of his parents, because he's got those Appaloosa characteristics.  Based on #1, that means he can only be LP/lp (2 in 3 chance) or LP/LP (1 in 3 chance).
5. If you've got LP and a PATN gene, chances are you're going to see it before the foal is weaned, if not at birth.  Every LP baby I've ever seen, if they had a pattern, it was there at birth or shortly thereafter.  Justice came out brown, continued to be brown through weaning, and honestly didn't show anything but brown until last spring.  So I'm willing to bet he's a varnish roan.

Since I don't plan to breed him (brain surgery this spring!), my wanting to know if he's got one LP or two is about half curiosity; the color of future generations does not depend on this.  It's fascinating that he's throwing out roan spots while his mother stays pretty much solid, because it implies that he's got something she doesn't - and it sure doesn't seem to be a PATN gene.

On the other hand, it is actually kind of important to know if he's night-blind.  Two copies of LP turned on and night-blindness are inextricably linked.  You can't separate them.  You got one, you got the other.  Not that I'm likely to go night riding any time soon, but it will affect how I approach taking him in and out of barns and trailers, and it will affect boarding if I should need to move him from where he is now.

Knowing when it's time to give up for the day

Today has been windy, sunny, and cool.  A little cold to actually be nice weather, but it wasn't bad.

Justice modeled his brand new adult-sized halter for some photos, and we wandered around the pasture for a bit, just hanging out.

It's a little big still, mom.

He gets green instead of blue, because I was informed by my family that both horses were brown and how would they tell them apart?  (Uh, I thought the star and snip might be a clue...)  So color-coding it is!

Granted, if he keeps up this pace of growing random white areas in the week since I saw him last, I may not have two brown horses for long...

All was otherwise quiet on the baby front.  The main herd was a different story.  Not sure if it was the wind or something else, but the one gelding in the group had his head up his butt and kept breaking and running for no apparent reason.  I startled him, I think, but usually you call his name and he comes over to check you out.  After that, everything is fine.  Not so much today; he stared at me like he'd never seen a human before, and eventually bolted.

Coming when called - the first time. Good girl!

Of course, when he blew, the rest of the herd started running too.  I went from having a quiet moment with Cessa to hearing galloping behind me suddenly... and then to throwing out an elbow to protect myself as Cessa took off after them.

Coming when called - the second time.  Again, good girl!

I figured something had spooked them, so I sauntered after and called Cessa again when they'd stopped.  I basically had time to pat her once or twice and the herd took off again.  She followed, but the super-calm mare that belongs to the BO's mom hung out with me for a few minutes. Then, all of a sudden, she bolted.

There comes a point where you acknowledge that you are surrounded by absolute lunatics, and it's really not worth it to keep risking life and limb.  Thaaaaat... was that point.  They weren't freaking out at anything I could see, and they didn't seem to be freaking out at me personally.  I didn't actually need Cessa for anything.  Time to leave them to get the crazies out of their system.

Of course, then I managed to both face-plant on my way out of the pasture and almost twist an ankle walking to the car, so maybe it's just today? lol

Magical color-changing pony

Today was one of those days where crap happened, the BOs weren't up for doing much, and to be honest - after my activities earlier in the day, I wasn't either!

Justice... is growing more white hair.

That white on his eyelids?  That wasn't there Christmas Eve.

I'm honestly, seriously starting to think he's got two copies of the Appaloosa (LP) gene.  I know his dam and sire.  His dam is going to be 7 this year, and aside from a few random appearing and vanishing spots is still solid dark brown.  When I say a few?  She spent part of the summer looking like someone put sunscreen on her nose, and now I believe she's maybe got one more spot somewhere?

His sire, on the other hand, is a roaned-out, minimal-pattern chestnut.  He's got some small spots, but mostly he's white with red accents, in that particular way Appaloosas roan.

We know Justice has at least one copy of LP, because he's got the characteristics.  There's a 1 in 3 chance he's LP/LP, since both parents are heterozygous.  As quickly as he's trying to roan out in comparison to mom...

Starting to look like a real boy (as long as we ignore the combo of baby neck and maximum what-is-that alert mode) - and about to outgrow his halter!

We also made an effort to conquer the puddle of doooooooom.

Or, you know, the puddle of moderate size and a certain amount of concern.

He had to think about it a bunch, but he did walk through it twice, so I'm calling that a victory!

Cessa and I just hung out a bit, taking stupid selfies and trying to figure out how on earth she gets entire seed pods tangled up in her tail and doesn't seem to notice.

So... why are you back there again? I'm just gonna find another one.

Apparently as long as I don't catch her and there's a chance for cookies, I've got a pocket pony.

Cookies. You mentioned cookies.

And I'm totally fine with that... for now.

Happy New Year...

So despite good intentions, I have yet to be out to the barn to mess with the beasties this year.

New Year's weekend, we had a barn party planned - and those cold temperatures had come back, so it was going to be an indoor party, thankyouverymuch.  But one of the BOs came down with some sort of illness, and we all assured her that party could wait for her to feel better and hunkered down in our nice warm houses.

During the week, it warmed up, but by the weekend, cold as hell again.  And snow on Friday didn't help - nor did the sick BO being in the hospital.  (She got out Saturday, and is doing well, but things were kind of wacky.  And cold.  Did I mention cold?)

This weekend is the rescheduled barn party!  And rain.  At least I'll get to wave at them prancing around in the mud...

(Photo from last February's attempt at a Valentine's Day shoot.  I'm thinking we need white lipstick for that nose, not pink...)

Christmas Eve

Nothing special around these parts, just a super-foggy day and a distribution of all the cookies.  We'll be more festive next time; the Santa hat is in the mail...

Winter Is Coming

Screenshot from earlier this week

Perhaps not surprisingly given the area of the country I live in - cold is not my thing.  In fact, the whole group of us at the barn tend to resoundingly and unanimously decide that if the weather isn't going to get above 50 degrees, that's a nope situation.

The forecast screenshotted above is for my house; the barn, being 40 or so miles farther north, is generally a few degrees colder.  That forecast also doesn't show the freaking wind chill, which is supposed to reach single digits.  Today narrowly avoided the nope because the temperature was going to be comfortable into the early afternoon - but that didn't mean any of us wanted to hang out for long! 

So I stopped at the weanling pasture to say hi to the little guy, and to check on Project "Make Justice Fat."  (He grew inches and winter hair at once.  It was... even more not pretty than his usual baby awkwardness.)

Ugh, that neck is so sad. Go play more, baby!

Fatter, taller, and still a cutie.  Awesome.

White spot check: butt spots still present, although not as many as before.  One small white spot on the muzzle.  And then there's the tail.

I halfway expect a white tail by mid-summer.

At this point, it was 45 degrees and falling.  The wind was blowing.  The sweatshirt was not enough.  Still, I'd said I was going to grab Cessa and blanket her, so off to the main pasture to collect her.

She wasn't thrilled with her blanket again, but did let us put it on her.  Once she's convinced that yes, it's going on, she's fine - but getting her there is still a bit of an adventure.

Level of impressed with the cold front: low.

Pretty girl.

All of the horses were on alert, because not only was the temperature dropping - by the time I got back into the car, it had dropped another five degrees - but the wind was blowing at a good 15-20 with gusts of much higher.  Cessa was a bit squirrely, but settled down once we walked away from the area where she was most agitated.

When we headed down to the arena to have one of the BOs check my blanket fit (more adventures in horse ownership: fitting the blanket isn't something I really had to do as a lesson kid...), the colts in the arena started running around.  We shrugged and figured they were wanting to play - which it did turn into play after a few minutes - and let it be.

Then I turned Cessa out, and we all cracked the hell up.

See, she went trotting off to the herd, who were standing there on high alert because winter and wind and hose in the trough making weird noises.  The herd took one look at her and took off running as though their lives depended on it.

Cessa chased after them - why are we running? - until they got to the far end of the pasture.  At that point, the herd decided there was a new horse in there with them (yeah, not so much, guys) and started chasing her off (she's usually high-ranking in the herd) and generally being a pain.  Miss Thing needs to lose some weight and a night or two of not standing at the bale of hay 100% of the time isn't going to hurt her at all, so we were still cracking the hell up.

I'm pretty sure she was sulking.

I have a Santa hat coming, so there may be festive pictures next weekend, assuming it isn't still this freaking cold...