Horse Color Genetics Index

Color genetics is a long-time hobby of mine, and I’ve written a number of posts about the genes that determine color and pattern in horses. I also have an extensive website on genetics and coat color in dogs.

Horse Color Genetics Index

The Basic Colors of Horses 10/31/10
Palomino Genetics 11/06/10
Pearl: a Palomino Complication 11/14/10
Dun: a Wild-Type Dilution Gene in Horses 11/21/10
The Agouti and Extension Loci in Horses 11/27/10
Champagne: Another Dilution Gene in Horses 12/5/10
Silver Dapple – Another Dilution Gene in Horses 12/12/10
Two Rare Dilutions and a Summary of Dilution Genes in Horses 12/19/10
The Genetics of White on Horses 12/27/10
The Grey Gene in Horses 1/3/11
The Roan Gene in Horses 1/9/11
Other Patterns of White Hair in Horses 1/17/11
White Body Markings on Horses 1/24/11
The Tobiano Gene in Horses 1/31/11
Sabino Spotting in Horses 2/6/11
The Frame Gene in Horses 2/14/11
The Splashed White Gene in Horses 2/28/11
Horse Colors: Manchado and Brindle 3/7/11
White Horses 3/20/11
The Leopard Gene in Horses 3/29/11
The Leopard Gene in Horses (Continued) 4/2/11
The Leopard Gene in Horses Part 3 4/10/11
The Leopard Gene in Horses 4 4/17/11
Horse Color Genetics: Darkening Genes 4/24/11
Horse Color Summary 1 5/1/11
Horse Color Genetics, Final Summary 5/8/11

Other Posts to do with Horses

The Horses of Homecoming 4/17/10
Obstacle Racing (Homecoming Glossary) 6/26/10
A Circus Horse with no Circus 7/11/10
Tourist Trap: What’s It About? 8/16/11

Indexing Blog Posts

500+ posts is too many for me to keep track of, and quite a few are “reference” posts, such as the ones on planet building or horse coat color genetics. So I’m putting in a new feature, an index page that links to posts linking to the posts on a given topic. (Sound confusing? Try doing it!)

These indexing posts start today (see below) and will appear occasionally until the reference posts are all indexed. After that I’ll just be updating the index posts, which will be accessible from the Index tab above.

Why an Index?

With 550 posts as of today, I’ve started to have problems remembering what I’ve already put on here. This is particularly a problem with posting existing content such as poems, short pieces from the Summer Arts Festival, or science explanations originally written for the Alaska Science Forum. I can’t remember which books or DVDs I’ve posted reviews on. It also is starting to be a problem when I want to link to a previous post and can’t remember when it was put up or what the title was. And there are posts on this blog that have permanent information, like the series on planet building and the one on horse color genetics, or the book and DVD reviews. I want to make it easier for my readers as well as myself to find things.

I made a start some time ago by adding an index page, which can be accessed from the menu at the top of any page. Right now, the only links are to index pages on my author site. This takes you out of the site and sometimes back in, which is rather clumsy. The index list is also incomplete.

I’m going to start posting an occasional entry which is strictly an index of past posts on a particular topic. These posts will be linked from the index page, and will link forward to the individual blog posts. As it takes a while to find all the posts that belong together, this will be a slow process—probably extending over the next few months. The first in this series, on DVD reviews, is already queued for January 3. Others will follow, most on Thursdays.

I probably won’t be indexing every post. Some, like those early posts which were simply glossary entries for my books, are on the author site and really belong there. Others, like the regular Monday updates on North Pole weather starting in November 2010, can be found easily enough just by using the calendar on the site. But I hope that by the time I have finished this, older posts of interest will be easier to find.

You’re It? Ten Random Facts About Myself.

I just got tagged by Samanatha Stacia to tell ten things about myself, and tag three other people. Well the ten things are fine, but have you any idea how many people that kind of tripling every day would involve?

Just for the heck of it (and because it’s a good example of what a regular doubling (or tripling, in this case) can do, I calculated how many bloggers would be affected if each one tagged actually tagged three others, and if those tagged posted their blogs the next day. Ready? Here’s what it does:

day	number
1	1
2	3
3	9
4	27
5	81
6	243
7	729
8	2,187
9	6,561
10	19,683
11	59,049
12	177,147
13	531,441
14	1,594,323
15	4,782,969
16	14,348,907
17	43,046,721
18	129,140,163
19	387,420,489
20	1,162,261,467
21	3,486,784,401
22	10,460,353,203
23	31,381,059,609
24	94,143,178,827
25	282,429,536,481
26	847,288,609,443
27	2,541,865,828,329
28	7,625,597,484,987
29	22,876,792,454,961
30	68,630,377,364,883
31	205,891,132,094,649

That’s over 200 trillion people in the first month! (The population of the Earth is only about 7 billion, which would be exceeded by day 22.)

Obviously many people who are tagged do not respond, people rather quickly start getting tagged twice (or more) and the whole thing breaks apart from its own weight. So I’ll play the game as a blog-publicizing exercise, but anyone I tag should not respond if they’ve already been tagged once. Regard it as advertizing for your blog.

1. I started talking before I could walk. (And I still like birthday cake.) I still also talk better than I walk.

2. I’ve loved horses ever since I can remember. (My parents claimed they had to pry me off the pony, which belonged to an itinerant photographer.

3. While still in grade school, I discovered my father’s subscription to Astounding Science Fiction, and later, his back issues to the late 30′s and read them all.

4. I’ve been telling myself stories (mostly about horses to start with) in third person past tense since grade school.

5. My first attempt at publication was in high school or thereabouts. I sent a werewolf story to John W. Campbell, editor of Astounding. He wrote back saying it was too much a fantasy story for Astounding, but I could write. (The story has since been totally rewritten at novelette length and I’m thinking of e-publishing it on Amazon.)

6. I took a poetry writing class at Harvard, even though my major was physics. (Unfortunately — or perhaps fortunately? I’ve lost those poems.)

7. I bred and showed Shetland Sheepdogs for over 25 years, and my first dog, Derry, became the first dog of any breed from north of the Alaska Range to earn an AKC tracking title. (He was also the canine telepath who inspired the pocket herders, a breed of dog that is important in my unpublished trilogy.)

8. At one time I developed and programmed scientific models in FORTRAN on punched cards, and later learned to make web pages with HTML and Netscape 1.

Dot

9. Although none of my Shelties after Derry had much herding instinct, I had three Shetland sheep and competed in herding trials with my Border Collie, Dot.

10. At one time, some 20 years ago, I was lead writer for The Alaska Science Forum, a weekly popular science column that went to media outlets all over Alaska.

And to my surprise, I find myself 70 years old.

My picks (the three latest in the WordPress group on SheWrites because quite a few I read already have been tagged) are:

Colleen Crinion

Pat Nance

Costa Jill

Tourist Trap: What’s it About?

This isn’t really a book review, or if it is it is a very biased one — I wrote the book. Maybe it would be more accurate to call it a much longer version of the synopsis on the back of Tourist Trap. A synopsis has to be very limited in length; this gives me room to introduce the characters and the conflicts.

Tourist Trap: the second novel about the Confederation that grew from Jarn. The white lead dog is Snowflake.

Tourist Trap is the second novel I’ve written about the Jarnian Confederation. This is a loose confederation of human-occupied planets, with a remnant population of R’il’nians, who hybridized with proto-humans to produce modern humans around 125,000 years ago. Some of the hybrid descendants followed their R’il’nian progenitor back to space; others remained on Earth and became our own ancestors. Most of the pure R’il’nians are extinct, but the remnant and their descendants from recent cross-breeding have the responsibility of protecting the human-occupied planets from other intelligent races and (more often) of preventing them from warring with each other.

In Homecoming (set around the time of George Washington’s birth) the last R’il’nian surviving in the Confederation, Lai, discovers that the human lover who left him years ago fled because she was pregnant with his child, in defiance of the Genetics Board. The child, raised a slave, is rescued at thirteen and given the name Roi — but he is found because he is struck down by a paralyzing disease. Homecoming deals with Lai’s discovery of a woman of his own species, Marna, on a distant world and their acceptance, Healing and education of Roi – himself an untrained Healer — who must finally accept that he, as having the most R’il’nian characteristics of Lai’s children, will replace his sociopathic half-brother, Zhaim, as Lai’s heir.

Tourist Trap starts a year and a half after the end of Homecoming. Roi, now eighteen, has been given a trip on Falaron, a planet terraformed from ice age Earth, as a graduation present. His three closest friends from slavery have been given to him as slaves, though as far as Roi is concerned the slavery is simply a legal fiction that allows him to act as their protector while they gain the education they will need to survive on their own.

The markings on this horse are a good match for Amber's horse, Splash.

Roi is well aware that his father and the other adults around him consider that he is lacking in independence because of his slave upbringing, and partly because of that is determined to handle the journey on Falaron without aid. Underneath, however, he is both afraid of Zhaim and fearful of becoming like his older brother.

Flame, slave-born and the one who has known Roi the longest, has every intention of staying with him and doesn’t much care whether she is his slave or free.

Amber, kidnapped into slavery as a child, also loves Roi. But she is very aware that she will grow old and Roi will not, so she has decided to stay with Timi. She trusts Roi to release her when she has the education she recognizes she needs.

Tim, also kidnapped into slavery, wants his freedom now, and has begun to resent the fact that Roi owns him. In partial response to this, he is pursuing a friendship with Zhaim.

This foal is obviously much younger than Roi's horse, Raindrop, but the color and markings are right. Photo courtesy of Gail Lord.

The Falaron guide, Penny, makes the fifth of the group. Dog sledding, hang gliding, a trip across a landscape much like Pleistocene North America by horseback, sailing across a large lake, river rafting and rock climbing are all part of the fun.

Penny starts out treating Roi and his friends as clients. But she finds herself caring more for all of them –especially Roi – than she really intended.

But Zhaim is using Timi, and intends that none of the five will survive their trip. He is not stupid, and realizes that either Lai or Marna would protect Roi if they had any idea of what he was up to. So he plots to get them far away from Falaron – Marna to combat a plague he engineers, and Lai to stop a holy war he has goaded on. Even before the two R’il’nians leave he uses Timi and the weather against the travelers.

The geophysics and weather patterns of Faleron were carefully thought out, as was the seasonality. Yes, I modeled it on the rain-shadow effect of the Rocky Mountains, but the weather patterns and climate are reasonable for mid-latitudes on an Earthlike planet.

I had fun writing this. I’ve had considerable experience with dogs and horses, and they, as much as the people, are individuals. Amber and Timi’s lead dog, Snowflake, is an older dog, arthritic, and a bit of a telepath – so was the first dog I owned. Snowflake might well be the leader on the cover of Tourist Trap. And the five horses they ride are individuals too. Roi’s Raindrop is a spirited animal that responds well to Roi but is far too much horse for Timi, who does fine with the rather lazy Dusty.

It’s science fiction, but the surroundings are primitive and the focus is on the people: R’il’nians, crossbreds and Humans alike. Try it. You might be surprised to like it, especially if you think you don’t care for science fiction.

Fairbanks Weather 8/8/11

Sunrise this morning was at 5:14 am and the sun will set at 10:37 this evening, for 17 hr 23 minutes above the horizon. It’s now pretty dark at night – dark enough that the Fair will be setting off fireworks Saturday when it closes – but if I stayed to watch them, it’d be too dark for me to drive home. The sun will dip over 9° below the horizon tonight – not astronomical twilight, but dark enough to see stars and aurora, if the clouds will just clear away. They’re not really expected to, today or tomorrow, but they might by Thursday. At least it doesn’t look like we’ll have any more frost warnings in the coming week! In fact, highs may be up to 70 again by the weekend.

Giant cabbage display, winner at lower left.

It wouldn’t be Fair week without rain, anyway. So far, Saturday was the only clear, hot (by Alaska standards; it got above 70) day.

I’ve mostly been getting photos of horses, checking the Alaskan Authors booth (they have my first book for sale) eating what Fair Food I can with an insulin pump, checking out the crafts booths, and checking other exhibits one or two a day. Yesterday I looked over the giant cabbage entry, but it wasn’t very impressive. The winner didn’t even make 50 pounds.

Photos of horses? Last winter I was blogging weekly on the genetics of coat color in horses. I need more photos, once I can get them off of my camera. Meanwhile, I went through and linked all of my horse color posts from my author website. After all, I mentioned under the Leopard (Appaloosa) gene that all of the horses in Tourist Trap were spotted.

I’m also feverishly checking the mail. I ordered copies of my second book, Tourist Trap, thinking it could be added to the Fair booth. They were shipped July 22 – but in spite of my repeated insistence that they be shipped USPS Priority Mail, they were apparently sent media mail – 4 to 6 weeks to Alaska, if I’m lucky.

My own garden is now providing beets, a few wax beans, and squash faster than I can eat them. My camera, alas, is still not talking to my computer, so until I can get it fixed I’m stuck with iPhone photos.

More on the Fair (and the quilt show) tomorrow.

Calypso

Twigs and branches, once reaching for the sky
Now bent and held by iron bands
To the likeness of a horse.
But is this not reality?

Sun’s energy,
Giving life to grass and leaves
Which in turn pass on that life
To the newborn foal.
Bound by the iron of blood
To the growing form—
Feet dancing, tail proud, neck arched.

And in the end
Giving itself back to earth
From which grow the twigs and branches
Reaching for the sky.

©Sue Ann Bowling

“Calypso”, a 2003 sculpture by Tamara Schmidt, greets visitors in the lobby of the Museum of the North on the University of Alaska Campus. The poem was inspired by the sculpture, which is life-sized.

The Animal Connection: Review

Last month I blogged about an article in The New Scientist based on a book due to be released soon. The book, The Animal Connection by Pat Shipman, is now available and was one of the first I bought for my iPad.

This is a book anyone interested in animals, domestication or human evolution should read. Dr. Shipman points out that hunters must observe animals and learn to anticipate them in order to hunt successfully. She links tool-making to the hunting of animals, pointing out that we are unique as predators in using tools, not teeth or claws, to hunt. The addition of meat to our diet may well have been what made us able to support increasingly large brains, as brains have a very large energy cost.

The need to get “inside the skull” of another species may also be behind much of the empathy and imagination we share.

Later, the need to share information about animals may well be one of the driving forces behind our acquisition as a species of language. Language, although one of the traits that define us as a species, does not fossilize, so arguments here tend to have more than a little arm-waving about them. The fact remains that animals, rather than plants or other people, are the main subjects of Paleolithic art.

If animals were living tools, as the author argues, they are tools whose best use must be based on mutual understanding, not on force. There is nothing really new about this; Xenophon’s tretise on horsemanship said it over two thousand years ago.

The future? To quote the author, “The post-animal world, if we choose to live in it, is a fearsome place that threatens to destroy the very best qualities of humankind.”

I tend to believe most of the arguments in this book partly because they reflect my own conclusions. I wrote a short story over ten years ago suggesting that the connection between people and dogs may have shaped both into a new symbiosis, and I am glad to see that idea now accorded some degree of scientific acceptance.

Book: The Animal Connection, by Pat Shipman. Published by W.W. Norton,
ISBN 978-0-393-07054-5

Six Sentences from Tourist Trap

Proposed Cover illustration for Tourist Trap

Thunder was audible to the riders as well as their mounts by the time they started up the slope, and the shadows of the clouds rushed toward and over them as they topped the rise. A wave of grass rippled out of the dimness toward them, and a chill gust from the northwest made Penny glad they had both put on tunics. Hastily she turned to untie her own poncho and put it on.

“There they are,” Roi said, pointing east to where sunlight still gilded the prairie. Squinting, Penny was able to make out a tiny white figure topping one of the distant rises. Then the shadow of the clouds swallowed the rise, and she lost sight of Token.

Other Six Sentence Sunday blogs:

Horse Color Genetics: Final Summary

Last week we reviewed the base color and dilution loci. Today we will do a final review of the interspersed white hair and white marking genes, along with the darkening genes. Although the blog series will end today, links will be put on my author site to all of the posts in the series.

There are two main loci responsible for interspersed white hair. These are Grey (born dark with white hairs becoming more numerous with age) and Roan (born roan with white hairs constant or decreasing with age.)

The Grey locus is the syntaxin-17 (STYX17) locus on equine chromosome 25. It causes an initial increase in melanocytes  followed by their depletion. There are two alleles at this locus: grey and wild-type, with gray being incompletely dominant. (Horses with two copies of the grey allele lighten faster than horses with one grey and one wild-type allele, are less likely to develop a fleabitten appearance, and are more likely to develop melanomas with age.) At this time the progression of graying (dark vs. light mane and tail) and the color of dark hair (usually black, but some individuals become rose grey, with the dark hair remaining red) are not known to be subject to genetic control. In any case the final result is a mostly white horse.

The Roan locus is close enough to the Extension locus that there is significant linkage. It is considered part of the KIT linkage group on equine chromosome 3. There are two alleles: roan (dominant) and wild-type. At one time possession of two roan alleles was thought to be lethal, but this has now been shown not to be true. Classic roan causes interspersed white hairs on the body, but the legs, mane and tail normally remain dark. The frosty pattern, in which the mane and tail are also affected, may be a variant of roan, but the genetic mechanism is at present unknown. Scars commonly lack white hair, causing dark corn marks.

Spotting loci are far more numerous, and some produce roaning as well as white areas.

Minor spotting genes may be responsible for white facial and leg markings. These genes are present in most breeds, and facial and leg white tend to increase in tandem. Animals with wide blazes and no white on the legs, or with high stockings and plain faces are very often minimally marked animals with one of the other spotting genes.

The Tobiano locus is closely associated with the KIT locus, and hence on equine chromosome 3. There are two known alleles, tobiano and wild-type, with tobiano being an incomplete dominant. Generally tobianos are crisply marked, with white crossing the topline. Legs are normally white and the face is plain or has minor markings. Minimal tobianos may have high stockings with plain faces; in the maximal pattern only the head may be colored. Roan or colored spots known as paw prints may occur in white areas on animals with two tobiano alleles. There is a dominant modifier which in the presence of both tobiano and cream produces what is called a calico pattern—the yellow of the buckskin or palomino is broken up, with some areas being red.

The Frame locus is on equine chromosome 17, and is at the locus that controls endothelin receptor b (EDNRB.) The alleles are frame and wild-type. The frame allele is lethal in double dose, producing the so-called lethal white foal syndrome, so all frame horses should have one frame and one wild-type allele. The minimal expression of frame is extensive white on the head with colored legs. The maximal extent may have color confined to the topline and legs. The fact that the frame allele still seems sometimes to come out of nowhere need further clarification—a masking gene may also exist.

The sabino pattern is a combination of spotting and roaning, and extremely variable in expression. It may also have more than one genetic explanation. The Sabino-1 locus is part of the KIT complex (equine chromosome 3) and has two alleles, sabino and wild-type. The sabino allele is incompletely dominant over wild-type, as horses with two sabino alleles generally have more white (even to being almost completely white) than horses with one sabino and one wild-type allele. There are other mutations near the KIT locus that cause white spotting, some of which appear to be lethal in double dose.

The Splashed White locus is yet another that seems to be near the KIT locus, though not at it. The locus probably has two alleles, splashed white and wild-type, with splashed white behaving as an incomplete dominant. The minimal effect of splashed white may not be detectable, or the horse may be more extensively marked with white legs, possibly white underbody and generally white on the head, sometimes to the extent that the whole head is white. Splashed white is also associated with deafness.

Manchado is a relatively rare type of spotting found in several breeds in Argentina, though that may be because of the Argentine fascination with coat color. Parts of the body, often including the top of the neck (and mane) are white, often with round colored spots. The genetic basis is unknown.

White with pink skin and dark eyes may be a separate gene, possibly lethal in horses with two white alleles. At the moment, this is somewhat up in the air.

The Leopard locus is the Transient Receptor Potential Cation Channel, Subfamily M, Member 1(TRPM1) locus. It has two alleles, leopard and wild-type, but an enormous array of patterns. Leopard is incompletely dominant over wild-type—horses with two leopard alleles generally have fewer leopard spots than those with one leopard and one wild-type gene, and have a high incidence of night-blindness.

Finally, darkening due to black hair in the coat may occur in at least three forms. Black hair may be scattered throughout the otherwise red parts of the coat, producing a sooty effect. Black tipping on otherwise red hairs appears to be associated with the agouti locus, and produces shaded effects where the back appears darker than the rest of the horse. Actual black striping of the coat, brindle, is rare but documented. Some types of roan, especially sabino, may produce a type of brindle with white stripes. The genetics are unclear in all of these cases.