Category: Genetics

Other Uses of DNA

DNA Molecule

A schematic of a DNA molecule. (Public Domain image from Wikimedia commons.)

So far I’ve been talking strictly about my results from the genographic project. This project is aimed at clarifying the history of the human species, but this is far from the only way human DNA sequencing is used.

Genographics focuses on mutations that are relatively old and allow us to track the spread of the human species around the planet. There are two other commercial DNA testing services that use a similar method of testing but are focused on slightly different uses. All use y-chromosome and mitochondrial DNA as well as the 22 sets of autosomal chromosomes, and all look for mutations specific to specific groups. But uses a set of relatively recent mutation that are most useful for finding recent relatives, while 23and me puts more emphasis on testing for genes know to be associated with health conditions. All three are useful adjuncts to conventional genealogical research, especially for those who have hit a “road block” with a known ancestor of unknown background.

But genealogy is far from the only use of DNA analysis. At the other extreme of price and usefulness is whole genome sequencing, where all 23 pairs of chromosomes are sequenced, letter by letter. This is expensive and rarely done, though the price is dropping fast. We are still talking thousands if not tens of thousands of dollars, not something to do for curiosity alone! However, such sequencing may be useful in finding an abnormal gene in a person with a health problem that cannot be pinpointed, and through knowing what the normal gene does even leading to a cure.

A far more common approach to health studies using DNA is based on the fact that many diseases are closely associated with specific genes. Finding such genes may aid in diagnosis, or (if the genes are found in prospective parents) may lead to counseling about the advisability of having children.

I’m running into this right now. There are a couple of variants of the BRCA gene that lead to an increased chance of breast and/or ovarian cancer, especially in relatively young women. I’ve had breast cancer, though at an age where it’s common. My recent (like this month) ovarian cancer has no obvious relationship to that breast cancer, from which I appear to have recovered, and the ovarian cancer was caught early enough (stage 1) that the chemotherapy I’ve been prescribed is mostly precautionary. But could I have a general susceptibility to this class of cancer? If so, would it be worthwhile removing my remaining breast tissue?  This is why genetic counseling should accompany or even precede this type of testing.

Finally, there are all kinds of forensic genetic tests. Like the genealogical tests, these are generally incomplete and depend on markers—regions where the DNA is known to vary markedly among people. I am no expert in these tests, but they have cleared more than one person on death row.

Neanderthal and Densovan

DNA Molecule

A schematic of a DNA molecule. (Public Domain image from Wikimedia commons.)

Homo has been spreading out of Africa since long before the evolution of “true” or “modern” humans.  But what exactly is a “true” human? What is a species?

Once it was simple. God made the species, which were unchangeable. Then the naturalists got into it, and the head-scratching began. The recognition that species could actually go extinct made more problems yet. Which modern species were they most like? Were they even “new” species, or variants of modern ones? Remember that the first “natural histories” included some very odd beasts from travelers’ tales, some of which were probably at fourth and fifth hand.

Comparisons within the human family tree have always been particularly fraught. Quite aside from the fact that many still refuse to accept the evolution of human beings, every paleontologist wants to be remembered as the discoverer of a new species. But it seems likely that Homo habilus, Homo erectus (who left Africa and included the subspecies Neanderthal and Denisova) and Homo Sapiens were valid species in that it is unlikely that an early Homo Habilis could have interbred with a late Homo erectus – though DNA is providing some surprises.

Even a relatively few years ago, when Jean Auel’s first book was published, the idea that Homo Sapiens, the upright and noble cave artists, could have interbred with brutish Neanderthals was laughed at by many anthropologists. Physically impossible! Any such rare hybrids would have been sterile, like mules!

Then DNA sequencing from bone fragments became possible. DNA of two variants of Homo Erectus, Neanderthal and Denisovian, was successfully sequenced. Bits of Neanderthal and Denisovan DNA were found in every human population except those of pure sub-Saharan African descent.

Love or war? We don’t know and most likely never will, but probably both. Obviously our DNA was still compatible. It is quite possible that the “extinction” of the Neanderthals by Homo Sapiens was more of a genetic swamping. We even know what some of the Neanderthal genes we retained were – part of our modern immune system. Makes good sense: the Africans would be wide open to cold-adapted parasites and diseases, while the Neanderthals had adapted to them over a couple of hundred thousand years.

We know far less about the Denisovans, though since I turned out to have a whopping 3% Denisovan, I’m going to be following their story with considerable interest.

DNA Molecule

A schematic of a DNA molecule. (Public Domain image from Wikimedia commons.)

I started with the family tree my mother wrote out in my baby book, added research from relatives on both sides of my family, and generally have a pretty good idea of where my ancestors came from. I’ve traced all branches back to before the Civil War, and in some cases to before the Revolutionary War. My baby book lists English, Irish, Scotch, Dutch and French origins, though quite a few generations back. I allegedly have some French-Canadian trapper ancestry though my maternal grandmother, and on that basis and physical appearance we sometimes think the family has a little Native American background. So I was interested in what Genographics would make of me.

Genographics give the percent of your total ancestry matching native groups from 9 different regions. The regios are:
Northeast Asia
South African
Southwest Asian
Native American
Southeast Asia
Northern European
Sub-Saharan Africa

Well, mine showed no Native American. My DNA results for the whole genome are fairly typical European: 45% Northern European, 37% Mediterranean and 16% Southwest Asian. That doesn’t rule out the possibility of a very tiny contribution from Native Americans, but it certainly doesn’t confirm it.

This doesn’t mean my recent ancestors came from these parts of the world! My profile is very similar to that of people who’ve lived for several generations in England, and even closer to those from Germany. The mixing probably took place several thousand years ago.

The Northern European component probably represents the original hunter-gatherer population of Northern Europe. These people may be descended from the Cro-Magnons. Genographics doesn’t say anything about skin or eye color, but I suspect blue eyes and light hair evolved in this component simply because they lived for a long time in a relatively low-sunlight environment where these traits would have had little cost and considerable benefit in production of vitamin D.

The Mediterranean component probably represents the partial replacement (with considerable interbreeding) of the hunter-gatherers by Neolithic farmers moving north and west from the early farming communities of the middle east. This movement is thought to have started around eight thousand years ago.

The Southwest Asian component probably had a similar origin, perhaps coming from father east in the fertile crescent, the origin of western Eurasian agriculture.

So no surprises, just a rather bland typical European background. What I found most interesting was the Neanderthal and Denisovian fractions of my genome – but more of that later.

My Maternal DNA

DNA Molecule

A schematic of a DNA molecule. (Public Domain image from Wikimedia commons.)

Every human being alive today has a maternal line, daughter from mother, that traces back to the same woman, who lived in Africa some 180,000 years ago. This comes from analyzing the mitochondrial DNA of people all over the world. There were small changes, mutations, of this mDNA over time, and these can be used to trace the branches of this woman’s descendants.

The first important mutation I carry is called L3. Although L3 is found today in Africa, it is thought to be the branch of the first woman’s descendants that first moved out of Africa, and is found today all over the world. This mutation is thought to have originated somewhere in East Africa some 70,000 years ago.

The next important mutation is called N, and it probably occurred in East Africa or western Asia about 60,000 years ago. This woman’s descendants probably traveled down the Nile and crossed into the modern Levant. They are very widespread today, but most important in the Near East and Europe. Chances are they were still very darkly pigmented, as they lived in a very sunny area. (Light coloration is thought to be an adaptation to a need to let sunlight through the skin to produce vitamin D.)

A mutation in a woman of the N group, probably about 55,000 years ago in West Asia, is called R. Apparently the descendants with the R mutation stayed with the parent N group, and both groups moved together through Turkey, the Middle East, and southern Russia.

A subgroup of R, called RO, occurred about 41,000 years ago somewhere in West Asia. This group produced the Cro-Magnons in Europe, but is most frequent today in Arabia and also moved into the Indus Valley.

The next important mutation in my female line was called HV. Like the M and RO groups, it arose in Western Asia. The Palestinian area is not only a political hotbed today, it is the origin of a large part of the “white” race. This mutation occurred relatively recently, around 22,000 years ago.

The next mutation is a little confusing, as the mutation to H is assumed to have occurred about 28,000 years ago, also in West Asia. It should be pointed out that the age estimates can be significantly skewed by such events as population bottlenecks. H is in any event the dominant maternal genotype in Western Europe.

The mutation to H1 is assumed to have take place a mere 18,000 years ago, still in West Asia. This line is again most common today in Western Europe. Some of these individuals may have been light skinned, in an evolutionary ploy to avoid rickets. I might point out that it is now recognized that at least two separate mutations to light skin have occurred, one in the West and one in Eastern Asia. Both help with the production of Vitamin D, but only the Western form gives an increased likelihood of skin cancer.

I have one final mutation, of undetermined age, called HB. This one is fairly rare. It may have arisen in Central Asia and runs between 1 and 2 percent of modern Europeans.

Overall, my ancestors in female line seem to have done a lot of traveling!

(The information above was taken from my results at the Genographic Project website. What does your mitochondrial DNA show?)

DNA: We All Have It

Where did we come from?

A schematic of a DNA molecule. (Public Domain image from Wikimedia commons.)

A schematic of a DNA molecule. (Public Domain image from Wikimedia commons.)

I just got the results from my Genographic DNA study, and I thought I’d share them. To start with, I thought I’d explain a little about DNA, and how the Genographics study uses it.

DNA is the abbreviation for deoxyribonucleic acid, and thank goodness it has a widely used abbreviation! If you enlarged a molecule of it enormously it would look rather like a twisted ladder with four different kinds of “rungs.” The genetic information is coded by the order of these kinds of rungs. I’m not going to get technical here, but if you want more information have a look at Wikipedia.

DNA is the information-carrying part of chromosomes. Most normal human beings have 46 chromosomes: 23 from the mother and 23 from the father. (The rare exceptions generally have some kind of medical problem, such as Down’s Syndrome which results from having three copies of one particular chromosome.) These chromosomes are in the nucleus of just about every cell in your body. In addition, the cell body has structures called mitochondria which are essential for metabolizing nutrients. These mitochondria have their own DNA, but since the cell body and mitochondria come from the egg cell, the mitochondrial DNA is inherited only from the mother.

There is one pair of the 23 which is special, called the sex chromosomes. These chromosomes come in two forms, X and Y. The Y-chromosome determines maleness, and seems to have little other genetic information. The X chromosome has a normal complement of genes. A normal woman has two X chromosomes. A normal man has one X (from his mother) and one Y (from his father.) Individuals with other combinations such as XXY occur rarely. The important thing for us is that Y chromosomes are passed only from male to male.

Thus there are three types of genetic analysis which can be done: nuclear, mitochondrial and Y-chromosome.

The nuclear DNA is what makes me, me and you, you. It comes from both parents, and is remixed in every generation. Your nuclear DNA can be compared with that of indigenous populations throughout the world, and interpreted as what percent of your ancestry came from what area.

Mitochondrial DNA is passed almost without change from mother to child. Thus my mitochondrial DNA is the same as my mother’s mother’s mother’s mother’s mother, a woman named Ellen Carr. Changes do occur, very slowly, and these can be used to track back how my maternal line traveled out of Africa.

I don’t have a Y-chromosome, so the Genographics results don’t give me any information on my father’s line. A cousin, a son of my father’s brother, has been tested by another company, so I know I am in Bowling Group 6. But I don’t have the pathway my paternal ancestors took out of Africa.

Next week I’ll retell the story Genographics told of my maternal line.

Dapple grey, trotting

AtoZ 13 logoIf you are looking for the A to Z post for today (F) scroll down or click on the button to the left.

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 in the index to all  posts in this 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.

Blazed face on chestnut

Blazed face on chestnut

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.

Tobiano horseThe 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.

Black and white frame horseThe 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. Think of a horse trotting through a puddle of white paint with its head lowered. Splashed white is also associated with deafness.

Lone Ranger andSilverManchado 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.

Appaloosa horse

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.

chestnutFinally, 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.

Horse Color Summary 1

As a final summary of horse color genetics, let’s go over the loci, what they do, and the alleles at each locus. My primary reference is Sponenberg.

BC bay headThe Agouti locus is widespread in mammals, and is involved with whether and where an animal produces eumelanin (black) or phaeomelanin (red) pigment. The alleles known in horses, listed with the most dominant first, are Wild Bay (Wild-type), Bay, Seal Brown and black. Agouti is hypostatic to Extension, meaning that the effects of the agouti alleles can be seen only if the extension gene allows the animal to produce both eumelanin and phaeomelanin. Note that at this locus, the redder the color, the more dominant.

ChescrThe Extension locus is the same as the melanocortin receptor one locus, or MC1R. Like agouti, it influences whether eumalin or phaeomelanin gets into the coat and occurs in most mammals. The alleles are dominant black (still not confirmed), wild-type, and chestnut. This locus may also have genetic control over the depth of black tipping. Only wild-type and tipping allow the agouti genes to show. In this series, more black is dominant over more red. Extension is epistatic to agouti.

Agouti and extension determine the base color of the horse—bay, brown, black or chestnut.

Dun fjord1crThe various dilution genes generally affect phaeomelanin and eumelanin differently, mane and tail hair and body hair hair differently, and not uncommonly are associated with patterns of dilution.

The Dun locus has two alleles. Wild-type is dun and is dominant over non-dun, but the wild type is rare in many breeds. When present, dun dilutes both black and red pigment on the body, but the degree of dilution varies a great deal. Head, legs, mane and tail are generally much less affected than is the central body, and dorsal stripes almost always occur. “Zebra stripe” markings often occur on legs and the shoulder region. The dorsal stripe may continue down the center of the mane and tail, with the edges diluted.



The Cream locus is also known as the membrane-associated transporter protein (MATP) locus. It probably has three alleles: Wild-type, pearl, and cream. The dominance hierarchy here is complex. A horse with two wild-type alleles is normal color. A horse with one wild-type and one pearl allele looks normal color except for slightly lighter skin. A horse with two pearl alleles will have red lightened to gold and black lightened to beige. A horse with one cream allele and one wild-type allele will have red lightened to gold and black lightened only very slightly. A horse with one cream and one pearl allele will have red lightened to pale cream or ivory and black lightened to beige. Finally, a horse with two cream alleles will be a very pale color, as red lightens to cream and black to a slightly dirty white.

champcrThe Champagne locus is the SLC36A1 locus. It has two alleles: Champagne (dominant) and wild-type. Champagne dilutes red to gold and black to brown or tan. The mane and tail are generally diluted less than is the body.

Silver Dapple8:4:12The Silver Dapple locus is the pre-melanosomal protein 17 (PMEL17) locus. It has two alleles, silver (dominant) and wild-type. The silver allele dilutes black strongly but has little or no effect on red. The allele also produces very strong dilution in mane, tail and lower legs, at times producing horses that appear black with white manes and tails. Far commoner are horses with a blue to chocolate body, often heavily dappled, with distinctly lighter manes and tails. At one time common primarily in ponies.

The Mushroom locus has not yet been located. Two alleles are suspected, wild-type (dominant) and mushroom (recessive.) Mushroom horses resemble silver dapples, but lack dappling and have tested chestnut at the extension locus.

Arab dilution is another possible locus. This is believed to be a recessive allele with a strong lightening effect on black but little or no effect on red. Both Mushroom and Arab dilution are very rare.

I will summarize patterns of white, including grey and roan, next week.

This is an update with photos of an article originally posted April 17, 2011.

Not all horses with the leopard gene have blankets of any size, and not all have spots. The gene can also produce two specific types of roaning, called frost and snowflake.

Ch varnish

Chestnut varnish roan. This horse has almost no white markings, and a full mane and tail.

These roan patterns are quite separate from that produced by the roan gene, which becomes less prominent with age and leaves head, legs, mane and tail dark. The leopard gene produces horses which are normally colored or at most have a few white hairs over the rump at birth, but develop roaning (frost) or scattered white spots (snowflake) as they age. In contrast to grey, the pattern eventually stabilizes rather than producing a pure white horse.

In frost, the roaning tends to be most prominent over the hips. So-called varnish marks are common — areas where the bones are close to the surface, such as the hipbones and nasal bones, retain pigment while the rest of the coat is roaned. An aged varnish roan may be almost white except for these varnish marks.

Varnish roan horse

Another chestnut varnish roan, this one with a blaze and three white stockings. This one has the white organized into a near blanket over the hips, with spots on the blanket.

Snowflakes are small white spots scattered randomly over the body, but often most numerous and prominent on the front part of the horse. They tend to become larger and more numerous with age, until in extreme cases the horse appears white with colored specks. This gives what is often called a speckled pattern, not to be confused with flea-bitten grey. Note that not all of the photos shown at the link are true snowflakes — the term is used very loosely.

Both types of roan may be combined with any of the blanket or spotting patterns, or may occur alone or together. Figure 8.140 in Sponenberg is a beautiful example of a combination of snowflake, varnish roan, blanket and leopard spotting all on the same horse. (Put Figure 8.140 on the search inside field.) Since the leopard gene can produce any of these effects, alone or in combination, breeding leopard-pattern horses can lead to some interesting results.

The remaining named horse in Tourist Trap, Amber’s mount Splash, is a bay varnish roan with a small spotted blanket, in color rather like the horse on the left side, but with black points and no blaze. He’s a gelding, about 14.2 hands – just enough smaller than the other four to have problems with fords. Roi has seen only solid colored horses on Central, and his first look at Splash gives this impression:

“Amber’s [horse], a little bay roan with curious dark lines on its nose, looked less exotic until it turned as she halted it.  Then it became apparent that it had a large white area, punctuated by dark bay spots, over its hips.”

I will summarize the equine color loci and alleles next week with links back to where they are mentioned, but I have covered most of the known color genes in horses. That doesn’t mean more won’t be found!

A last comment: Horse Power, with the Leopard horse on the cover, is FREE today on

This is a repeat with some updating and additional photos of an article originally posted April 10, 2011

Lace blanketNot all horses with white markings produced by the Leopard gene are leopards. The white markings are generally symmetrical and present at birth, but they vary a great deal from horse to horse and may even be absent entirely. The minimal expression is white over the top of the rump, and the broad term for the pattern is blanket. Note that I am speaking only of white produced by the leopard gene. Leg and face white are generally independent of the leopard gene.

Edges of the white blanket may be crisp, flecked or roaned.

Appaloosaa horseSponenberger divides the white patterns by percent of white at birth. The modification I am using in Tourist Trap is:

10% or less white spots over hips
10% to 20% lace blanket
20% to 40% hip blanket
40% to 60% body blanket
60% to 80% near leopard
90% to 100% leopard

Note that “leopard” in this table includes both leopard and few-spot leopard, and that the size of the blanket has nothing to do with whether spots are present. If one copy of the leopard allele and one of the wild-type allele are present, whatever white areas are on the horse will normally have spots of the base color. If two copies of the leopard allele are present, the white markings will have few or no spots, and the pattern is often called snowcap or few-spot.

Lace blanketThe Pattern-1 gene is heavily implicated in the amount of white, but it is almost certainly not the only modifier.

Spots will normally be of the base color, but may show a concentration or dilution of color. Thus they may appear darker or lighter than the base color. The horse on the book cover on the right sidebar shows spots on the neck, suggesting that at least some of the spots are darker than the body color. (That horse, by the way, is a stand-in for Raindrop’s granddaughter.)

The description of Roi’s horse, Raindrop, in Tourist Trap is that of a body-blanketed grulla approaching a near-leopard. She has white coronets and spots significantly darker than most of her body, which is already dark and somewhat bluish for a grulla. Roi’s first sight of her gives the following description:

Grulla appaloosa foal

If this foal’s blanket enlarges with maturity, she could grow up looking like Raindrop. Photo credit Gail Lord.

“One of the two led horses had a black-spotted white body, but its neck, legs and chest were a dark mouse gray, set off by a black head and mane and a black and white tail.” Raindrop is later referred to as having a sparse mane (black) and being the color of polished slate. The dark dorsal stripe typical of duns would have been in the white-blanketed area, and hence invisible.

Genetically, she would have had two recessive black alleles at the Agouti locus, at least one wild-type allele at the Extension locus, at least one dun allele at the Dun locus, and one leopard and one wild-type allele at the TRPM1 locus.

Next week I’ll talk about the roan, flecked and snowflake patterns produced by the Leopard gene. Again, these patterns are often called Appaloosa in the United States, but they occur in horses worldwide.

The pattern most people first think of in Appaloosa horses is the one that gave the gene its name—leopard. This pattern gives a white horse with round or oval spots of base color. There may be shading of the genetic base color on the flanks, behind the elbows or on the head.

Appaloosa horse

Most people would call this horse a chestnut leopard. In fact he combines a white rump, extreme roaning or snowflake, and clearly defined spots. Note the haloes on several of the spots.

Genetically, a leopard must have at least one Pattern-1 allele in order to have most or all of the body white. In addition, it must have one leopard allele and one wild-type allele at the TRPM1 locus. Two leopard alleles will lead to a few-spot leopard, with only a few colored spots. Other factors leading to the leopard pattern undoubtedly exist, but are still unknown.

The mane and tail may be mixed in color if some of the mane and tail hair grow from colored spots. The spots may have roan edges, called haloes, which normally develop after birth. Blacks tend to have more and larger leopard spots than do chestnuts, with bay being intermediate. Also, horses with black mixed in the coat (sooty) will sometimes have the black and red colors form separate spots.

Three of the horses in Tourist Trap have leopard markings.

Appaloosa horse

Another view of the same horse. Note the white “lightning strike” markings on the forelegs.

Token is the mare ridden by Flame. She is fairly tall—around 16 hands. She is a chestnut leopard, white with copper spots. Genetically, she is homozygous for the most recessive of the extension alleles, has two copies of the Pattern-1 allele and one of the leopard allele. She is wild-type at all dilution, pinto spotting, grey and roan loci. She could have genes for minor white marking on face or feet, but they cannot be seen.

Dusty is the gelding ridden by Timi, who would just as soon not be riding. He is the calmest and laziest of the group, and the easiest for a novice rider to handle. He is also the least responsive to leg pressure. Dusty is a buckskin leopard, around 15 hands tall. He has wild-type extension genes, bay alleles at the agouti locus, and one cream and one wild-type gene at the cream locus. His pattern-1 and leopard alleles are the same as Token’s. He has quite a lot of white in his mane and tail, so they are not noticeably sparse.

Penny is the guide and her horse, Freckles, is a bay leopard gelding. Freckles is a little keener than the horses assigned to Penny’s clients, but he’s a bit younger and the cross-country trip is part of his training. Freckles’s underlying bay color is a little sooty, so he has both red and black spots. Genetically he is the same as Dusty but with sooty and without the cream allele.

The other two horses have the leopard allele but are not leopards, and I’ll talk about them next time.

This was first posted, without photographs, April 2 2011.