Children are similar to their parents because of genetics, the way traits are inherited from one generation to the next. Traits such as eye color, hair/fur color, and height are determined by genes, which are made of DNA.

Here's a small piece of DNA. The left side shows how the atoms are arranged. It looks pretty complicated, but it's actually made of just four different types of pieces. We call them A for adenine, T for thymine, C for cytosine, and G for guanine. The right side shows how the pieces fit together. A is always across from T, and C is always across from G.

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If we start with that A at the top and we read along the one strand, we get A, G, G, A, C, G, A, A, T, C, G, T. Because of the way the pieces match, we know the other strand will always have an A where this one has a T, a T where this one has an A, a C where this one has a G, and a G where this one has a C. So the letters of just one strand are all we need to know, and we can read the DNA like a book.

DNA forms chains of letters that are very, very long. Think 100 million letters long, roughly. To store the DNA, it's packaged into a chromosome. If you think of DNA as a series of letters, you can think of a chromosome as a book. Each chromosome stores a single, extremely long, piece of DNA.

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At least, it usually has a single strand of DNA. While a chromosome is copying itself, it can have two identical strands. That's when it makes the familiar X shape.

A gene is the DNA used as instructions on how to make a particular protein. Proteins are well known for their role in muscles, but they actually do much more. Almost everything your body needs to get done, it uses proteins to do. Each different type of protein is made using the instructions from its gene.

If you think of a chromosome as like a book, then a gene is like a chapter.

The drawing below shows a gene within a chromosome. The gene is colored blue, and the rest of the DNA is colored gray. It's all DNA, so what makes this one section different? The gene is read as instructions on how to make a protein. The DNA on either side may help decide when and where to make the protein, but not how.

The gene drawn above is called agouti, and its instructions make the agouti signalling protein (ASIP). This protein's job is part of how pigment cells decide whether to make a red or black pigment. The horse's agouti gene is 3595 letters long, and if you're curious you can see them here.

At some point in the past, a mutation deleted 11 letters from the agouti gene in one horse, creating a separate version of the gene with different instructions, which makes a different protein. We call the different gene versions alleles. The gene's sequence before the mutation is one allele (called the wild type), and the mutated sequence is another allele.

Wild type: T G G A G A T T A . . . A C G C C A C T T G T C A G G G C C C . . . G A G G G G T G
Mutated (11 letters deleted): T G G A G A T T A . . . A C G G G C C C . . . G A G G G G T G

The agouti gene in the horse happens to have two known alleles, but other genes can have different numbers of alleles. For instance, the KIT gene has over 30 known alleles - over 30 variants in the letter sequence of that gene, including those causing the dominant whites and the sabinos. Or a gene can have only a single allele, if every member of the species has the same sequence of letters there.

When we want to talk about an allele, it's really awkward to have to say things like "the wild-type agouti allele" or "the agouti mutation that deletes letters 2174–2184". Instead, we give them shorter names. The wild type agouti allele is usually called A (but may also be called A^A or ASIP⁺) and the mutated agouti allele is usually called a (but may also be called A^a or ASIP^a).

By convention, uppercase names are for dominant alleles while recessive alleles use lowercase. Alternately, the wild type allele of any gene can be named +.

When deciding what to call an allele, the most important thing is that someone reading or listening knows which allele you mean.

If we compare genetics to instructions on how to build a car, then these comparisons might make sense:

• Genome - The full instructions on how to make a car.
• Genetics - Anything to do with instruction manuals in general.
• Mutation - A change to the instructions. For instance, making the wheels square (oops!), or changing the paint color to red, or making the windshield a bit more aerodynamic.
• Chromosome - A book. One single volume, if the instructions were long enough to need multiple.
• Gene - A chapter about how to make a specific part of the car, like a tire or the windshield.
• Protein - An actual physical part of a car, like a tire or windshield.
• Allele - The exact chapter from a specific edition.
• Haplotype - The exact [portion of a book longer than a chapter] from a specific edition.
• Codon - A word.
• Base pair - A letter.
• Nucleotide - A glyph? The analogy's kind of breaking down, sorry.
• Nucleic acid - Paper and ink.
• DNA - A nice thick paper and waterproof ink that's good for long-term storage.
• mRNA - A really thin tracing paper and pencil for making a copy of a chapter and taking it over to the parts machine.
• Ribosome - A machine that makes mechanical parts.

In general, an animal has two copies of each gene. One came from its mother, and the other came from its father. When it has children, it randomly chooses one of the two copies to pass on to each child.

Each copy of the gene is made of a particular sequence of letters, that is, each copy is one allele. For instance, each copy of the horse's agouti gene can be either the A allele or the a allele. So a horse can have A/A, A/a, or a/a. Order doesn't matter; a/A is the same as A/a.

In horses, the A allele of agouti is responsible for the bay coat color (brown body, black mane, tail, and lower legs) and as you'd expect a horse with two copies of A is bay. Meanwhile, the a allele causes a solid black horse, and a horse with two copies of a is black. But what about a horse with one copy of A and one copy of a? That depends on which allele is dominant.

An allele is dominant if only one copy needs to be present for it to show. On the other hand, an allele is recessive if it needs two copies to show. Another way of saying this is that if a horse has two different alleles of a gene, and one of the alleles is dominant over the other, the horse will look the same as if it had two copies of the dominant allele. It's standard to name dominant alleles in uppercase and recessive alleles in lowercase.

Of the agouti alleles, A is dominant and a is recessive. That means a horse with A/a is bay just like a horse with A/A. At the gene level, the two different copies A and a have different instructions that make different proteins. The copy with the A allele makes a protein that works properly, whereas the copy with the a allele makes a protein that does nothing in particular. A horse with A/a will make half as much working agouti protein as a horse with A/A, but it's still enough to function as normal. That's why A/a appears the same as A/A.

Not all genes have one dominant allele and one recessive allele. Sometimes both alleles are equally dominant, sometimes there's more than two alleles that sort neatly from most dominant to most recessive, and sometimes there's more than two alleles but they don't sort neatly.

An easy way to calculate what color foal you can get from breeding two parents is to use a Punnett square. The parents go in the big squares on the top and left, and the 4x4 group of squares shows what colors the foal can be. Each foal gets the allele above it from one parent and the allele to the left of it from the other, and then by knowing what the alleles do you can figure out which color the foal will be.

In this example, breeding one horse with A/a to another horse with A/a has an equal chance of making each of the four foals shown. Three out of four are bay, so the chance of a bay foal is 3/4, and one of the four foals is black, so the chance of a black foal is 1/4.