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---  Pigment  ---


Genetics 000
Dark Colors

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Pigment is the substance that gives COLOR
to hair and skin.

Only two kinds of pigment are ever present in horse hair:

Black   (E)   --   and   --   Red   (e) 

These two substances, black and red pigment, form all horse colors!

Black / red is the "first",
or most basic,
horse color gene

Which kind of pigment is determined by only one pair of genes, and is only the very first step in determining the final COLOR of the horse.

Look, again, at our imaginary string of genes from one chromosome, from one cell, from one horse.  

One set, or PAIR, of genes is circled:

We're imagining that these two circled genes are the PIGMENT genes, which are the genes that tell the cells whether to make RED pigment only, or to ALSO MAKE BLACK pigment*.

EACH of these two genes, that make up the pigment pair of genes, contains directions to produce either black pigment or red pigment.

The pair can both be red, both be black,
or they can be one of each.

*A general note about pigment in horses:

All horses produce red pigment in all of their hairs
(except white or gray hairs,
which are as clear and colorless as glass.)

They would also produce black pigment in all of their hairs,
unless that black pigment were blocked.

Keep reading to learn that two red genes (ee) block black pigment.

  • E and e are the codes/abbreviations for black or red PIGMENT

    •  The E, or black, gene is the DOMINANT gene of this pair; so, if it is present, its "directions" are always followed - the hair cells of that horse will make black pigment. When the black pigment is present, it "covers up" (or extends over) the red pigment, so the horse looks black (unless color modifying genes change it).  Another way to think of this is that the E gene ALLOWS black pigment to EXTEND into the hairs.

    •  The e, or red, gene contains the direction to block ALL black pigment, leaving only red pigment.  But, it is the RECESSIVE gene of this pair, so its "directions" are only followed if it is the ONLY gene in the pair -- ee (if there is no E gene present).  A horse with only red pigment is chestnut, or red, (allowing only unrelated genes to modify the red.) 

  •  Possible pairs at E/e (pigment)

    •  ee would block black pigment, causing the horse's only pigment to be red (chestnut/sorrel).  If a horse with ee were to become the parent of a foal, it could only contribute an e to its foal, since that's all it has.

    • EE would allow/cause the horse to have black pigment. 
      Black pigment covers the entire horse if no other color
      modifiers affect it.  If a horse with EE were the parent of a
      foal, it could only contribute an E, since that's all it has.

    • Ee would also allow/cause the horse to have black pigment, (the same as EE) because E is dominant over e
      (Remember, it would not be written eE.) 
      A horse with
      Ee could give either  E or e to its foal.

  •  There is a DNA test which can tell you exactly which "E/e" genes your horse is carrying, even if you can't tell "by looking".

  •  Some laboratories, authors, etc., call this test, or the genes themselves, "red factor".


By the way...

When the second gene in a pair "doesn't matter" in a discussion, because the other gene would be either the same or recessive to it, its place will often be marked by an underlined blank space.

If you see E_ or A_   , for example:

E_ could stand for EE or Ee, and

A_ could stand for AA, AAt or Aa . (A, At and a are the topic of the next section.)

DNA testing labs often use their own abbreviations.  For example, some testing labs use N for the "negative", or absence, of any gene.  Example:  Z/N  =  Zz  (only one silver gene)

(To continue with the simplest explanations, click Agouti, now.  But for ...)


Other genetic terminology:  you don't need to learn these terms in order to understand horse colors as presented on this web site.  However, you may run across them being used by others.  In case you want to learn them now, or look them up later, they are listed here.

  • Melanin: all pigment

  • Eumelanin: black pigment (E)

  • Phaeomelanin: red pigment (e)

  • Allele: one of a pair of genes (e is an allele of E)

  • DNA: the protein of which genes are made

  • Nuclear DNA: the genes in the nucleus, which we are studying

  • Mitochondrial DNA: the genes in the mitochondria, another structure inside the cell.  Only comes from the mother.  Not important for this study.

  • Locus: the position where a pair of genes (two alleles) is located.  The plural of locus is loci.

  • Extension gene: the gene that allows black pigment to "extend" over the horse.  (This is where the letter "E" comes from.)

  • To continue with the logical "flow" of the site, click Agouti next.


To follow the educational, logical progression of this web site, click "Next", below.

Back Pigment Agouti

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