From: A1.MHH@isumvs.iastate.edu (Mary Healey)
Subject: Re:Horse color genetics - LONG
Organization: Iowa State University, Ames IA
Date: Fri, 22 Jan 1993 15:41:24 GMT


Re: Horse color genetics program

Sue Bishop writes:
>  Not that hard if you use the 'square' method.  Just make a big
>  square, list possible variations of the mare vertically, possible
>  variations of the sire horizontally.  Works great, takes a few
>  minutes and the margin of error is small.
>
>                Bay stallion x Grey mare
>
>  Stallion out of bay mare and chestnut stallion, so genotype is almost
>  certainly Bc.
>  Grey mare out of chestnut mare and grey stallion, known to have
>  produced greys, chestnuts and bay, depending on what she is bred to.
>  Genotype almost certainly Ggcc
>
>       Stallion              Bc          bc
>                       _________________________
>           M      Gc  |     GBcc    |   Gbcc    |
>           a           _________________________
>           r      gc  |     gBcc    |   gbcc    |
>           e           _________________________
>
>  I think that's right, with this combination you get 50% grey, 25%
>  bay, 25% chestnut.
>
>  Tracy, do I have it right?
>
>  Sue

Sue -
     I'm not Tracy, but you don't have it right.  Deep breath.
Here we go, plunging into the genetics jungle.  BRIEFLY, color in
horses is controlled by several loci (DNA on different parts of a
chromosome).  Most of these loci have several alleles
(possibilities).  The loci seem to be common to many domestic
animals (dogs and horses, for example, are considered to have
similar loci, but few of the same alleles).  The list (off the
top of my head, so it may be wrong/incomplete) is:

A ... agouti series.  This determines the extent of dark pigment on
      an animal's body.  There are three alleles (in order of
      dominance)
              A - "bay" pattern.  Dark pigment restricted to
                   mane, tail, legs.
              at- (that should be a superscript t) Dark pigment over
                   most of body (except muzzle, flanks).  Is
                   considered necessary in seal brown horses.
              a - Dark pigment extends over the whole body.
      A is dominant to at and a.  Or incompletely dominant to at,
      and dominant to a, depending on which reference you use.

B ... Black/brown.  This determines the color of the dark pigment.
              B - black
              b - brown
      B is dominant to b.  So a horse with black pigment is at least
      B-, but a brown horse is always bb.

C ... The albino series.  There are no true equine albinos, so all
      horses are assumed CC (or cc, I can't remember).

D ... Dilution series.  This acts on all pigments, to lighten red to
      yellow, and reduce black.
              D - "normal" - fully colored
              d - dilute - palominos, duns, buckskins, perlinos,
                  cremellos
      The dilution series is additive.  That is DD, Dd and dd all
      produce different phenotypes (colors).  DD is fully colored,
      Dd is partly dilute (palomino, dun, buckskin), and dd is very
      dilute (perlino, cremello, some "white" horses)

E ... extension series.  Controls the production of dark pigment
      (regardless of color or pattern).
              E - "normal".  Extends dark pigment over body.
              e - restricts dark pigment to eye.
      E is completely dominant to e.  So a bay horse may be EE or
      Ee, but a chestnut is always ee.

G ... grey series.  G (grey) is dominant to g (non-grey)

R ... roaning.  RR is lethal, Rr is roan, rr is non-roan.

T ... tobiano.  T- is patterned, tt is solid colored.

O ... overo.  O- is solid colored, oo is patterned.

Appaloosa, if I remember rightly, is a single locus, multiple allele
(as in 4 or 5 or more) case, modified by other genes at other loci.

Now, back to the example.   A bay stallion (A-B-DDE-ggrrttO-) is
mated to a grey mare (--------G-------).  If these are from
traditionally solid-colored, non-roan stock, then we're working with
an A-B-DDE-gg stallion and a --------G- mare, and we can drop the
R, T, and O series, since all animals will be rrttOO.  Grey masks
everything, so unless you know her original color, the one dominant G
allele is all we can state for sure.
   The stallion is by a chestnut sire and a bay dam, so we can fill
in his E series, A-B-DDEegg.  The mare is out of a chestnut dam
(----DDeegg) by a grey stallion(--------G-), so she is ----DD-eGg.
I'm assuming the phrase "known to have produced greys, chestnuts
and bays, depending on what she is bred to" is referring to the
grey mare, and not to her dam.  We already know she is out of a
non-grey dam, so this information doesn't help, unless she produced
a bay foal by a black (aaB-) or brown(aabb) stallion.
   Still with me?  I know this is long, but it's not a simple topic.
IF both stallion and mare are heterozygous (have different alleles)
at every locus where one is unknown except D - the grey stallion
could be Dd, but lets not get carried away.  So, the bay stallion
may be AaBbDDEegg, the grey mare may be AaBbDDEeGg or, dropping the
homozygous (same alleles) at D, the stallion is AaBbEegg, and the
mare is AaBbEeGg.  Since at is relatively rare, and because this
is getting pretty windy, we'll assume Aa instead of Aat.  This
will give the following possible combinations:

    Stallion:
         ABEg     ABeg     AbEg     Abeg     aBEg     aBeg     abEg     abeg
  ABEG AABBEEGg AABBEeGg AABbEEGg AABbEeGg AaBBEEGg AaBBEeGg AaBbEEGg AaBbEeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  ABEg AABBEEgg AABBEegg AABbEEgg AABbEegg AaBBEEgg AaBBEegg AaBbEEgg AaBbEegg
          bay      bay      bay      bay      bay      bay      bay      bay
  ABeG AABBEeGg AABBeeGg AABbEeGg AABbeeGg AaBBEeGg AaBBeeGg AaBbEeGg AaBbeeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  ABeg AABBEegg AABBeegg AABbEegg AABbeegg AaBBEegg AaBBeegg AaBbEegg AaBbeegg
          bay     chest     bay     chest     bay     chest     bay     chest
  AbEG AABbEEGg AABbEeGg AAbbEEGg AAbbEeGg AaBbEEGg AaBbEeGg AabbEEGg AabbEeGg
M        grey     grey     grey     grey     grey     grey     grey     grey
a AbEg AABbEEgg AABbEegg AAbbEEgg AAbbEegg AaBbEEgg AaBbEegg AabbEEgg AabbEegg
r         bay     chest   ch/bay*  ch/bay*    bay      bay    ch/bay*  ch/bay*
e AbeG AABbEeGg AABbeeGg AAbbEeGg AAbbeeGg AaBbEeGg AaBbeeGg AabbEeGg AabbeeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  Abeg AABbEegg AABbeegg AAbbEegg AAbbeegg AaBbEegg AaBbeegg AabbEegg Aabbeegg
          bay     chest   ch/bay*   chest     bay     chest   ch/bay*   chest
  aBEG AaBBEEGg AaBBEeGg AaBbEEGg AaBbEeGg aaBBEEGg aaBBEeGg aaBbEEGg aaBbEeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  aBEg AaBBEEgg AaBBEegg AaBbEEgg AaBbEegg aaBBEEgg aaBBEegg aaBbEEgg aaBbEegg
          bay      bay      bay      bay     black    black    black    black
  aBeG AaBBEeGg AaBBeeGg AaBbEeGg AaBbeeGg aaBBEeGg aaBBeeGg aaBbEeGg aaBbeeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  aBeg AaBBEegg AaBBeegg AaBbEegg AaBbeegg aaBBEegg aaBBeegg aaBbEegg aaBbeegg
          bay     chest     bay     chest    black    black    black    chest
  abEG AaBbEEGg AaBbEeGg AabbEEGg AabbEeGg aaBbEEGg aaBbEeGg aabbEEGg aabbEeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  abEg AaBbEEgg AaBbEegg AabbEEgg AabbEegg aaBbEEgg aaBbEegg aabbEEgg aabbEegg
          bay      bay    ch/bay*  ch/bay*   black    black    brown    brown
  abeG AaBbEeGg AaBbeeGg AabbEeGg AabbeeGg aaBbEeGg aaBbeeGg aabbEeGg aabbeeGg
         grey     grey     grey     grey     grey     grey     grey     grey
  abeg AaBbEegg AaBbeegg AabbEegg Aabbeegg aaBbEegg aaBbeegg aabbEegg aabbeegg
          bay     chest   ch/bay*   chest    black    black    brown    chest
-----------------
*ch/bay are animals with the "bay" pattern, but brown instead of
 black pigment

The totals are:  grey   64 (50.0%)
                 bay    26 (20.3%)
                 chest  15 (11.7%)
                 black  11 ( 8.6%)
                 ch/bay  9 ( 7.0%)
                 brown   3 ( 2.3%)

This is, of course, a worst-case/most possibilities scenario.  But
you can begin to see why a computer program to calculate the
possibilities would be very difficult to write.

Mary H.
Animal Breeding Section
Dept. Animal Science
Iowa State University
(BTW I work with cow and pig records, seldom horses)