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This short course is given in layman's terms to give a general understanding for the average person to understand the basic concepts on how genetics work.
It is by no means exhaustive and in some cases more detailed exlanations can explain some genetic things more fully than what we will do here.  

Read through the information and see how much you can learn :)

And so we start.

We have a horse that is crCR, EE, Aa, n/P1 and nn for MH - what do these codes tell us about this horse? by the time you are done you should be able to read this and more.

How do genetics work?

* A horse has 64 Chromosomes. That is 32 pairs.
* There are thousands of genes along each chromosome each in fixed positions known as the locus,  The individual genes determine the characteristics of the horse.
* To put things very simply (in fact it is more complicated) the horse inherits one gene from the father and one gene from the mother for each characteristic.
* Each gene is symbolised with a letter or combination of letters. The use of a capital letter indicates that the gene is dominant and lower case indicates that the gene is recessive. 

What is the difference between Dominant and Recessive?

* Dominant and recessive refers to whether the genes will affect the horse.   If the gene is a dominant gene only one copy is needed to be able to see its affect on the horse.  So the horse inherits one gene from each parent - lets look at color for an example - 
A buckskin, a Palomino and a Cremello all have one thing in common - they have a cream gene.  The options for a cream gene are as follows nn, nCR (sometimes written as crCR or some other variation) or CRCR.  Cream is considered a dominant gene.

- the nn means neither parent contributed a cream gene so the horse will not be a palomino, a buckskin or a cremello
- the nCR means the horse inherited an n from one parent and a CR from the other parent - this horse will be either a buckskin or a palomino (or a smokey black)
- the CRCR means the horse inherited one cream gene from each parent
and is a double dilute.

A lowercase n tells us that the cream gene is dominant - if it would be an uppercase N that would mean the gene is recessive - okay so now we put this together.

Dominant example - if the horse only has one cream gene you can see it on the horse - eg palomino or buckskin (smokey black) whose genetic code is nCR
- if the horse inherited 2 copies and is CRCR then the horse is a double dilute - a cremello, perlino or a smokey cream

Smokey Cream

now if we flip that and look at it from the sire and dams side - a buckskin stallion's cream genetic code is nCR - he has one "negative" and one positive gene for cream - so when he sires a foal he will give that foal an n for cream (no cream) or a CR for cream

the same would go for a palomino mare - her code is also nCR - she will give her foal either an n or a CR 

So if we breed that palomino to that buckskin the foal could inherit an n from his sire or a CR and for the other gene he could inherit an n or a CR from the dam - so the foal may inherit 2 n's and be nn (he inherits no cream genetics) or he may inherit one n from his dam and one CR from his sire (or vice versa) and he would be either a buckskin or palomino (or a smokey black) - or the foal could inherit a CR from each parent and in that case would be a cremello, a perlino or a smokey cream 

Now a caveat on the above which we used as an example for a visual example - there is an option for n/CR which does not obviously sow itself even though cream is dominant - that is smokey black - some people say you cannot see cream on a smokey black - while it may not be obvious most smokey blacks do show the cream.

Where dominat genes really come into play is with genetic diseases.  Genetic diseases that are dominant only need one gene fro the horse to show the disease - Recessive diseases must have one of the genes from each parent in order to show the disease.  PSSM1 is an example of a dominant genetic disease and Herda is a an example of a recessive genetic disease.  A horse that only inherted 1 P1 gene from either the sire or the dam is considered to have PSSM1 - where if a horse is N/HERDA that horse is only a cerrier of the HERDA gene and will not show HERDA symptoms - it must inherit the HERDA gene from each parent in order to show the disease.

A common misconception is that dominant means that the foal will inherit the gene - and that takes us to the next important concept to understand... 

What is the difference between Homozygous and Heterozygous?

The common misconception that dominant means that the foal will inherit the gene is actually refering to the term homozygous - there are three ways that horses can inherit a gene - they can be nn for the gene, they can have one of the genes (going back to our color esample) and be nCR or they can inherit both genes and be CRCR - a horse that is nCR is considered heterozygous for Cream and will only pass on the Cream gene statistically to 50% of their foals - a horse that is CRCR is called homozygous for cream and will pass one cream gene on to 100% of their foals.  A cremello stallion would be homozygous for cream and therefore will pass one cream on to 100 percent of  his foals - this is what makes horses that are homozygous for a certain color so desirable as thei woner can confidently predict the color of the foals. (Again with some caveats). 

Why are some horses symptomatic and some not?

This question gets asked alot - there are many factors that affect horses with genetic diseases - we will not cover those here.  From a genetic standpoint though - genetic disease testing has only come about in the last number of years - the science is a fast paced changing world as scientists develop new tests and find new gene mutations and figure out how genes work with each other.  Figuring out why some ae more symptomatic than others likely relies on gene combinations, some of which we dont even know about yet.  As we become aware of new information we will update this site and try to keep things current as things unfold in this exciting time.

Mutant Genes

Sometimes over the course of time there is a a breakdown in a gene - and a new genetic disease is born - that gene then gets passed on to offspring and more and more horses inherit a problem from an ancestor. 

What codes are used?
* Color Codes: 

Genetic codes are not standardized across the world - some labs will write them one way and some will choose a different way.  Below we will give some of the ways codes are written.  Some use lowercase letters to refer to an n - meaning the horse did not inherit that gene.

HEre are examples of a horse heterozygous for cream and the different ways it might be written:

nCR  or n/CR or crCR or crCr 

Other color codes are as follows:

Dominant Colors:

Black/Red for some reason this one is fairly standardized - and it is done with E's  

                                  ee is a red based horse Ee or EE is a black based horse - Black is Dominant so a horse only needs one E to show black
All horses are either red based or black based.   All the rest of the genes modify the horses base color.

Agouti is written as aa or aA or AA (another form of Agouti which produces Brown is written as At)   Agouti restricts the black on a black horse to the main, tail and lower legs (Think Bay)  Agouti cannot be seen on ee (red based horses)

caveat - this is where color can get confusing - a bay can look red but it is a black horse - the way I like to think of it is like this:  all horses are red - for a black horse it is like it is a red horse was dipped in black.  For a black horse with agouti, it is like a red horse was dipped in black but all his body was masked except his mane tail and legs, so they are black but his body remains red.   

Grey is written as gg or Gg or GG depending on if it is negative for grey, heterozygous for grey or homozygous for grey - Grey is a wild card when it comes to color in horses - it causes all kinds of spectacular coloring as the horse slowly changes from its base color it is born as to completely grey (looks almost white) by old age.  Grey can even cause an ee horse to appear to have black markings.

Other modifiers

Dun is written as dd, dD or DD - dun adds a dorsal stripe and darkens the points (lower legs, mane and tail) and adds leg barring (look like tiger stripes on the upper leg) - so a red dun would have a darker mane and tail (and lower legs) as opposed to a chestnut who's mane and tail is the same color as the body, or a sorrel who's mane and tail are lighter than the body.

Cream is written as crcr or crCR or CRCR - cream lightens the body to a creamy color - think palomino or buckskin - a double cream horse ALWAYS has blue eyes and pink skin (cremello, perlino and smokey cream).  Unlike a smokey black (who you can barely see the cream gene affecting, a smokey cream is a black horse with no agouti and it is lightened the same amount as a perlino or cremello - for most double creams you cannot tell them apart without testing them. Perlinos do have a slightly orangy look to their manes and tails so guesses can be made. 

Champagne is written as chch, chCH, or CHCH - it is very similar to cream in how it acts

Silver is written as zz, zZ or ZZ - it is recessive - so unless two copies are present you will not see it.

More color gene info will be added in the future.

So what else do we know about the horses below?

Smokey Cream


ee ee Ee or EE Ee or EE ee
aa, Aa or AA aa, Aa or AA aA or AA aa aa, Aa or AA
So what do we know about the horse first mentioned?
He was crCR, EE, Aa, n/P1 and nn for MH
The EE tells us he is black based, the Aa tells us he has agouti so his black is restricted to his points, and the crCR tells us he has one cream gene.  HE is a buckskin.   What does n/P1 and nn for MH mean?
for that we have to look to the GENETIC CODES for Diseases.
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