What are Punnett Squares, Genes, Alleles, Loci ...?

Genetics basics

You’re finally getting good at Hunt & Jump, and ready to get serious about breeding beautiful colored foals!  You know that some genes, when mixed together, cause a ‘heavy burden of white’ and the foal will not survive.  They’ve shown you all the charts: (insert colors chart, numbers chart, Punnett square)     You’ve paid for gene testing and have the results in front of you, and you don’t have a CLUE what you’re looking at!

Gene Testing Results
Ee aa CC dD gg ff SS pp zZ chCh KitrKitto SpSps LLlpECA3P+ECA3P+ rbRb OlwO WF: Minimal

Genes and Alleles - It takes two.

Each of those letters and numbers in the list above are genes.  Genes live on chromosomes, chromosomes group together to tell bodies how to make other bodies.

Genetics means it’s about genes.  But we have to dig even deeper to figure out how things get passed along from mother and father to their offspring.  

To make a gene you need 2 alleles, (pronounced Ah-lee-els)

Every horse requires a set of 2 alleles to produce a specific color gene.  

EX:  Ee  aa  CC  dD

The horse gets one allele from its father, and one from its mother.  

(Usually the fathers’ allele is listed first.)  

In the above example dad gave the kid an E allele and mom gave the kid an e allele.  

Both mom AND dad each gave the kid one a allele, and one C allele. 

Dad gave the kid one d allele, and mom gave the kid one D allele.  

Two alleles make one gene. 

Thing to Remember #1.  

When there are 2 of the same size letters, that means the horse is Homozygous for that color.  Either aa or CC.  Homozygous means they are the same.  Very often people shorten the word Homozygous to Hom, or Homo.  

When there is one Upper case letter and one lower case letter that means the horse is Heterozygous for that color.  Either Ee or dD.  Heterozygous means they are different. Very often people shorten the word Heterozygous to Het, or Hetero.  

Dominant and Recessive – Who’s the Boss?

EX:  Ee  aa  CC  dD

Alleles can be either dominant or recessive. 

A dominant allele takes precedence over a recessive allele.

In our example snippet the upper case E is dominant and the lower case e is recessive.  

Both a’s are recessive

Both  C’s are dominant

The d is recessive and the D is dominant

The way this all works out is a bit tricky.

A dominant trait is what you will actually be able to see on the horse (or in our situation, on the horses picture)

If a dominant trait is paired up with a recessive trait then the dominant trait is the “boss” and the dominant trait is the one that will be visible.  

Recessive traits only show up if there are TWO recessives.  

So in this case, because E is dominant, whatever E tells the gene to do, is what is going to happen.  The aa gene is taking the day off.  

Thing to Remember #2

There are 2 kinds of genes.  

Back to Basics - 

There are only 3 basic colors of horses.  Chestnut, Black, and Bay (called Agouti in the “better” scientific circles)

Every other color is some kind of mix and match of different variations of different genes and how they get along with those three colors.  

Lets shorten our snippet a little further to:  Ee  aa   

Chestnut and Black are controlled by the E gene. 

Bay/Agouti is controlled by the a gene.  

All about Punnet Squares. What, why, and limitations