In color genetics, we often want to think of genes as switches that are either off or on and separate from one another. This is good for explaining simple inheritance and gives people with no background in genetics an easy introduction. However, when you start to learn more complex subjects like linkage, you have to understand that this is an oversimplified approach.
Gene are not simple, they are actually very complex. An average gene is made up of around 100,000 base pairs. A base pair is a grouping of DNA that looks something like this (shamelessly stolen from wikipedia)
Genes are also not separate from one another but are one continuous DNA strand with the gene breakpoints being decided on by science to aid in the location of protein production and mutations. So you can think of an allele of a gene like a train track, each “letter” (“actually they are symbols for nucleic acid) is a car, but they are all attached together. Linkages occur because these “train cars” that are “linked” to one another want to “stick” to one another and are usually inherited together. This means that if alleles of genes are linked they will “usually” be inherited together because they are on the same “track”. For example in horses, since KIT and Extension are linked, if a horse is Ee and Rnrn his roan allele will be “linked” to one of his extension alleles. Lets say that E is linked to Rn. This means that every time an offspring inherits “E” it will also inherit “Rn”. All of the offspring that inherit “e” from this parent will also inherit “rn” (non roan).
Occasionally, however, “train cars” that are “close” to one another, instead of being inherited together, are instead inherited separately. Even the individual “cars” in each base pair have a chance (a very low one) of being inherited separately. This very small chance between “cars” (ie letters) adds up, in a way, so that the farther apart any two “cars” are the higher the chance that they will be inherited separately. Eventually, they get up to a 50/50 chance of being inherited separately which is what we see most of the time with genetic mutations. When genes are “close” together like Extension (MC1R) and KIT in horses they tend to want to “stick” to one another but are far enough apart so that we can see them occasionally separate. This “breaking apart” is called Crossover.
When a crossover occurs, it occurs with the offspring not the parent so that even if a crossover has occurred in one offspring, the chance of is happening again remains same for the parent (in the example chosen around 7%). However, in the offspring, the crossover “change” will remain. Lets consider our example stallion again who has one “E” and one “e”. His roan is linked to his “E”. A crossover occurs with one of his offspring which results in the “e” being linked to RN” instead of “E”. In the line of that offspring the “e” will continue to be linked to roan unless (until) a crossover occurs reversing the linkage. However, in the original stallion the roan will continue to be linked to “E”.
Linkage and crossover occurs between genes on the same chromosome. For example the only known linkage in color genes in horses is between KIT and Extension (MC1R) which are both on equine chromosome 3. Therefore all mutations on KIT will be linked to extension. This includes All of the Sabino mutations (SB1, dominant white, white spotting, anything designated with a W, classic Roan, Tobiano, and probably Rabicano). Since genes do not always appear on the same chromosome in all species, these same genes may not be linked in other species. Rabbits for example have no known linkage between KIT and Extension (ie Broken and the E locus).