Another concept which can 'mysteriously' affect the outcomes of breeding trials is that of linkage. Two types of linkage exist, trait linkage and sex linkage. Additionally, many appearances may be controlled by multiple alleles, such traits are called polygenic.
The physically connected pairs of genes don't exist on one long continuous strand. Rather, they exists in large groups of strands called Chromosomes. Oddly, strands have a tendency to break apart and sort in sections rather than in individual pairs of genes as most breeders assume. In other words the alleles of many adjacent loci (plural for locus) may be passed to an offspring as a set, rather than as individual genes.
A friend describes this as similar to flipping coins: When flipped loose, all sorts of heads and tails combinations are easily produced. But when some of them are taped together and flipped, some combinations are impossible to produce. But a persistent breeder knows that eventually the tape will come loose and he'll get the desired combination.
This explains why certain double homozygous forms of reptiles can be incredibly difficult to produce. A well-known example is that of the famous 'Blazing Blizzard' Leopard Gecko. These are nothing more than the two traits of 'Blizzard' and 'Tremper Albino' existing in the homozygous state in one specimen. Learning of the value of these specimens, many breeders quickly bred albino and blizzard specimens together to create the needed double heterozygous specimens. These double hets were then bred together the next year, with breeders expecting the usual one in sixteen offspring to be the 'Blazing Blizzard'. Damn few were produced, with many breeders producing as few as one in two thousand which turned out to be 'Blazing Blizzard'!
While all these breeders understood that something had gone wrong, few understood it was a simple case of trait linkage.
All of us are familiar with the famous 'X' and 'Y' chromosomes responsible for sex determination in humans (XX=Female & XY=Male). In snakes, it's the 'W' and 'Z' chromosomes (ZZ=Male & WZ=female) that are responsible for sex determination. Regardless of the name, these chromosomes each contain a whole bunch of strands of loci containing many many alleles.
Many of the loci which exist on the 'Z' chromosome do not exist on the 'W' chromosome. This can have unusual effects. In males, two copies of the 'Z' chromosome are present and the usual genetic rules apply to all loci contained within. However in females, those loci in the 'Z' chromosome corresponding to the missing loci from the 'W' chromosome will necessarily contain only one allele. Therefore, any allele present at these loci will have total control over the function of that locus. Thus even a recessive allele at these unpaired loci will be expressed! This state is properly termed Hemizygous.
While all of the previous information on genetics we've presented in these pages may have seemed complicated, they are as nothing compared to the next concept we'll introduce.
Polygenic and Autosomal Mutations
So far, everything we've discussed has been based on the assumption that a mutated allele at a single loci has been responsible for the changes in appearance reptile breeders covet. This is termed autosomal.
But what happens when multiple loci are responsible for altering a single change in appearance? Such results are termed polygenic, and they are unquestionably the most difficult to predict. In fact, for most polygenic traits there simply is no way to fully understand what is happening behind the scenes. Others, such as Bloodred Cornsnakes involve combinations of recessive alleles, incomplete dominant alleles, and groups of alleles best thought of as polygenic. It's like predicting the weather, there are just too many variables to ever be 100% accurate.
In truth, most appearances in animals (well, all life actually, including humans) are controlled by polygenic factors. Often these types of traits are termed 'selective traits or are achieved through 'selective breeding'. But there's plenty of margin for error in such projects, and even the best laid plans will oft times go awry.
Breeding race horses is an excellent example. It's generally well-known that breeding two prize-winners together will increase the odds of producing a derby winner. But it certainly doesn't guarantee it. And there's always a chance of producing a winner from relatively poor stock, as in the recent movie 'Seabiscuit'.
Sadly many coveted morphs of reptiles are no exception to these rules. Popular morphs of Leopard Gecko such as Jungle, Tangerine and Carrot-Tail are all good examples. Many breeders have bred two fine examples of these together and gotten junk, and many have bred two less than spectacular examples together and gotten some really impressive specimens. More often than not, the results are about what you would expect - a mixed bag of babies containing some nicer, some poorer and most about the same as the parents used. In general, it's wisest to simply acquire the best examples of a type that you can locate and hope for the best.
Why all the variation in offspring? Well, remember that these polygenic types are created by achieving the proper combination of several alleles at several loci. Some of these may be recessive alleles, some incomplete dominant, and some may even be dominant. Many may be trait-linked as well, and some may even be sex-linked. Most will not be discernible to the eye individually. Consider that the parents used in breeding trials are likely heterozygous for some or all of the alleles involved and you get quite the potential for variation. Trying to get all of these to turn out correctly gets progressively harder as the number of alleles involved increases.
To go back to my friends analogy of tossing coins in the air, try to imagine that the goal of producing that coveted reptile is akin to trying to land twenty pennies all heads up. Don't forget that some the pennies may be taped together as well!
We would love to write something here in closure such as "this concludes our lessons in genetics" but we can't. The subject will never be closed. New traits continue to pop up, mysteries are revealed through investigation, new combinations of traits reveal hidden secrets and so forth. It's a fascinating subject that will never grow tiring. Hopefully, the information put forth here will prove beneficial in developing an understanding of how it all works and enable the unraveling your own mysteries.