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Note: Answers are not entirely "exact." They are pretty much, "you got the idea or you didn't" type questions, so you should know if you have the concepts down or not. If you're not sure, feel free to reply with questions/arguments so we can all keep learning. (Believe me, it's entirely possible I brain-farted on any of these and you might catch me on one, hehe, so please do argue away.)
Basic:
Define Heterozygous and Homozygous.
Homozygous means that the two corresponding alleles are the same.
Heterozygous means that they are different. Note that most of the mutations we deal with are recessive, and it is easy to read a lot of posts/comments on genetics and pick up the idea that "het" means a gene which is not expressed. This is different from the true meaning, and is important to understand when dealing with dominant and codominant traits. Also note that an animal that is "het for amel" is actually (technically) "het for amel AND normal" but it is generally silly to point out the "normal" part since that's a "duh" statement.
What is the difference between Phenotype and Genotype?
Phenotype is the physical appearance of a particular animal.
Genotype is the actual genetic makeup of an animal.
For example, a Normal animal is phenotypically normal, and genotypically normal. A "het for amelanistic" is phenotypically normal, but (key difference) genotypically "heterozygous for amel."
What is the difference between Dominant, Codominant, and Recessive?
A recessive allele must be "homozygous" to express itself--to have a noticable effect on the phenotype.
A dominant allele will express itself, and keep all other alleles from expressing themselves.
A codominant will affect the phenotype only "partially" when heterozygous, and totally when homozygous.
What are the possible genotypes for a simple trait called A?
Assuming only the wild-type and mutant allele: AA, Aa, and aa. Or "wild-type, het, and mutant."
If a trait is recessive, what is the genotype of an animal that expresses this trait?
Homozygous for the recessive allele. If we're talking about trait "A" then the genotype could be described as "aa."
If a trait is dominant, what is the genotype of an animal that expresses this trait?
This is kind of a trick question. It can be either Aa or AA. In other words, either het or homozygous for the dominant allele.
If a trait is codominant, how many phenotypes exist for the possible genotypes?
Three possibilities exist. AA, Aa, and aa are all different. For example, let's pretend we have yellow and blue "genes." The 3 corrseponding possibilites are yellow, blue, and (the het would be) green.
If an animal is het for a recessive trait, what does it look like?
It looks like whatever the dominant type (usually wild-type) allele dictates.
If you breed "A" (an A-mutant, which shows that trait) X "het for A" what will the offspring look like?
Half will be heterozygous, normal-looking. The other half will express the recessive trait.
An allele is simply a different "version" or "copy" of a gene that always goes in one specific place. Maybe this should have been a beginner question since all those answers relied on this definition. (d'oh!)
Define Locus. This is a specific location on a certain chromosome. Different alleles can appear at this locus, and which alleles are present is what determines the final genotype and phenotype of an animal.
When both parents are het for the same recessive trait, what is the best description of their normal-looking offsprings' genotype?
When both parents are het, 25% of the offspring will express the mutation. The remaining 75% will consist of 2 hets and 1 non-het (wild type) animal. So, out of those three, two will be hets. Thus, 66% (or 2/3rds) are het. The best description of the normals is "66% possible het."
What do P, F1, F2 mean?
These describe the Parent, First Filial, and Second Filial generations in line breeding. In more common terms, this would be the parents, children, and grandchildren.
When both parents are "double-het for A and B,"
What is the expected ratio of phenotypes in the offspring?
The standard for this cross is 9:3:3:1, Normals, type A, type B, and type AB.
[*]How would you describe the genotypes of the offspring that only express mutation B?
Since they express B, they are obviously homozygous for B. Since they do not express A, but both parents are het for A, they would be best described as "66% het for A."
If an animal has never been bred but is known to be het for trait A, what can be said about its parents?
One of its parents is homozygous for this recessive trait. The other parent is either heterozygous or not carrying that gene at all (homo for wild-type)
Where A is recessive and D is a dominant trait: breeding "A het for D" X "het for A" will give you what results?
The idea here was to trip people up on "het" being so closely associated with recessives.
Looking at the A trait, you will get a 50/50 split between those that do and do not express A.
The D trait, since it is dominant, will also be split 50/50.
The end result (by phenotypes) is a 4-way even split of normal, A, D, and AD.
Given that 3 alleles exist for trait A:
A1 (dominant wild-type),
A2 and A3 (recessive to A1, and codominant to each other)
How many possible genotypes are there? (example: 11, 12, 13, etc.)
Six genotypes: 11, 12, 13, 22, 23, 33
How many possible phenotypes are there?
Remember, the "1" allele is dominant, so 11, 12, and 13 will all look normal.
But... 22, 23, and 33 will all look different because these are codominant amongst themselves. That makes 4 possible phenotypes.
If you breed "22" X "33":
What will the offspring look like?
They will be "23" which means they will look like something in between type 2 and type 3. Example: if the types 2 and 3 were red and yellow, they would all be orange.
[*]Are the offspring homozygous or heterozygous?
Remember, Het is only genotype, so the appearance means nothing here. They have allele 2 and allele 3. Those two alleles are different, therefore they are heterozygous.
What trait(s) in cornsnakes resembles this trait?
This one would be extra credit. Motley, Striped, and their normal corresponding wild-type allele match this description.
What are the advantages and disadvantages of inbreeding?
In short...
The advantages:
Inbreeding makes it much more likely to pair up similar--and most interestingly--rare recessive genes. For example, when you discover the first ever example of a cornsnake expressing some new trait, you can breed it to anything to create the "het" offspring. You can then breed those offspring back to the original mutant, pairing up the recessive gene into more animals. Breeding the F1 siblings together also accomplishes this, but not to the same degree.
Inbreeding also allows other similar, but more subtle genes to be brought together to create more "extreme" expressions of a given trait or set of traits.
You might have an entirely new gene already present in your collection, or present in a wild-caught animal. Even if you are entirely unaware of this new "gene" you are more likely to uncover its presence (and maybe a new recessive trait) by inbreeding.
The disadvantages:
Inbreeding brings together recessive genes... (sounds familiar?) but there are also a lot of recessive genes that are extremely bad when expressed. This can create genetic weaknesses or even "incombatibility with life." Well-known examples are hip problems common to some breeds of dogs, and some of the infertility and picky-feeder-hatchling problems experienced by the original striped and bloodred lines in cornsnakes.
The good news is that outcrossing (breeding in unrelated bloodlines) can immediately bring in a fresh set of dominant genes to counteract the recessives, and bring new vigor to the projects. Look up "hybrid vigor" for more information. This has been very successful in eliminating the major problems in bloodred and (I believe) striped lines in cornsnakes.
The bad news is that, if these traits are very complex, it will take a lot more inbreeding to recover something like the original traits once again. ...which is probably why nobody outcrosses Collies trying to get rid of hip dysplasia. (and maybe why a lot of bloodreds don't live up to my "pie-in-the-sky" expectactions?)
You find a wild amelanistic male, bring it home, and breed it to a never-been-bred amelanistic female in your collection. All of the offspring are normal. Explain.
The new male is actually expressing a new nonallelic form of amelanism. That is, you have discovered "amelanism type B" which is incompatible with the current form.
(extra credit)
An easy way to visualize how this is possible is to imagine that 3 genes control the pigment production: genes A, B, and C which respectively code for proteins A, B, and C. The proteins ABC are chained together to make our pigment.
The current form of amelanism is a defect in gene A. The "new" form is in gene B. If only one defective A gene and one defective B gene are present, the other non-defective genes in the pairs can still produce everything that's needed to make the whole chain of ABC, and so you still have the pigment.
While in the 5th generation of line-breeding normal cornsnakes, you mate 4 brother/sister pairs. Every clutch results in 20 hatchlings. In all but one clutch, the offspring are all normal, as you would expect. Out of 20 of the hatchlings in the other clutch, 5 of them show a new (never-before-seen) trait.
Let's call our new trait "Z" here. Notice that if you have one het parent, each F1 is 50% possible het. Statistically, 1 out of 4 pairings should line up to where both mates are het for Z. (the other 3 possibilities: only one/other are het, or neither are het) This weird one, however, is the one clutch out of four where you got the mutants showing up.
What is most likely to have happened?
Obviously, a new trait has appeared. Since you have been line-breeding, it is unlikely that this trait was present at the beginning of the project. One possibility is a spontaneous mutation. (another is really bad luck for a few generations...)
[*]What is the most likely mode of inheritance of this trait? (simple/complex, dominant/codominant/recessive?) 1/4th of this clutch are expressing mutant Z. This suggests that it is most likely a simple-recessive trait with a het-to-het mating.
[*]Where would you suspect the trait to have originated?
My best educated guess would be looking at the grandparents of the first expressed mutants, as this is the closest point at which it could have occured.
[*]Statistically, how many of the 80 offspring would be het for this new trait? Since the one grandparent was het (that we know of) we can assume (statistically) that the pairings were
"het X het" (10 of these 20 are het).
Het X normal (10 of these 20 are het)
normal X het (10 of these 20 are het)
normal X normal (0 of these were het)
...so we can expect about 30 of the 80 to be het.
(Ok, I admit that last 30/80 was just plain evil... hehehe!)
A new recessive allele appears in a wild population. When expressed, this trait makes survival in the wild impossible. At what point does being heterozygous for this trait create a selection disadvantage?
My answer is "whenever a het breeds to another het" because 25% of their offspring will definitely not get the chance to pass these parents' genes down to future generations, resulting in a "disadvantage" for the hets. I'm sure it can be made a million times more complicated with math, but I was just looking for the idea behind selection.
Thanks to everyone who stuck through all the rambling and nonsense. And of course, all feedback, questions, corrections, and "Serp, you moron, you totally messed up that answer!" are 100% welcome.
Some 'lines' of stripes still have lingering fertility problems. The line my stripe male comes from has some 'glitches' in fertility still. The breeder I bought him from was more than happy to disclose this to me at the time of purchase though. (Good guy/breeder.) He told me he has only experienced fertility problems in stripe X stripe. But no problems with stripe X het stripe or het X het.
If there is a conclusion to be drawn from this genetically, its over my head. I am not exactly a genetics wizard. God bless 'Mick' and her Progeny Predictor.
joe clark
Ps: I have outcrossed my stripe to an amel this year, and only plan on producing stripes from amel/stripe hets or stripe X amel/stripe hets. Next year he will be outcrossed to a ghost and anery motley.
it's really useful. Kinda brings back all my memories when I was in high school biology....I learned all those back then but completely forgot about them already...hahahahha
It's the first answer in the Intermediate section. I should have put that one (and locus) in the Beginner section, since it's part of the vocab there.
Also, Webster's defines it as: 1 : any of the alternative forms of a gene that may occur at a given locus
2 : either of a pair of alternative Mendelian characters (as smooth and wrinkled seed in the pea)
If you're not sure, feel free to reply with questions/arguments so we can all keep learning. 
