Thse next few paragraphs mention various aspects of the Mendelian story not covered in class, which you should review on your own.
a) Dominance
It became clear in the summary of Mendel's paper that he was aware that not all trait variants (we would now say alleles) exhibit dominance relations of the kind possessed by the 7 traits in his experiments. In general hybrids (or as we shall say from now on, heterozygotes) can exhibit phenotypes which are intermediate between, or more extreme than both homozygous phenotypes, concepts that only make sense if the phenotype is quantitative on at least an ordinal scale. Terms like full or partial dominance are used in this context, and overdominance describes the more extreme case. For qualitative traits, heterozygotes may resemble one or the other or neither homozygous phenotype. When all three genotypes AA, Aa and aa are distinguishable, we say that A and a are codominant, and generally avoid the use of upper-case letters, using instead (say) a1 and a2.
b) Multiple allelism
One of the earliest and nicest examples of multiple allelism is furnished by the ABO system of blood groups. Because there were initially 4 (there are now more) distinguishable phenotypes (O, A, B and AB), it was first thought that the genetics of the ABO system was best explained by postulating 2 bi-allelic loci segregating independently. However, a nice statistical argument by the mathematician (later geneticist) Bernstein showed that the population and family data were better explained by a 3 allele system, with partial dominance: AA and AO are type A, BB and BO are type B, while OO is type O and AB is type AB. Thus alleles A and B are codominant, but are dominant in relation to O. See the book by C. Stern (Principles of Human Genetics) for a discussion of Bernstein's work.
c) Gene expression.
Although not vital for the course, it is better to avoid naive notions of genetic determinism. The relation between genes (alleles) at a locus and phenotype can be very complex, being potentially influenced by the whole previous history of the organism, including environmental characteristics. The fact that identical twins frequently differ in characteristics with strong genetic components testifies to this. Many genetic disease have different frequencies at different ages, for males and females, according to diet, and so on.
A term we will meet arise in this context is penetrance, which (when fully specified) is the proportion of individuals with a given genotype that exhibit a given phenotype. For example, suppose (with Mendel) that we have a trait with variant forms designated by A and a. Then strict dominance means simply that the penetrance of individuals with genotype AA or Aa is 1, while that of aa individuals is 0. Of course here the phenotype is the dominant variant of the trait. Incomplete dominance might then be described as penetrances between 0 and 1.
Another term relevant to this subsection is phenocopy. Imagine that a phenotype is produced by a particular genetic composition (more or less invariably). This does not mean that every individual exhibiting that phenotype must have the associated genotype; individuals that do not are sometimes referred to as phenocopies.
d) Gene interaction.
A simple story. Suppose (cf. Mendel) that we cross two pure-breeding lines designated A and a and find that the hybrids all look like A. Following Mendel, we now either self or form an intercross of these hybrids, and find a segregation ratio of 9:7 A to a in this first generation of hybrids, known as the F2 generation. What is going on?
One possible explanation, known to be true in some cases, is as follows. There is a pair B, b of alleles at another locus, segregating independently of those at the first locus; B as well as A is required to manifest A, and our original pure breeding lines were in fact AABB and aabb.
Under these assumptions, our F2 generation is (like Mendel's dihybrid cross) the result of crossing AaBb with AaBb, and (following Mendel) should be 9:3:3:1 AB, Ab, aB and ab. Of these only the 9 AB manifest A, and the remaining 7 are a.
In such cases, B is said to be complementary to A. The phenomenon is a kind of 2-locus dominance, and is called epistasis. (This term is also used for any kind of gene interaction.)
Chapter 11 of Strickberger's excellent book "Genetics" gives illustrations of no fewer than 15 different patterns of segregation frequencies resulting from independent segregation at two bi-allelic loci. The differences arise from different combinations of full or partial dominance, or codominance, together with different kinds of interactions. And this is with only 2 independently segregating loci; what if there were 3 or 4 or....involved in a trait? The large number of possibilities illustrates what a difficult business it is guessing gene action from phenotypic frequencies in crosses. Fortunately, the latter-day version of this game has further data - marker genotypes - to assist in the guessing. We will be looking at such data shortly.
e) Lethality.
This is another complication that can obscure the simplicity of Mendelian segregation ratios. A classic example in all the books refers to a dominant yellow strain A of mice (after Cuenot, 1905 which I have not seen). An intercross Aa x Aa of the heterozygotes Aa yields Aa and aa in ratio 2:1, while a backcross Aa x aa gives Aa and aa in ratio 1:1. What is going on? In this case the data are explained by supposing that AA is lethal; that is, no-one has ever bred an AA mouse (so the books say).
Often in experimental genetics, a serious deviation from the proper (Mendelian) ratio is observed at a marker, and explained by postulating a lethal or near- lethal gene near that marker. The above is what they mean in such cases. (How correct such explanation are, is another question.)
f) Sex.
Of course you will all read about sex-linked traits, but you should also
be aware that parental (maternal, paternal) effects are also a feature of
certain traits. That is, it can matter which parent passes on a given
trait variant to offspring, even when that trait is not sex-linked. And
there are also traits influenced by mitochondrial genes, which are largely
tramsmitted maternally.