In my new genetics course I'll soon be teaching about how genotypes determine (or influence) phenotypes in diploid organisms. For these Week 3 classes I want to give the students some reading material, both to read before the lectures and as a study reference for material covered in class. But there's nothing suitable in any of the genetics textbooks I've looked at, so I need to create it myself. Below I'm going to try to work out how best to present this and to design the reference I'll have them read.
The Week 2 lectures (= this week), will discuss natural genetic variation, how mutations generate this variation, and the phenotypic consequences of genetic differences in haploids and homozygous diploids. In the last of these lectures I want to consider the differences caused by standing genetic variation as well as lab examples. And here I should raise the issues we'll deal with next week, explaining that diploidy complicates the relationship between genotype and phenotype, and that the next week's classes will all focus on building a solid understanding of this relationship in diploid organisms.
Somewhere (in the Friday Week 2 class or in the Monday Week 3 class) we'll need to consider that there are different kinds of phenotypes. Some are strictly qualitative - presence or absence of an antigen or blood type, presence or absence of a disease - but many are best treated as quantitative, especially when we consider natural variation. These include obvious things like height and hair colour, and less obvious things like about of an enzyme or metabolite present in a cell or bodily fluid.
I'll also need to introduce the idea of 'risk' as a quantitative phenotype - this is best done in the context of natural variation and genomics.
The first Week 3 class will just be about interactions between alleles of single genes. I'll start with some of the same examples I used the Friday before, asking students to predict the phenotypes of individuals heterozygous for mutations whose homozygous phenotypes we've already established. These should include intermediate phenotypes, 'both-type' phenotypes, and dominant/recessive phenotypes, and genes with more than two alleles.
The existing terminology is terrible, since everything is described in terms of dominance, whereas dominance and recessiveness are really only two extremes of the range of heterozygous effects. The problem is maintained by the practice of beginning genetics courses with Mendel, and of introducing all the important concepts with dominant/recessive allele pairs and the A/a allele representation. Only long after students learn this (mainly by rote) are they told about genes with more than two alleles and about 'Variations on Dominance' (Introduction to Genetic Analysis), 'Modifications of Dominance Relationships' (iGenetics), or 'Complications in the Concept of Dominance (Genetics: Principles and Analysis). These books, and all the other genetics textbooks I've seen, present 'co-dominance' and 'incomplete dominance' or 'incomplete dominance'
Oh, and in the preceding Friday class I also need to raise the important issue of how we name alleles - when the A/a convention is appropriate and when it isn't. I'll tell them that its usually only appropriate for made-up examples in classrooms, because genetics researchers have different conventions for the real organisms they study. (There's no point teaching students these conventions, because they are not only arbitrary but are different for different organisms.) I'll also tell the students that I will only use the A/a convention for alleles known to be dominant/recessive to each other, and that they should be careful to only use them it they are confident that this is the case.
I really wish we had good terminology for the different kinds of effects. I don't want to use 'codominant' and 'semi-dominant' (or 'incompletely dominant'), but the only alternative is to describe the actual relationship in each case. Maybe I can at least standardize the words I'll use in this course: 'blended' for a heterozygote phenotype that's halfway between those of the homozygotes, 'both phenotypes' for co-dominance.