Why F1 generation predictions are identical and dominate though literal results can be different?

Question

In my genetics unit, I am doing a major assignment on the F1 and F2 generations of canola plants, looking at the two traits of stem colour and plant height.

We made predictions about the F1 and F2 generations and then compared them to the plants we grew. While I understand why and am able to explain how the phenotypes of the F2 generations differed slightly from the predictions, I cannot explain the F1 generation.

As the parents are homozygous dominant for one trait and recessive for the other, all offspring genotypes were "TtPp' meaning all phenotypes should be dominant. However, only 74.07% presented as such in the plants we grew.

Are there any theories, reasons or resources I could use to explain a 26% difference?

Answer 1

Alas, there always are! The search terms you're looking for to learn more are 'penetrance' and 'expressivity'. Penetrance refers to "how many individuals of a given GENOTYPE display the PHENOTYPE that is expected?".

Let's say that purple stem color is dominant, designated by P. So Pp should be purple, if everything is the way it was for Mendel (who brilliantly picked phenotypes that did NOT display any of this nonsense!).

However, suppose that it's not that simple. Suppose that there is some regulator, and the plant must make AT LEAST 1000 units to show purple. Usually, it gets this right. But let's say that the amount made is also dependent on how much sunlight is present; if there is little sunlight (such as in a classroom), then plants are "living on the edge" as to whether they produce 1000 units or not. Maybe there are also other genes involved, some of which add 20 units if you get one allele; fail to add units if you get the other allele.

So each plant has its own situation BESIDES the Pp genotype. If a given plant makes 1200 units, then its stem will be purple. However, if another plant, Also having Pp genotype makes 988 units, it fails to meet threshold and stays green.