Contributed by Vic High:
Basically, when you are cubing a mother plant, you are taking her paired alleles and making them homozygous for each trait that you want to become true breeding. Some paired alleles will already be homozygous but most of the important ones will be heterozygous in the case of an F1 other-to-be-cubed. Mind you this can only be true of those traits that are controlled by basic dominant/recessive genes. This isn't always the case and sometimes genes can be codominant. Here is an example of the implications.
let A & B & C be codominant genes, d being a recessive gene on the same loci. Now for simplicity we will just look at the genotype and ignore the phenotypic effects of each genotype. Lets say our mother-to-be cubed has the genotype AB and the P1 male is Cd (both being F1s).
Notice that you can never really get a completely true breeding situation with this sort of gene. To fully capture the mother's trait you must maintain the heterozygoous AB condition. Crossing two parents with the same characteristic AB will give the following offspring:
AA, AB, AB, BB
Note only 50% of the offspring will ever be able to recreate this mother's genotype (and in this case phenotype)
Ok, now that aside, lets explore the practical issues of trying to cube that mom. Crossing the AB and Cd you the following combinations:
AC, Ad, BC, Bd. You then select from these to do your first backcross to your AB mom (creating the .75 generation)
ABxAC = AA, AC, AB, CA - 25% resemble mom in this case
ABxAd = AA, Ad, AB, Bd - 25% resemble mom again
ABxBC = AB, AC, BB, BC - 25% resemble mom again
ABxBd = AB, Ad, BB, Bd - 25% resemble mom again
As you can see, it really doesn't matter which males you selected for your first backcross as they all brought you equally close to your goal. Notice that it will also take a sharp eye to pick out the special offspring that will take you closer to your goal in the second backcross. Hopefully this shows how difficult it can be to stabililize a trait caused by codominant genes.
This was just the first factor affecting cubing success. Also, it only dealt with a single genes and you are often trying to stabilize dozens of gene pairs when cubing.