Zygotes will germinate overnight into 4 or 8 cells. These can be separated by manipulation with a glass needle under a dissecting scope, so that each cell will produce an isolated colony for analysis. In many cases the genetic analysis can be achieved by replica-plating the colonies onto selective plates, or individual colonies can be picked with sterile toothpicks and restreaked. In the course of mating a small percentage of the zygotes will form stable diploid cells that can be grown mitotically. The selection of such cells can be enhanced by including selectable markers in the two parents, A common system is to use two arginine-requiring strains that are located very close to each other on the same chromosome.
Diploid strains are useful for examining dominance relationships between alleles.
In addition there is a period between cell fusion and the formation of a zygote or diploid in which the cells retain two distinct nuclei. The nuclear genetics of Chlamydomonas is well established. There are a large number of mutants that have been characterized and the Chlamydomonas Genetic Stock Center at Duke maintains an extensive collection of mutants, as well as many combinations, including some excellent mapping stocks. Chlamydomonas has the distinction of also having a large number of chloroplast mutants as well as several mitochondrial mutants. In addition to classical genetics, all three genomes can be transformed.