When it comes to breeding tomatoes, the first step is deciding on what the parents will be. Parents are chosen for many traits, such as plant habits, productivity, disease resistance, fruit shape, fruit color, and—most important—flavor.

For example, let’s say we want to cross Cherokee Purple to Sweet Scarlet. Both tomatoes have good flavor, but other than that, they are very different. Now let’s compare the known genetic traits of each of them.

Cherokee Purple has two dominant traits—regular leaves and an indeterminate growth habit—but the fruit color, purple, is a recessive trait because it has a clear epidermis. Any time a tomato has a clear epidermis (skin) as opposed to a yellow epidermis, it is a recessive trait. Sweet Scarlet is completely opposite in that it has two known recessive traits—it is a dwarf and it is potato leaf—but it has one dominant trait: Being a red tomato, it has a yellow epidermis.
So what does this mean when deciding which parent should become the mother/host and which parent should become the father/pollen donor, and why are we looking at dominant and recessive traits? If you fast-forward past the actual “cross” to the first generation of seeds that grow out from the cross (F1), the offspring will generally express all dominant traits. For this reason, it’s best to choose the plant with the highest number of recessive traits to become the mother. If this plant is crossed with the pollen from the father that shows mostly dominant traits, then you can be sure the cross was a take in the first generation because you will see dominant traits appear from a mother that did not express them.

In the F1 generation resulting from a cross between (mother) and Cherokee Purple (father), you will get an indeterminate plant with regular leaves and red fruit. The leaf and plant habit genes come from the father, and the red fruit genetics come from the mother. Not until the next generation (F2) will you see the genetics diversify and begin to pair up and settle out.