Hybridization occurs when pollen from one pepper plant is used to successfully pollinate the flower of a different pepper variety, resulting in seeds that have genetic material from each of the parent plants. "Successfully pollinate" is the key term as not all pepper plants can cross with each other. In some instances, plants from one pepper species can cross with a pepper plant of another species, though generally, hybridization is most likely to be successful with plants within the same species.
With hybridization, the offspring plants typically have traits that are a combination of its two parents. Sometimes traits will closely resemble one of the parents, while in others, the combination results in a plant/pepper that differs significantly. The process of hybridization paired with selective breeding can be used by nearly anyone to create new and exciting chile pepper varieties.
A first generation hybrid between two different types of pepper plants is referred to as the first filial generation or, using shorthand notation, as F1. Seeds taken from these F1 plants are known as the second filial generation, or F2 seeds, which would produce F2 plants. Seeds taken from those plants would be known as F3, with the next generation being F4, and so on.
If the F1 hybrid's parents are two different pepper cultivars, then its siblings (other F1 plants from the same two parent varieties) will usually be different from each of the parents, but very similar to each other. This is because a cultivar is nearly homozygous – meaning the corresponding genes within chromosome pairs are nearly identical – and it will produce pollen and eggs with nearly identical genetics. This is what gives a cultivar similar, predictable offspring.
F1 seeds formed by a crossing of two cultivars, received one chromosome for each pair from each of the genetically different parents. While these seeds have genetics that are a combination of the two parent varieties, they (and resulting F1 plants) will be very genetically similar to each other. This is due to the genetically uniform pollen from Cultivar A pollinating the genetically uniform eggs of Cultivar B.
Alternatively, F2 seeds taken from these F1 plants, even if self-pollinated, can vary considerably from both the parent(s) and each other. F1 hybrid plants, while genetically similar to each other, are no longer homozygous, having chromosome pairs with differing genetics. When the F1 plant produces pollen and eggs through the process of recombination, it will randomly exchange chromosome pair DNA to produce pollen and egg cells with random combinations of genetic material from both of the parent cultivars.
Whereas the F1 seeds were a predictable mix of DNA from Cultivars A & B, the F2 seeds are an unpredictable mix of their DNA. The resulting F2 seeds, thus, are likely to have significant DNA differences among them – potentially producing a wide variety of observable traits as plants.
If desired traits (color, size, shape, heat-level, etc.) are noticed, selective breeding can then be used lock-in and potentially magnify these traits. If such traits are consistently and continually selected for propagation, then each subsequent generation (F3, F4, F5, etc.) should produce less variation and more consistency. If done properly, one could use this process to create their very own pepper cultivar with seeds that "come true" to consistently produce the desired traits.
The above was based on hybridization by crossing two cultivars. On the other hand, if the F1 hybrid is a result of a crossing where one, or both, of the parent plants weren't cultivars – meaning not homozygous – then the resulting F1 seeds are likely to produce sibling plants with significant differences among them. The degree of F1 differences being related to the underlying degree of chromosome pair differences for each of the parent plants.
While many times you'll want your seeds to produce the intended plant, sometimes it's fun to get new and unexpected pepper plants pop-up through accidental hybridization. We accidentally found (and found again, and again...) that non-intended hybridization is actually quite common. We typically grow anywhere from 20-40 varieties of peppers in about 400-600sqft. When using seeds from those plants, we usually find around 10-20% of our new plants are not what we expected.
Many times the differences are minor, like a small amount of purple tint toward the top of what would normally be an all white pepper. Though, some hybrid plants have significant differences and desirable characteristics (beauty is in the eye of the beholder!). If you feel ready to provide a good home for this unplanned pepper, you can attempt to selectively breed your newly discovered hybrid into a variety of your very own.
If you'd like to design your own hybrid, so to say, you'll first need to check to make sure the two cultivars have the potential to cross with one another. If so, you'll want to clip the flower buds from one of the varieties just before the flower opens (so you know it'll have pollen from only that plant). Then, while holding them over a cup, take a tweeters and gently pull off all the flower petals from the bud. Place the buds in a small cup to dry. In a couple of days, you should be able to gently shake the cup to create a small film of pollen on the cup's bottom.
Once you have the pollen from the first variety, you'll want to find a flower just as it's getting ready to open on the second plant. While taking care, to keep this flower bud attached to the host plant, use a tweezers to gently pull apart the flower petals and use a cotton swab to apply pollen from the cup onto this flower. Fold a small piece of paper gently over the artificially pollinated flower and tape the edges to seal it.
About a week later, you should be able to remove the piece of paper and have the very beginnings of a new pepper. Mark the pepper by loosely placing a small twisty-tie around the pepper stem. When ripe, pick the pepper and harvest its F1 seeds. These can then be used to start the selective breeding process.
If resources and space permit, repeating the hybridization process with multiple parent plants, can help to broaden the F1 gene pool and help to produce hardier plants. With the genetic diversity of only two parents, it's more likely that an undesirable recessive trait could be propagated. Crossing two plants of one cultivar with two of another, can produce four batches of F1 seeds – providing a broader range of genetics to select from and cross the following year. Furthermore, additional planned hybridization can be used within subsequent rounds of the selective breeding process to introduce or emphasize certain traits.