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Plant Breeding for Gardeners

Use proper hybridization to preserve the unique traits found in your favorite garden plants.

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Adobe Stock/Polina Ponomareva

 This article is also available in audio format.  Scroll down just a bit for the link and enjoy listening.

Imagine that it’s harvest time, and you find a tomato that’s a bit larger than the others in your garden. Inspired by this, you decide to try breeding extra-large tomatoes. You begin by collecting the seeds from this large tomato, and the next year, you plant 20 tomato plants from those seeds. At harvest time of that year, you select the largest tomatoes and save their seeds. You then repeat this cycle for 20 years. For two decades, you plant 20 plants every year, each seeded by the biggest tomatoes from the previous year. What do you think would happen to those plants?

If your tomato plant was a commercially available open-pollinated (OP) cultivar — an heirloom variety, for example — then the most likely result would be that your tomatoes would remain the same size for 20 years. On the other hand, if the original tomato plant was a hybrid cultivar, multiple things might happen. In some cases, the seeds might not be viable. Even if they were, the tomatoes you grow might be nothing like the tomatoes that grew from the hybrid seed. In either case, the odds are small that you’d end up with larger tomatoes overall.

At this point, you may be asking, “But isn’t that how plant breeding works?” Yes, but it matters what type of seeds you use at the outset, and what you cross them with. To interpret the results of our hypothetical tomato experiment, let’s think about the material we started with. From there, we can go deeper into what it takes to successfully cross plants in your garden to preserve desirable traits.

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Image Adobe Stock/Sarah

You can save seeds of open-pollinated cultivars if you wish to maintain certain genetic traits in future plants

Generations of Genetics

OP vegetable seeds come from cultivars that “breed true.” If these cultivars are fertilized by another plant of the same cultivar, or are self-fertilized, then they’ll produce a plant with the characteristics of that cultivar. This is because all the plants of an OP cultivar are nearly genetically identical. Variations in the plant, such as fruit size, are thus usually caused by different environmental conditions. So, if you selected the largest tomatoes from a patch of OP tomatoes for 20 years, then the genetics of your selections would be the same as the plants you originally culled, and you’d simply be growing that cultivar year after year. Though it’s technically possible that an OP cultivar might have a small amount of selectable genetic variation present, it probably wouldn’t affect any easily recognizable, desirable traits. If that were the case, plant breeders would’ve bred for it already.

In the case of hybrid seeds, the grown plant is the result of a cross between two different cultivars. Any resulting viable offspring would contain a mix of genes from the two parent cultivars, but not in the same proportion as the original hybrid. So, planting seeds from these offspring and subsequent generations similarly wouldn’t give you the larger tomatoes you’re looking for.

Also, if larger tomatoes are produced, they could be explained by improved gardening practices; maybe you amended your soil or added more fertilizer. There’s also a tiny chance that a random mutation increased the size of tomatoes grown from the seeds. However, if you planted the selected seeds in similar conditions every time over 20 years and gave them the same level of attention, they’d still only grow to the size of your original tomato crop. The genetics of the plants wouldn’t have changed.


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Image Adobe Stock Ehaurylik

Choose two plants that are open-pollinated, such as heirlooms, to begin hybridizing.

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The Language of Hybridization

Geneticists and plant hybridizers use a variety of specialized terms to discuss genes and plant generations. The following definitions cover the use of the lingo in this article.

ALLELE: A form of a gene, noted with a letter or abbreviation. In our example, there are two alleles for flower color, “r” for red, and “w” for white. Dominant alleles are capitalized, and recessive alleles are lowercase.
DOMINANT: An allele that’s expressed when one or two copies are present, written as a capital letter.
F1: The first hybrid generation; each successive generation is numbered in order.
GENOME: The entire genetic makeup of an organism.
GENOTYPE: Which alleles are present for a given gene. In our example, this could be “ww,” “wr,” or “rr” for the flower color gene.
P: The parent generation.
RECESSIVE: An allele that’s only expressed when two copies are present, written as a lowercase letter.


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Image Adobe Stock/fotorauschen

When crossing plants, you can use a paintbrush to transfer pollen from male parts to female parts.

The Basics of Breeding

So, how does plant breeding work? Modern plant breeders increase the rate of mutation, and screen large numbers of plants for mutants — sometimes called “sports” — that may have a useful trait that can be bred into an existing cultivar. Evolution works in a similar manner. It “screens” large numbers of mutants over numerous generations and selects for mutations that improve the ability of an organism to reproduce. Unfortunately, gardeners don’t have the luxury of growing large numbers of plants for endless generations.

Luckily, hybridization is within the reach of an avid gardener. To start the process, a gardener selects an OP plant with a specific characteristic they desire. They’ll cross that plant with another OP cultivar in the same species with overall good characteristics. Generally, plants within the same species can be crossed, but sometimes even distantly related plants can also cross.

Let’s say you’re growing a large, easy-to-grow, disease-resistant type of white flower. While growing this plant, you come across another cultivar of that same type, but with red flowers. However, the red cultivar is a smaller, less-hardy plant than your plant with white flowers. Your goal is to grow a big, healthy plant — like the white cultivar — but with red flowers. Here’s how you could do that.

dried zinnia flowers and seeds

First, you have to hybridize the white and red flowers.  To do so, take pollen from the red cultivar and use it to fertilize female flowers on the white cultivar, or vice versa. When the fertilized flowers shrivel, harvest the seeds. Each seed should contain a mix of genetic material, half from the white cultivar and half from the red. Plant the seeds during the next growing season.

A couple of things could happen when these plants — your F1 hybrids — bloom. In the best-case scenario, you’ll grow red flowers, and all the plants will be intermediate in vigor between the white and red parent plants. In this case, cross your F1 hybrids back with the original white cultivar. This will probably yield a mix of red- and white-colored flowers in your next generation, each containing three-quarters of its genetic material from the white cultivar, and one-quarter from the red.

Cross the red-flowered F2 hybrids back with the original white-flowered cultivar again. Repeat this process with each succeeding generation of hybrids until the plants resemble the white cultivar in all respects, except for the flower color. Every generation, the percentage of the red cultivar’s genetic material present in the offspring will decrease by half. By the eighth generation, 99.6 percent of the hybrid plant’s genetic material will derive from the white cultivar, while only 0.4 percent of the genetic material — including the genes for the red flower — will come from the red cultivar. In the final generation, cross your hybrids with each other and grow out one last generation of flowers. Retain seeds only from plants that yield 100 percent red-flowered offspring; these plants carry only the genes for red flowers. Plants with the genes for both white and red flowers will produce one white-flowered offspring for every three red-flowered offspring.

Hypothetical Hybrids

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Image Adobe Stock/Serjik Ahkhundov

Crossing open-pollinated cultivars to select for desired genetic traits will take multiple plant generations.

The results of this case are based on four assumptions: that the flower color is determined by a single gene; that the white flower contained two alleles for white flower color; that the red flower contained two alleles for red flower color; and that the red allele is dominant to the white allele. In genetics, the abbreviation for dominant alleles is expressed as a capital letter, and a lowercase letter is used for recessive alleles. Therefore, we could call the genotype of the white cultivar, with regard to flower color, “ww.” Likewise, the red flower would be “RR.” An individual with alleles from both white and red flowers — a “wR” individual — would have red flowers. (Perhaps the allele coded for a red pigment that would mask the white color when present.)

It’s possible, though, that all the flowers on your F1 hybrids are white. In this case, each plant has genes for white and red flowers, but the red color isn’t being expressed. The simplest explanation for this is that the red flower color requires both of the flower color alleles to be of the red type — meaning the red flower color allele is recessive. If so, you’ll need to generate red-flowered plants by crossing one of your F1 hybrids — which are “Wr,” because in this example, the white gene is dominant — with another F1 hybrid. This should yield three-quarters white-flowered plants (“WW” and “Wr”) and one-quarter red-flowered plants (“rr”). Then, make a backcross of a red flower to the original white cultivar, and repeat the two-generation process of crossing all-white hybrids with each other to reveal red-flowered hybrids. Finally, cross these plants back to the original white cultivar.

Select Characteristics

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Image Adobe Stock/Kiwanchaichaiudom

Most of the time, hybrid cultivars won’t breed true-to-type, or even viable, seeds. Yellow and red hybrid cattleya orchid.

For these experiments, we assumed that multiple genes controlled height and vigor in the original white cultivar. By continually backcrossing to the original white cultivar, the percentage of its genome in the hybrids would increase each generation, and more of the many genes required for taller, healthier plants would eventually come to reside in those plants.

This is the simplest case you might encounter. In other cases, a given trait might be the result of a combination of genes working together, and may disappear in your hybrids. In biology, almost anything can happen. However, hybridizing OP plants, and then repeatedly backcrossing your hybrids to one of the original plants, is how many plant cultivars are bred.

With this method, you could create plenty of breeding combinations. For example, you could attempt hybridizing two chile peppers — one spicy and one with a larger fruit — and try to move some heat into the bigger pepper. You could breed a pumpkin with warts and a pumpkin of a preferred size and shape to move the warts into the other pumpkin cultivar. In fact, squash, gourds, and pumpkins can interbreed in most cases, and they come in a wide variety of colors, shapes, and sizes. Plus, they have large, separate male and female flowers that make hybrid crosses easy. Whatever you experiment with, just remember to start with OP cultivars — not hybrid or F1 cultivars — and be prepared for the unexpected.

Adding plant breeding to your botanical repertoire can make gardening more enjoyable and give you a multi-year project to undertake. When in doubt, if you see a potential mutant in your garden, save its seeds. It may just be a developmental mutant, but it also might have genes that you’d like to keep around. If the variation seems at all interesting, try saving and replicating it by saving the seeds and backcrossing.


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Image Adobe Stock/Chanakarn

Closeup of hibiscus (rosa sinensis) flower revealing male and female parts.

Fertilizing Plants for Genetic Crosses

To cross one plant with another, you’ll need to learn a little about plant and floral anatomy. Flowers contain the sex organs of angiosperms (flowering plants). Some species grow as either male or female plants, each bearing male or female flowers, respectively. In others, such as most squash and melons, each plant grows both male and female flowers. And in plant species such as tomatoes and beans, each individual flower contains both male and female parts.

At the center of a female flower or the female part of a flower, a structure called the “pistil” holds the ovary and structures (called the “stigma” and “style”) that lead to the ovary. The stigma receives the pollen, while the style leads the pollen from the stigma to the ovules in the ovary.

The male portion of a flower consists of filaments — called “stamens” — capped with a structure called an “anther.” Pollen, which encapsulates the plant’s sperm, forms in the anther. When this pollen lands on a female stigma, it grows tiny tubes that extend down the style to the ovary and transfers sperm to an ovule, where it fertilizes an egg.

When making a cross, you need to transfer pollen from the male part to the female part. You also need to prevent other plants’ pollen from reaching the stigma of the female plant. In the case of separate male and female flowers, making a cross is easy. Once the female flower opens, use a small bag to cover it to prevent unwanted pollen from fertilizing the plant. Secure the bag around the flower stem with string or a rubber band. Then, collect pollen from the male plant by rubbing the anthers with a small paintbrush or cotton swab. You can also simply pick the male flower. Uncover the female flower, and brush the stigma (the tip of the pistil) with the pollen-covered brush or cotton swab. If you picked the male flower, brush the male parts of it directly against the pistil; you may need to remove the petals in order to do this. After the pollen transfers, cover the female flower again until it’s fertilized. In most cases, the female flower will close shortly after fertilization.

If the plants you’re crossing contain flowers with both male and female parts, things get slightly more complicated. In this case, remove the stamens from the flower you’re using as the female in the cross before the anthers release any pollen. In many cases, pollen won’t be ready immediately after the flower opens, so if you clip the stamens right after they open, you can prevent self-fertilization. After removing the stamens, bag the flower, and collect pollen from the male flower in the cross.

It’s easy to make crosses with squash, pumpkins, and melons. They have separate male and female flowers. Corn is likewise easy to cross — just rub a male tassel (which holds the pollen) against the silks of the cob (which are the stigmas and styles leading to the ovule). Crossing tomatoes and other plants with small flowers of both sexes can be more difficult. In tomato plants, for example, several stamens are fused and arranged to surround the female reproductive structures.

Before attempting any crosses, find out what you can about the anatomy of the flowers on the plant you’re breeding. It may take some practice to become proficient at making crosses, especially in cases where you have to remove the stamens.


Chris Colby is a writer and editor with a background in biology. He has an in-ground garden by the side of his house and a container garden on his driveway. He mostly grows vegetables, but he’s becoming increasingly interested in native plants that feed bees, butterflies, and other beneficial garden insects. He lives with his wife and an undisclosed number of cats in Bastrop, Texas.

Updated on Jul 21, 2021  |  Originally Published on Jun 8, 2021

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