Updated at: 26-05-2022 - By: Sienna Lewis

New and improved tomato varieties are created through the cross-breeding of different tomato varieties. From backyard gardeners trying for a better tasting tomato to university research programs looking for new varieties that can endure less friendly regions, it is performed by all kinds of people. It is thanks to these projects that a number of novel tomato varieties have been introduced to the market.

The selection aspect of tomato breeding was the focus of my article in Growing For Market in April 2020. To continue the discussion, I’ll go over how to build crosses and run breeding programs in the next piece.

The nuts and bolts of crossing tomatoes

The pollen of one tomato variety can be transferred to the pollen of another tomato type by physically moving the pollen. A sequence of steps are required to reach this goal. First, a mother and a father are selected from among the available varieties. Smaller-fruited cultivars make excellent moms for my hybrids. Large beefsteaks generate fewer seeds per fruit and take longer to ripen, according to my experience.

Different Types of Tomatoes - Comprehensive Guide - Fresh Exchange

If a tomato plant has both male and female reproductive systems, it could be a mother or father. Aside from the fact that tomato blossoms contain both male and female parts, they’re often used for interbreeding purposes (self-crossers). In the wild, tomatoes will self-pollinate if left to no man’s land. As a result, saving seeds from an open-pollinated tomato will almost always result in a plant that looks exactly like the parent plant.

You need to take the next stage in the process to avoid self-pollination if you want to cross a different type. In order to avoid self-pollination, you must emasculate the flower intended to be the mother in order to eliminate the male reproductive components.

Tweezers are used to extract the floral structures from a few flowers that have been chosen as mother plants. The flowers to be emasculated are those that have not yet unfolded their light yellow petals. The anthers of the flower have not yet been detached from them, so to speak (see figure 1 above). Because they haven’t started to discharge pollen or have a stigma that may receive pollen, the oldest unopened blooms are ideal for emasculation (see drawings below).

I remove the sepals, petals, and the cone of anthers (pollen-bearing structures) that surround the ovary/style/stigma, working my way inward from the outside in (female structures). The stigma and style are less likely to be damaged if the anther cone can be removed as a single unit after the base sepals and petals have been removed. When the tags break off or are ambiguously placed, the sepals can serve as an indicator for hand-pollination.

Several YouTube videos demonstrate the general emasculation and pollination process of tomato flowers.

After I have emasculated a few flowers, leaving only the ovary/style/stigma intact, I remove all of the older flowers and also all of the younger flowers on the same branches as the emasculated flowers. This accomplishes two things. First, removing all nearby flowers makes it easier to tag and follow exactly which flowers have been crossed. Removing nearby flowers also reduces the competition for resources by other developing fruits in that region of the plant.

All of the older flowers and all of the younger flowers on the same branches as the emasculated flowers are removed once I have emasculated a few blossoms. As a result, this accomplishes two important goals. It is easier to tag and track which flowers have been crossed if all the neighboring blossoms are removed. Other developing fruits are less likely to compete with each other if neighboring blossoms are removed.

Identifying project goals

It is better to put in extra effort to create a few great new varieties than to create a huge number of new mediocre variations, which is why it is important to explicitly define project goals. Is it possible to create a truly superb variety of a new variety? For tomato breeding, this is especially true, as there are already a large number of excellent varieties to pick from. In fact, I believe that more “excellent” varieties are not necessary nor desirable in today’s environment.

For new breeders, I recommend making no more than three crosses in the first year. Tomato cultivars that you enjoy should be used as the parents in your cross. With tomatoes you cultivate every year and like eating, there is virtually no chance of producing “poor” tomatoes.

On the other hand, if your project begins with the goal of fixing existing flaws, you’ll likely end up with a large number of subpar tomatoes. As a result, starting small allows you to gain a clearer picture of the choosing process. Because of this, you will be less likely to establish populations that are too tiny so that you miss out on seeing rare and extraordinary trait combination.

Starting small allows you to experiment with new combinations of traits. With the ability to notice, follow, and build new initiatives that spring out of the unexpected strands that are seen when starting with F2 and F3 populations big enough to produce as many characteristic combinations as possible even if you start with clear goals helps restrict your focus. Following up on unexpected, but often quite beneficial lines of inquiry hinges on starting with tasks that are small and manageable.

Crossing to generate new inbred (OP) lines

To generate new inbred lines, we do crosses. Seeds from seven generations of self-pollinated individuals must be used to create these “true-breeding” or “open-pollinated” varieties. The vast majority of genes in a line take around that long to become homozygous. It can take longer on rare occasions. Self-pollinated tomato lines that continue to reproduce after seven generations typically generate progeny that are almost identical to their parents.

Tomatoes self-pollinate because the pollen-producing cone of anthers surrounds the female stigma, where the pollen is deposited, making it relatively simple to breed them. In contrast, the plant’s initial blossoms, which are normally more open when pollination occurs, are less likely to be closed. As a result, harvest seeds from fruits whose anthers entirely envelop the female structures of flowers.

False breeding or OP lines can either be utilized as finished goods (true breeding or OP lines), or they can be used as parents to produce hybrids that are “finished” varieties (as opposed to true breeding or OP lines). To make hybrids that can be tested and put to use right away, this method relies on crossbreeding.

If your primary goal is to develop true-breeding lines, there are some qualities that appear to be relatively susceptible to optimization in true-breeding lines. Two features that, in our opinion, can be improved in pure breeding lines are flavors and colors.

In efforts intended to develop inbred lines, it is also quite simple to optimize unique plant behaviors (such as dwarfing). As a result, if your goal is to create a true breeding/open-pollinated line, these features should be prioritized.

Keeping track of breeding information

To get a strong handle on project management, it’s best to start small and work your way up to larger tasks. I use two methods to keep track of and arrange information about my tomato breeding. On the #1 coin envelopes I use to store seed, I record both pedigree and trait information (see photos). I also use Excel spreadsheets to keep track of my tasks and cross-checks. I find myself continuously modifying the way I organize breeding knowledge based on these two main strategies.

Growing Tomatoes - Grow it Local

As a means of storing and organizing my breeding endeavors, I use seed envelopes and storage boxes. Typically, one plant’s worth of seeds is included within each seed envelope. To begin a breeding program, only use seed envelopes that contain the original hybrid seed, which is derived from fruits created from crossing two female flowers.

Variety A is always stated first on the envelope holding the hybrid seed, which is labeled “Variety A x Variety B.” The date the seed was gathered is listed below that. Because the fruits that produce hybrid seed resemble those of the female parent, there are typically no remarks below the date in this generation (See Figure 2a).

Below the initial cross, a “X” has been circled on the envelope for the following generation (which contains the F2 seed). A seed with an X in the center denotes that it is a hybrid plant’s self-pollinated fruit. I’ll add a date this time, as well as some information about the features I’m looking for (See Figure 2b). A plant’s appearance should be identical to that of its parent plants in the first generation of hybridization (F1).

More information on the F2 plants is usually included in the envelopes for the following generation and the F3 seeds. There is now a number at the top of the envelope that denotes which F2 plant was harvested (Fig. 2c). Using the “-1” signifies that the F1 generation seed was taken from the first (and often only) plant. The “-3” on the envelope denotes that it includes seed from the third F2 plant collected. Because of these characteristics (red cherry, long shelf life & flavor score), they’re often the most significant ones. Each year’s field analysis will produce a list of additional characteristics.

F4 seed (Fig. 2d) was extracted from the second plant developed from the F3 seed packet in Figure 2c, according to the pedigree on the envelope. On the seed packet, it is also stated that characteristics, in this example color, continue to segregate well after the F2 generation.

Having several plants available from the F2 generation onward allows projects to grow. There is no limit to the number of lines a previous generation can produce in the current generation. As a rule, I don’t choose more than four or five lines every generation for each original cross in order to keep projects under control. There are a few dead ends as a result of this

One way to organize all of the envelopes/seeds from a cross is to store them in a small box. Figure 3 shows one of the small plastic boxes that I use to store seeds. In this case, the hybrid seed is in the front of the box and each successive generation is stored behind the generation preceding it.

Keeping all of the envelopes and seeds from a cross together in a compact box is a good method to keep them organized. I keep seeds in small plastic boxes like the one in Figure 3, which you can see more of. Hybrid seeds are at the top of a box, and each subsequent generation is stacked on top of them.

Another point to make about project organization: It is quite easy to conserve seeds from too many plants at the conclusion of each growing season. Many projects can become daunting if we try to expand on all the accessible lines. That’s why deciding whether to drop or put on hold lines with low promise is so critical. It’s important to keep in mind that when more lines are developed, the chances of being able to fully analyze and select from our best lines decrease.

Crossing for F1 synergy

When we first started using crossbreeding as a method of selecting for new breeding lines, it worked well for many years. Hybrids have become an important part of our breeding strategy throughout the years, but they are no longer only a vehicle for developing new breeding kinds. This is something we’ve noticed over the course of many years of cultivating hybrids, true-bred tomatoes, and tomatoes at every stage in between, and we’ve found it to be an important factor in the development of new kinds.

True-bred varieties continue to be released, but we also actively make and evaluate hybrid lines with the objective of producing different F1 kinds. True-breeding types can’t always match the benefits that hybrids can provide in certain situations.

We use the rin feature, for example, to dramatically extend the shelf life of fruit, with little or no affect on texture or flavor. In tomatoes, the term “ripening inhibitor” (Rin) refers to a natural feature that delays the softening of a tomato, while ripe flavors remain intact. The article “The guy behind the tomatoes” from the February 2018 GFM has more information on Rin.

When only one parent inherits the rin gene, the increased shelf life is most effective. Alternatively, the optimum qualities of both shelf life and flavor can be found in the rin heterozygote (rin/+). The fruit quality of rin heterozygotes is superior than that of either parent, making this a clear example of hybrid trait synergy. An example of a rin/plus hybrid tomato, “Agi Red” has a long shelf life and outstanding flavor and texture.

Disease resistance and plant architecture are two more features that we’ve found to be more easily optimized in hybrids (and far more difficult to tune in true breeding lines). In reality, the ratio of leaf to fruit production is skewed in one one or the other in most of our true-breeding parent lines.

For example, if you cut back on the number of leaves the plant produces, you’ll end up with a lot more fruits, because you’ll need less energy. Second, there are parent lines that don’t produce enough leaves to cover the flowers and fruits they produce.

There are several examples where one parent produces leaves while the other parent produces many flowers and fruits early in growth. This is the case with our new Green Bee hybrid tomato. It eventually becomes impossible for the plant’s leaves to produce enough fruits to keep up with the number of blossoms it produces. When it comes to the Green Bee hybrid, however, the balance between leaves and fruits appears to have been improved. The hybrid bears significantly more fruit than any of its parents.

Tomato hybrid vigor has also been frequently noticed by our team, in addition to trait synergy. Hybrids have many more potential genes than either parent, thus this isn’t a surprise, given that each parent contributes alternative gene forms for many genes.

The way we do things now is to plant parental lines right next to rows of hybrids that are descended from those same parental lines. Hybrid rows tend to be significantly larger, more vigorous and capable of producing more fruit than their “parental” rows. Qualitative and visible changes can be seen here. The discrepancies are so readily obvious that no measurements are required to demonstrate them. Crop yields are substantially higher on hybrid rows than on non-hybrid.

There are some exceptions. Many times in our fields, the OP variety “Captain Lucky” was mistaken for a hybrid. The plants are huge, productive, and resistant to disease…. In addition, we have a few cherry parents that appear to be as productive as our hybrid cherry cultivars. In spite of these outliers, it is clear that there appears to be a growth/vigor penalty that accrues as you move from hybrid to true breeding.

Accidental Cross Breed Tomato Great Find in My Garden! Bellmere Tomato by Mark - YouTube


Tomatoes are bred by gardeners for a wide range of reasons. David M. Francis, PhD, a geneticist and tomato breeder, is working on developing tomato plants that are more resistant to bacterial spot and bacterial canker. Fruit quality, color, smoothness, and fracture resistance are all goals of the program. “Tasti-Lee,” a vine-ripened tomato developed by John Scott at the University of Florida, boasts superior flavor and color, as well as more antioxidants than any other variety. A Purdue University horticulture professor, Avtar Handa, has produced a longer-lasting tomato. Other scientists are working to improve the size and yield of tomato plants. It’s possible that some gardeners simply wish to experiment with new flavors.

Choosing Plants

Those who work in the tomato breeding industry look for plants with certain traits they’d want to see merged into a single variety. The size, color, and resistance to disease of the plants are all taken into account by researchers. In order to identify and generate cultivars that demonstrate desirable features, professional researchers identify genes and make DNA markers.


Breeding techniques differ widely depending on the level of expertise of the person doing the breeding. Even the most seasoned academics employ a variety of approaches. Tomato blossoms are emasculated by removing the anther cone by gardeners. Gather pollen with a dissecting needle, then apply it to the stigma with another dissecting needle. In order for the procedure to be successful, the ovary must be expanded. Pollination sites can be identified with the help of colored twist ties. Cross-pollination can be prevented by placing a paper bag over the blossoms. Afterwards, the breeder will only have to wait and see what happens.

Additional Considerations

There are some new tomato varieties that don’t produce better-tasting tomatoes. It’s often a trial and error process. When two plants with favorable traits are combined, it does not mean that the resulting plant will have all of the beneficial attributes of both. A combination of both is possible, or it could have completely different characteristics. Ongoing studies are focusing on producing tomato plants that can withstand changing weather conditions.