How We Breed Exceptional Tomatoes- The Science Part

How We Breed Exceptional Tomatoes – The Science Part

Breeding great tomatoes is both an art and a science. The creative eye of an artist is needed to imagine which traits, when combined, could create a novel and valuable variety. At the same time, the rigor and knowledge of a scientist are required to organize breeding populations, keep careful records, and understand the probabilities of obtaining plants with the desired characteristics.

 

Making a Cross

To create a new variety, a breeder begins with two existing tomato varieties, each carrying traits worth combining, such as flavor, size, shape, color, or disease resistance.

These are called phenotypic traits, features that are visible or measurable in the plant, such as fruit shape, leaf type, or growth habit (for example, indeterminate vs. determinate). The word pheno comes from the Greek phainein, meaning “to show” or “to appear,” emphasizing that these are characteristics you can observe.

Behind every phenotype lies the genotype, the plant’s genetic makeup encoded in its DNA. While the phenotype is what you see, the genotype is the unseen code that gives rise to those traits. Genes can exist in different forms called alleles, and these alleles explain variation within traits. For example, whether a tomato is determinate or indeterminate, or whether its fruit ripens evenly red or develops green shoulders.

Some traits are controlled mainly by a single gene. For example:

• The self-pruning (sp) gene determines whether a plant is determinate (bushy, sets fruit all at once) or indeterminate (vining, keeps producing flowers and fruit).
• The uniform ripening (u) gene leads to evenly red fruit instead of blotchy green shoulders.

But many traits are polygenic, meaning they result from the combined action of many genes. Examples include:

• Flavor, driven by sugars, acids, and hundreds of aroma compounds.
• Yield, influenced by plant vigor, fruit set, and resilience.
• Disease resistance, often strengthened by combining multiple resistance factors to defend against diverse pathogens.

Because polygenic traits are complex and influenced by the environment, breeders grow large populations across multiple generations, selecting plants that show the best phenotypes while keeping the underlying genetics in mind.

The practical step of making a cross involves carefully removing the anthers (pollen-bearing parts) from a flower on the chosen female plant to prevent self-pollination. Pollen from the male parent is then dusted onto the stigma. The pollinated flower develops into a tomato, and the seeds inside, the F1 generation (“first filial”), are collected.

 

The F2 Generation: The Breeder’s Treasure Hunt

When F1 seeds are planted, the resulting plants are usually uniform. Each plant looks and performs much like the next, consistently showing the traits chosen by the breeder.

This happens because every F1 inherits the same combination of alleles from the two carefully selected parents.

But when F1 plants are allowed to self-pollinate, their seeds, the F2 generation, reveal something exciting. In the F2, the alleles from the original parents reshuffle into new combinations.

As a result, F2 plants no longer look identical. Instead, the population displays a wide range of variation within traits: differences in plant height, leaf shape, fruit color, flavor, and more.

This is where the breeder’s skill and eye are critical. From this diverse mix, the breeder selects individuals with the most desirable traits and saves their seed for the next generation.

 

Stabilizing a Variety

The selected F2 seeds become the F3 generation, which shows less variation but still isn’t completely uniform. With each new generation, F3, F4, F5, and beyond, the breeder continues selecting the best plants and saving their seed.

After 8–10 generations, the variety becomes stable. At this point, it is considered true breeding or open-pollinated (OP). OP varieties “breed true,” meaning that if a gardener saves seeds, the next generation looks the same.

Many beloved heirloom tomatoes are OPs, including Cherokee Purple, Brandywine, San Marzano, Mortgage Lifter, and Black Krim. These varieties have been passed down for generations and remain popular for their flavor, uniqueness, and resilience.

 

OP Varieties vs. Hybrids

While OP varieties are wonderful for gardeners and small farms, they can lack vigor in large-scale production. Because they are inbred (genetically uniform), large plantings of a single OP variety can be more vulnerable to pests and disease.

That’s why breeders also create F1 hybrids by crossing two different OP varieties. Hybrids benefit from hybrid vigor (heterosis), which makes them stronger and more productive than either parent. A classic analogy is the mule, produced by crossing a horse and a donkey. Mules are famously hardy, though sterile. In tomatoes, F1 hybrids often yield more, resist disease better, and produce more uniform fruit than OPs.

One advantage of hybrids is their consistency, which is highly valued by farmers who need predictable harvests.

However, seeds saved from an F1 hybrid won’t grow true. The F2 will be highly variable, so hybrid seed must be recreated each season. This is why hybrid seed is more expensive: it requires careful hand-pollination and multiple generations of parental preparation before the final cross.

 

The Result

Through this combination of art and science, we create both stable OP varieties and vigorous F1 hybrids. OPs give gardeners the joy of seed saving and tradition, while hybrids provide farmers with the reliability and performance needed for larger harvests.

At Bene Seeds, our goal is to bring you exceptional tomatoes — delicious, beautiful, and bred with care for growers of every scale.

 

Glossary of Terms

Allele – A version of a gene. Each allele has a slightly different DNA sequence, and these small differences can change how a trait appears. For example, the gene controlling tomato fruit color has different alleles: one leads to evenly red fruit, while another causes green shoulders.

Determinate vs. Indeterminate – Two tomato growth habits controlled by genetics. Determinate plants stop growing after a set number of flower clusters, producing a compact, bushy plant that ripens fruit all at once. Indeterminate plants keep growing and flowering throughout the season, producing a vining habit and a longer harvest window.

F1 Generation – The “first filial” generation. These seeds come from crossing two parent varieties. Because each F1 plant inherits the same combination of alleles from the parents, they tend to look and perform uniformly, showing the chosen traits reliably.

F2 Generation – The “second filial” generation, produced when F1 plants self-pollinate. In the F2, the parental alleles reshuffle into new combinations. This creates a wide range of variation within traits, such as differences in fruit color, size, or flavor.

Genotype – The genetic makeup of a plant, written in its DNA. The genotype provides the blueprint for traits, but the final outcome depends on how genes interact with each other and with the environment. For example, two plants with the same genotype may show differences in sweetness if grown in different soils.

Hybrid – A plant created by crossing two distinct parent lines. Hybrids combine the strengths of both parents, often producing higher yields, better disease resistance, or more uniform fruit. Because their alleles are reshuffled, seeds saved from hybrids won’t grow true to type.

Hybrid Vigor (Heterosis) – When hybrids outperform their parents in traits like growth, yield, or stress tolerance. This happens because crossing brings together diverse alleles, which can mask weaker ones and create new beneficial interactions. In tomatoes, hybrid vigor often results in stronger plants and more abundant harvests.

Open-Pollinated (OP) Variety – A stable variety developed by selecting plants over many generations until traits are genetically fixed. OPs “breed true,” so seeds saved from them will grow plants that resemble the parent. Many heirloom tomatoes are OPs, valued for their flavor and tradition.

Phenotype – The observable traits of a plant, such as fruit shape, color, or flavor. Phenotype is the result of the plant’s genotype interacting with its environment. For example, a tomato’s flavor depends not only on its genes but also on sunlight, soil, and water.

Polygenic Trait – A trait controlled by many genes working together, often with small combined effects. Traits like yield, flavor, or disease resistance fall into this category. Because the environment also influences them, breeders evaluate large populations to find plants with the best overall performance.

Self-Pruning (sp) Gene – A gene that controls whether a tomato plant is determinate or indeterminate. A mutation in this gene causes plants to stop growing after a certain point, producing the determinate habit.

Uniform Ripening (u) Gene – A gene that leads to evenly red fruit by removing the green “shoulders” seen in some heirlooms. While it improves appearance and consistency, it can reduce flavor because the green shoulders are often richer in sugars and aroma compounds.