Building a Better Tomato

Molecular marker breeding is leading to seed innovations at Bayer CropScience

Heard It Through the
Tomato Vine

Ancient Aztecs were early fans of the xitomatl (pronounced “heetomahtel”)—in Nahuatl, “fruit (tomatl) with a belly button (xictli).” Later, in 16th century France, the tomato was known as the “love apple” for its purported aphrodisiac properties. The Italian word pomodoro translates to “apple of gold.”


Botanically, the tomato is a fruit berry. Culinarily, it’s a vegetable because of the savory rather than sweet flavor. Nutritionally, tomatoes contain lots of vitamins A, C and K along with potassium and antioxidants, plus lycopene to protect skin against sunburn and UV ray damage, especially when cooked.


The TV show “America’s Test Kitchen” reported that tomatoes last three or four days longer with the stem side down. Store tomatoes at room temperature; refrigeration dulls the flavor. Gardeners can improve tomato yields by watering more thoroughly but less often, as light daily watering leads to shallow roots. To avoid overwatering (one of the most common tomato-growing mistakes), wait until the leaves curl at the edges. Watering vines 25 percent less typically results in tomatoes with better flavor, yield and hardiness.

Today’s top seed engineers are looking both ahead and to the past in developing better produce varieties for the future. Our grandparents and prior generations of gardeners saved select crop seeds best suited to local conditions for cultivation the following year. In the case of tomatoes, decades of selective breeding resulted in landrace seeds exhibiting specific regional traits. These cultivars were developed over time, adapting to their native environment and promoting hardy genetic crop diversity with strong disease resistance.

Bayer CropScience seed experts Coert Engels, MSc, and Pieter van Poppel, PhD, based in the Netherlands, recently shared with Fluidigm an insider perspective on tomato breeding advances. Their team is developing tomatoes for cultivation methods and climates all around the world, and since each area has its own demands and approach, their breeding efforts must focus on a range of specific traits.

Bigger, better, faster, more

Lab science innovations are guiding production-scale breeders to engineer high-yield seeds that grow new hybrid varieties quickly and resist diseases, pests and environmental stressors like drought and higher saline conditions. Agronomic traits increasingly provide improved uniformity, shelf life, stability, washability, density and hardiness—all of which boost grower profits and food supply, and make for better tomato pizzas and caprese salads down the line.

Modernized seed breeding includes resistance to disease species of fungi, bacteria and viruses and insect pests like aphids, whiteflies and nematodes known to cause serious problems in tomatoes. “Tomato plants need to be high yield, pathogen resistant and adapted to local growing conditions.” And, Engels explained, “The fruit must have good shape, color, firmness, storability, size and taste. Our tomatoes must meet the demands of growers but also traders, retailers and consumers.”

Molecular breeding applications

Molecular-marker breeding offers several advantages for produce seeds, facilitating plant-gene identification and selection of planned characteristics such as resistances. Benefits for cell and tissue culture include propagation of specific germplasms for developing doubled haploid lines in vitro to broaden crop genetic pools.

“Understanding molecular plant characteristics speeds up the new seed variety production process,” said Engels. “Time to market averages 10 years from R&D to marketplace release. Molecular biologists can save years of development work by analyzing leaf samples to quickly identify the presence of a desired gene without waiting for plants to mature.”

SNP-ing tomatoes from the vine

According to van Poppel, a scientist in marker-assisted breeding, Bayer CropScience uses the Fluidigm EP1™ system in combination with the 96.96 IFC and the 192.24 IFC for endpoint genotyping.

“We map novel traits of interest in segregated populations using genome-wide markers and marker-assisted backcrossing instead of single-trait linked markers,” van Poppel explained. “Genotyping on Fluidigm IFCs provides optimal numbers of SNPs and samples.”

Engels agreed: “Every population requires specific marker selection, which can be done using Fluidigm IFCs. Once quantitative trait loci are mapped, then single-trait linked markers assist with advance selection. Phenotyping tends to be costly, seasonally dependent and time-consuming. Markers allow breeders to track agronomic traits like color and stature. And for progeny selection, genome-wide markers enable marker-assisted backcrossing.”

Bayer’s new varieties are bred for aforementioned traits of yield, appearance, shelf life, disease resistance and drought and flood tolerance. They’re also bred for the key trait of flavor (100 or so genes are linked to flavor perception alone). While the idea is to develop hybrid varieties with desired quality combinations from pure inbred male and female parental lines, Engels observed that it may take as many as seven generations of isolated self-pollination inbreeding for gene purity. Molecular markers help with rapid selection of desired traits.

“It’s impossible to change hundreds of genes in one breeding step,” Engels said. “Marker-assisted breeding instead focuses on controlling the genes that have a large phenotypic effect.” He explained how Bayer is developing SNP markers that closely link to traits by combining phenotypic information from individual vines with genotypic data to gradually improve genetic lineage.

Boosting seed value

Bayer uses hybrid vigor control methods for crossing selected parental pure inbred lines because hybrid varieties generally have higher yields and are more tolerant to stressors than conventional varieties. When breeders optimize breeding, resulting plants exhibit hybrid vigor, or heterosis. “Using broad germplasm bases and exotic lines leads to greater genetic distance of parental inbred lines and thus higher heterosis,” he noted.

Several improvements in recent years have resulted from choosing the right parents in order to develop high-performing hybrids, yet heterosis is only part of the story. With worldwide germplasm hybridization exchanges, breeders cross and select varieties with desirable traits to develop new seeds for global crop improvement efforts.

When Bayer develops a new seed, it applies for plant variety protection (PVP). Regulators may grant such a request to prohibit third-party reproduction of a specific variety, yet other growers may continue using the plant for germplasm improvement, regardless of origin.

Engels recapped how Bayer is breeding seeds for tolerance to specific growing conditions such as drought, freezing or salinity: “We’re developing technologies and protocols for vegetable seeds to optimize quality, production, processing and to increase value. Coating and pelleting seeds enables more uniform germination, while priming enables simpler, targeted seed-sowing.”

“Once we find specific genes correlating with tolerance or resistance to particular stressors,” he added, “we look for molecular markers to make further testing and future development easier and faster.”

Heirloom Tomato Primer

Each summer, bushels of bright heirloom tomatoes beckon fetchingly from the produce aisle. Heirloom varieties are those with a family or community history of being grown and passed on generationally—similar to heirloom furniture or jewelry. Most can be traced to the early 20th century. Their rainbow hues and quirky appearance make them a seasonal staple in California cuisine, with names as colorful as the fruits themselves: Cherokee Purple, Orange Banana, Black Cherry, Ivory Pear, Green Zebra, Blue Beauty, Pink Ping Pong, Round Yellow Chicken and Berkeley Tie-Dye are a few.

Their ubiquity in markets and on menus can make it seem like new heirloom varieties are being developed in novel shapes and shades. But agronomists are simply rediscovering forgotten varieties and reviving older varieties from seed banks. While there are about 5,000 types of heirloom tomatoes, many bear only a few seeds each, so it can take years of regeneration before those varieties become available in seed catalogs.

While all heirlooms are open-pollinated (OP) rather than hybrids, not all OPs are heirlooms. OP varieties breed naturally when pollen transfers within same-variety plants from parent seeds, meaning new seedlings share characteristics from the previous generation.

Heirlooms and OPs both cross-pollinate. Combining two different parent varieties of the same species produces hybrid varieties. Hybrids do not remain true after the initial cross and cannot be saved from one generation to the next unchanged. Most mass-market tomato plants fall into this category. While heirlooms tend to have lower yield and are harder to harvest all at once, they also have wonderful flavors that makes them perennial summertime favorites.

Despite the increasing popularity of heirloom varieties, they represent less than 1 percent of the tomato market due to their lower yield and tendency to be more challenging, disease-prone and costly. Some heirlooms and wild tomato species carry traits such as disease resistances, though, and have already been used in breeding for decades.