Keygene’s leg-up in the hot tomato race began more than 15 years ago when it developed a DNA fingerprinting technique called AFLP (Amplified Fragment Length Polymorphism) that enables it to identify a specific strand of genetic pairs in a chromosome. Wageningen-based Keygene, which was founded by a consortium of the world’s leading seed companies inside and outside of Holland, licensed the AFLP technology to a wide array of labs—and it’s most famously used now in crime scene analysis to identify criminals’ genetic material. Royalties from AFLP licenses still pay for a good deal of the lab time Keygene’s researchers spend crossing thousands of wild tomatoes with older varieties. 

Each cross, undertaken by conventional means, may include as many as 3,000 plants. A typical breeder would have to allow all of those plants to mature and bear fruit, then present those fruit to a tasting panel to select the best. But by using AFLP analysis, researchers can quickly identify not only which plants lack sufficient disease resistance, but also which will have other undesirable qualities—low productivity, short shelf life, small size, etc.—when the plants are no more than tiny seedlings in a plastic cup sustained by growth hormone. On average, well over 95 of them can be immediately eliminated and the rest then back-crossed to arrive at the most promising new varieties.

Two of the best known tomatoes now on the European market, Tasty Toms and Tiger Tomato, developed with Keygene technology, have won rave reviews for tangy sweetness combined with a two-week shelf life. Tigers are a largish cherry tomato size with gold stripes on a red-to-magenta ground while Tasty Toms are full red, medium sized, and grow in grape-like clusters. Keygene’s Van Tunen emphasizes that the breeding “technology” used for both was molecular but not transgenic. Molecular, genetic markers were used to enhance the crosses that produced seeds for each tomato. 

Most of the commercial lettuce cultivated in California depends on Keygene technology, focused on breeding resistance to aphids that, in conventional lettuces, can destroy an entire season’s produce.

Critical to Keygene’s successes with fast breeding cycles are the extraordinary software advances that enable bio-technicians to run gene scans. “It cost us $25 per [genetic] base pair to sequence the DNA in 1990,” van Tunen explains, and today it costs $0.00005 per base pair.” Or, as he says, while walking through Keygene’s lab quarters in Wageningen, “a few years ago we could sequence 100,000 base pairs per technician per day. Now we have a machine that can sequence 1 billion per day.”

 “These are what we call texture genes,” de Boer says. Texture, because this array of genes governs the firmness, durability, and elasticity of the cellular walls within a fruit or vegetable. As apples and other fruits ripen and mature, they give off ethylene gas, which advances maturity into decay. Put some apples in your fridge in a bag with lettuce and celery and you’ll see how quickly the green leaves turn yellow from the effects of ethylene. Some ethylene receptors absorb the gas more quickly than others, contributing to cell wall softening, which is why some apples lose their crunch faster than others.

De Boer says the company only sequences the genes that are active at a certain time period. For example, in fruits, only a subset of a plant’s 20,000 or 30,000 genes is present in the actual fruits. And only a subset of this subset is active during ripening. “We determine which genes are involved in the ripening process and which genes are involved in ‘disorder development,’ which can lead to damaged tissue prone to infection by pathogens, which leads to rot,” he says. Even if the particular genetic profile may prevent outright decay for months, it can still leave the fruit unpleasantly soft.