What can you do with a home DNA machine? One unexpected answer: grow better truffles

Dec 2, 2016 /
Paul Thomas

Personal DNA testing machines are bringing lab-grade genetic technology within the reach of more people. A look at how a scientist-turned-farmer is using DNA testing to cultivate the most elusive — and prized — of foods.

Truffles are lumpy, odoriferous, edible fungi with an unforgettable taste — and unforgettable prices. Chefs and restaurants pay thousands of dollars per pound for the best specimens, which is why your plate of truffle fries cost $17, your plate of truffled pasta $120. The high price is largely due to scarcity — wild truffles are hard to find and can only be foraged with the help of trained pigs or dogs. With wild supplies on the decline worldwide, cultivation is an appealing option — but it’s incredibly difficult for a few big reasons.

Which is why one truffle farmer was thrilled to discover a low-cost DNA machine that is helping him to crack one of the toughest problems: waiting four to seven years for a black truffle to grow, only to find it’s a different fungus altogether.

At the heart of DNA science is a technique called polymerase chain reaction, a.k.a. PCR. PCR allows a short DNA sequence to be copied in bulk so we can visualize, interpret and understand the genetic information it contains. This technique is now used in everything from analyzing DNA samples at a crime scene to detecting viruses like HIV.

Up to now, PCR has required bulky, expensive and complicated equipment, so it’s mostly been restricted to scientists and academics. But a revolution has been brewing as entrepreneurs are building cheaper, simpler and smaller DNA machines. Broadening access to DNA analysis is what motivated molecular biologist Sebastian Kraves (TED Talk: The era of personal DNA testing is here) and geneticist Zeke Alvarez-Saavedra to create their shoebox-sized miniPCR, which was released in 2015. Since then, says Kraves, “we’ve seen people come up with the most unimaginable applications.”

Among those once-unimaginable applications: truffle cultivation.

Truffles: hard to forage but even harder to grow. Unlike most mushrooms, which grow on decomposing organic matter, truffles grow in a symbiotic relationship with the roots of trees. In order to produce truffles, a germinating tree seed must be inoculated with the truffle fungus even before it’s planted. And because truffles are a weak fungi and require very specific nutrient, pH and moisture levels to thrive, after they start growing they can be easily displaced by stronger fungi during their four-t0-seven-year journey from germination to harvest. “You need to do everything right at every step of the way,” emphasizes farmer Paul Thomas. Thomas, a UK-based forager, began developing his own truffle cultivation system as a biology PhD student. After receiving his degree, he decided to make the truffle-growing business his full-time job.

As with many other luxury goods, black truffles and their high demand have led to the introduction of knockoffs. Tuber indicum, a species originating in China and known as the Chinese truffle, looks amazingly similar to the high-value Tuber melanosporum, or the Périgord black truffle. “Even under a microscope, they can look almost identical,” says Thomas. One main difference is scent — black truffles have it, Chinese truffles don’t — and this lack of aroma is partly why Chinese truffles have little culinary value. (Epicures also claim the Chinese truffle has an inferior flavor, and the cost reflects it — connoisseurs will pay ten times more for a black truffle.) Chinese truffles were used as food for pigs … until unscrupulous vendors realized they could mix Chinese truffles with black truffles and the Chinese fungi would take on the scent of the fragrant black fungi.

The difficulty of telling the two truffles apart has made it easy for cultivators to accidentally plant the wrong truffle, a mistake that can be devastating given the time and labor involved. “Imagine you’ve waited five or six years of your life or more tending your plantation, and it produces a truffle and it’s the wrong species,” says Thomas.

A farmer finds a high-tech solution: DNA testing. Thanks to his background in advanced biology, Thomas recognized that DNA testing could hold the key to distinguishing between Chinese and black truffles. Frustrated by the cost and restrictions of traditional DNA equipment, he was excited to get a miniPCR machine. By analyzing a small piece of truffle with it, Thomas can look for a telltale area of DNA that is present in the black but not the Chinese truffle. Now, besides cultivating his own truffles, he also acts as a consultant to other growers, selling them seedlings that have been tested to ensure they’re inoculated with the desirable fungus, assessing and sampling the growing truffles, and helping distribute and verify the valuable harvest.

The next frontier: truffle mating. Thomas is trying to use the miniPCR machine to solve another puzzle of cultivation. Truffles were long believed to be self-fertilizing (or selfing); it was thought they did not need to interact with another truffle to reproduce. But when the Périgord black truffle genome was sequenced in 2010, it was revealed that there were different mating types; subsequent research has narrowed that down to two primary types. In order for a truffle to produce fruiting bodies — that is, the part of the mushroom we humans like to eat — the two mating types have to interact, but how exactly this happens is unclear. Thomas believes that a better understanding of how truffles mate, combined with the ability to genetically identify mating types, could allow growers to increase their yields and make cultivation much more reliable. And while this might not bring down the price of those $17 truffle fries, it will ensure you’re getting what you paid for.


Sebastian Kraves
Paul Thomas