Blueprint for produce: How fruits & vegetables are designed for the market

Researcher Juan Marraguin uses a fruit pressure tester on a Harper melon in the demonstration garden of seed producer HM Clause in Davis.

Take a deep sniff of a standard cantaloupe at your local supermarket and you might not be able to tell whether it’s ripe or not.

That’s because the Harper melon has taken over the produce bin. Previously, the cantaloupe variety you would see in the store was likely the Western Shipper, a breed that, despite its prosaic name, would peak in aroma and flavor when ripe. Other than a greener tinge under its tan netting — the fuzzy vein of raised lines above the smooth skin — the Harper looks almost identical to the Western Shipper. It’s easier to harvest and ships better, and is still plenty sweet. But the flavor doesn’t compare to the Western Shipper.

“In the early years, most of our effort was really geared toward grower traits — yield, degree of netting, size, shape, maturity. That was really where the early genetic improvement was being made,” says melon breeder Bill Copes, in the demonstration garden of the international seed company HM Clause in Davis.

Cantaloupes are just one of the dozens of types of produce that you may see in the supermarket without realizing how much they’ve been meticulously configured to appear, or smell or taste. Soon, you may see sliced mushrooms that don’t brown and beefsteak tomatoes that actually taste good as plant scientists take advantage of emerging technology, like genome editing, that offers even more breeding precision but comes with a fair share of controversy.

Melon breeder Bill Copes tastes a Harper melon as he and his team conduct an evaluation at seed producer HM Clause’s demonstration garden in Davis. Copes is part of a team working on a three-year study at UC Davis, sponsored by HM Clause, to identify the honeysuckle perfume and juicy-crisp texture found in melons down to the biochemical level, in the hope of reintroducing those traits to the workaday Harper. “Customers want flavor back,” he says.

Typically, a decade of breeding goes into creating each type of vegetable or fruit you see in the store, to develop essential traits like shelf life, disease and pest resistance, drought tolerance and increasingly, adaptability to automated harvest. Now, breeders say new genetic tools are speeding up the process and allowing them to focus back on flavor without sacrificing those practical characteristics.

With UC Davis a top agricultural research center, the Central Valley’s excellent growing conditions and new farm technology constantly emerging from Silicon Valley, a lot of that seed development is happening quietly in the Bay Area’s backyard.

“The seed industry is essential to agriculture — we have to have seeds to start — but it’s sort of a hidden part,” says Kent Bradford, distinguished professor at UC Davis’ Seed Biotechnology Center. “It’s where the new technology comes in.”

With new access to more genetic information, such as genome mapping of individual plants and the ability to tie traits with genetic markers, seed scientists are also interested in tools like gene editing, which they say could cut research and development time exponentially. That could, in theory, make it possible to grow beefsteak tomatoes that transport well and don’t taste like cotton balls.

However, some of this newer biotechnology is still in the early stages and hasn’t yet been regulated by the federal government.

“You can make very targeted changes,” says Bradford, referring to a recent study by scientists in Shanghai and Purdue University in Indiana that showed how CRISPR, a type of gene editing, could be used to delete or add traits to crops like rice in just one generation. “Instead of doing 10 years of breeding to get that in, you just reproduce that gene in your current cultivar. You’re done.”

Harper melons grow in the demonstration garden in Davis of international seed producer HM Clause.

Because plant breeders in Davis are developing vegetables for a worldwide market, they have to breed not just for specific growing conditions but also consumer expectations that vary by place. Many of these are merely cosmetic. Americans think dark green stripes signal ripeness in a watermelon, so breeders design them that way even if it’s not necessarily true, says watermelon breeder Jerome Bernier of Monsanto, which has a (non-GMO) vegetable seed unit in Davis. Most Europeans still prefer the smaller seeded kind, and yellow-fleshed varieties are popular in China, he adds.

Back in HM Clause’s demo garden, vines explode with examples of round, burger-width tomatoes, perfect for slicing and bred for the American food-service market. Other rows bear elongated tomatoes — more similar to what we call romas — which are popular in Guatemala, Argentina and Mexico, all with small variations in shape and texture that, for whatever reason, each population identifies as an ideal tomato.

Copes’ work with UC Davis involves training tasting panels to identify positive and negative traits in melons. This summer the panel evaluated texture components, from firmness to crunchiness to juiciness, across a range of melon types. Once the data is analyzed, they’ll try to track the traits to biochemicals in the fruit.

“Once we can measure those chemicals and characterize them then we have a good shot at breeding for favorable compounds,” Copes says. “It’s trying to take a scientific approach toward flavor development.”

Harry Klee at the University of Florida is taking a similar sensory analysis approach with tomatoes and then working to identify where flavor chemicals reside on the tomato chromosome. In a study published in January (“A chemical genetic roadmap to improved tomato flavor”), he described how tomato flavor comes from a mix of sugars, acids and volatile compounds that interact in a way not yet understood by breeders.

Traditional breeding of hybrids involves crossing parent plants with desirable traits. Each cross takes a year to grow, then the process has to be repeated to refine the traits.

Breeders have had access to genetic information since the 1950s, and genetic engineering of foods has been allowed in the U.S. since 1994, but the cost of regulation and public concerns about safety have limited its use largely to big crops like corn and soy, with very few fruits or vegetables.

In 2000, marker-assisted selection became available, meaning breeders could locate specific parts of the gene associated with certain traits rather than have to grow out several generations of a plant. As genome mapping has become less expensive, marker-assisted selection is becoming more widespread.

Harper melons in the demonstration garden in Davis of international seed producer HM Clause.

Genome editing techniques like CRISPR could allow breeders to cut and paste the genes responsible for a tomato’s magical flavor compounds from heirlooms into a standard tomato’s DNA. But most commercial seed companies are holding off on gene editing until they know how they’ll be regulated.

In July 2018, the U.S. Department of Agriculture is due to finalize new rules for how to label genetically engineered foods after the Obama administration required their labeling. While genetically engineered corn and cotton both have foreign DNA, or genes from another species, gene-edited foods don’t necessarily. For that reason, they might not be regulated the same way, says Andy Lavigne, president and CEO of American Seed Trade Association.

For example, earlier this year the USDA gave the green light for gene-edited button mushrooms to go to market without regulation. Scientists at the Chinese Academy of Sciences in Beijing and Pennsylvania State University narrowed down and deleted the genes associated with the enzymes that cause browning in the mushroom.

Belinda Martineau, a former genetic engineer who helped develop the Flavr Savr, the first genetically engineered commercial tomato, thinks there should be more caution around CRISPR because the technology can sometimes hit the wrong targets and could result in unanticipated mutations.

“While it is hard to anticipate what possible damage such unintended mutations could cause in crops, most mutations are deleterious,” says Martineau, who is now a writer at the UC Davis Institute for Social Sciences.

For Klee, who hopes to use the technology for tomatoes, the first changes could be fairly modest.

“Producing a modern commercial tomato that can be shipped across the country in the dead of winter but has the taste of a backyard grown heirloom is probably not going to happen,” he wrote on his lab’s website. “But we do think that as we elucidate the genetics that determines flavor, we can make huge improvements.”

Author: Tara Duggan