By combining traditional plant breeding with ever-faster genetic sequencing tools, researchers are making fruits and vegetables more flavorful, colorful, shapely and nutritious
Scientific American
By Ferris Jabr
Armed with toothpicks and sour cream, Michael Mazourek and three friends marched into the field of 600 chili pepper plants. One by one, they pierced the habaneros and brought the juices to their tongues, cooling and cleansing their palates with cream now and then. Habaneros are typically some of the hottest chilies around, ranking as high as 350,000 on the Scoville scale of pepper pungency—40 times hotter than the jalapeno. The habaneros Mazourek and his team had grown in this experimental field at Cornell University were in no way typical, however. The four graduate students knew that, due to an unidentified genetic mutation, a portion of the peppers would not be very spicy. Exactly what they would taste like was a mystery.
If a particular habanero’s juices indicated that it was relatively mild, they bit into it like an apple. Some of the peppers were smoky; others astringent. Some tasted faintly of sausage; others had the foul funk of gym socks. But the most interesting peppers by far possessed all the complex aroma and flavor of a habanero, yet none of its heat.
A few months earlier Mazourek had received a shipment of seeds from researchers at New Mexico State University. These seeds, they said, grew into habanero plants whose red peppers did not even register on the Scoville scale. Knowing that Mazourek was a plant breeder interested in pepper pungency, the New Mexico scientists thought he might like to study the tame habaneros himself.
Mazourek raised the seeds he got in the mail into adult plants and mated them with ordinary habaneros. Inside greenhouses he carefully transferred pollen between flowers on the two kinds of plants with tweezers, ensuring that the resulting offspring and, eventually, the 600 grandchildren would have a mix of their parents’ DNA. After growing that third generation in a quarter-acre field, he recruited some fellow scholars for the intrepid taste test.
As the friends ate the unusual peppers, they snipped off leaves from each plant, which they later crushed and liquefied to examine the DNA within. By syncing the results of the DNA analysis with what their palates had told them, the team managed to identify a specific genetic mutation that explained why some of the peppers lacked heat. Chili peppers get their fire from an oily molecule called capsaicin, which is produced by glands within the fruit—those leathery, seed-covered white or yellow bits that people usually cut out of a pepper. As it turns out, the same bucket brigade of chemical reactions responsible for making capsaicin is also essential for concocting a bouquet of associated compounds that give a pepper its scent. The heatless habaneros had inherited a mutation that nearly—but not completely—shut down their capsaicin factories, leaving the glands just functional enough to eke out a drop of capsaicin and fragrant molecules here and there.
Seeing a unique opportunity, Mazourek and his colleagues spent the next several years making crosses between various plants in an attempt to create a single variety that reliably produced habaneros with plenty of zest but no heat. Having illuminated pungency genetics, they no longer had to wait for plants to grow up and work their taste buds overtime simply to find out if the peppers were spicy or not. Instead, they could take a leaf from a young plant, analyze its DNA and determine whether it would produce blazing or bland peppers before deciding whether to raise it to maturity—a trick that made the whole breeding process more efficient. Today, their prized pepper is persimmon orange, a bit longer than a typical habanero and wonderfully piquant. They call it a habanada, as in no burning heat—nada, zip. Cornell hopes to license the habanada to a major seed company soon for wider distribution.
Mazourek belongs to a new generation of plant breeders who combine traditional farming with rapid genetic analysis to create more flavorful, colorful, shapely and nutritious fruits and vegetables. These modern plant breeders are not genetic engineers; in most cases they do not directly manipulate plant DNA in the lab. Rather, they sequence the genomes of many different kinds of plants to build databases that link various versions of genes—known as alleles—to distinct traits. Then, they peek inside juvenile plants to examine the alleles that are already there before choosing which ones to grow in the field and how best to mate one plant with another. In some cases breeders can even analyze the genetic profiles of individual seeds and subsequently select which to sow and which to disregard, saving them a great deal of time and labor.
Plant breeders have, of course, always used the best tools available to them. But in the last 10 years or so they have been able to approach their work in completely new ways in part because genetic sequencing technology is becoming so fast and cheap. “There’s been a radical change in the tools we use,” says Jim Myers of Oregon State University, who has been a plant breeder for more than 20 years and recently created an eggplant-purple tomato. “What is most exciting to me, and what I never thought I would be doing, is going in and looking at candidate genes for traits. As the price of sequencing continues to drop, it will become more and more routine to do sequences for every individual population of plants you’re working with.”
In particular, these tools are helping breeders pivot their attention toward qualities of food that are important to consumers, instead of fixating solely on the needs of growers. Aided by genomics and related molecular tests, breeders have managed to create a cornucopia of new foods that are already available at some grocery stores and farmer’s markets, including cantaloupe that’s firm and ripe in the winter, snack-size bell peppers, broccoli that brims with even more nutrients than usual, onions that do not offend the eye and tomatoes that do not disappoint the tongue.
Sowing change
People have been changing plants to suit their purposes for at least 9,000 years. Just about every fruit and vegetable we eat is a domesticated species that we have transformed through generations of artificial selection and breeding: saving seeds only from plants with the most desirable characteristics and deliberately mating one plant with another to create new combinations of traits. In this way our ancestors turned a scrawny grass named teosinte into tall plump-eared corn and molded a single species of wild cabbage into broccoli, cauliflower, Brussels sprouts and kale.
Until the early 20th century, most crops were open-pollinated, meaning that farmers allowed wind and insects to transport pollen between plants. Over time, however, farmers and scientists alike had noticed that allowing closely related individuals to exchange pollen sometimes resulted in small, sickly plants. Conversely, when plants with very different traits mated they often produced hybrid offspring that were healthier than either parent—plants that grew taller and larger and yielded more fruit, for example. In 1908 George Harrison Shull of Cold Spring Harbor Laboratory in Long Island, N.Y., published a paper demonstrating that a controlled cross between two highly inbred lines of corn created hybrid plants that were incredibly healthy and uniform in their traits—a very desirable outcome for farmers. Although the precise reasons for this “hybrid vigor” remain unclear, many major crops grown today are hybrids created in this fashion.
Instead of working solely with whatever variation was present in a given crop, researchers in the 1920s began exposing plants to radiation and mutagenic chemicals to deliberately induce new genetic mutations, some of which serendipitously proved advantageous. Deep red Rio Star grapefruit, dwarf Calrose 76 rice that does not fall over as easily as taller varieties, fungus-resistant Gold Nijisseiki pears and hundreds of other kinds of vegetables, fruits and grains we eat today are the result of such “mutation breeding,” which has become less popular over time.
By the 1980s, scientists had devised a much more precise way of changing a plant’s DNA: genetic engineering, which is usually defined as adding, removing or otherwise directly altering genes in a plant using laboratory tools. Foods engineered in this way, commonly known as genetically modified organisms (GMOs), first appeared on the market in the U.S. in the 1990s. Although more than 70 percent of processed foods in the U.S. contain ingredients made from GMO corn, soybeans and canola, very few of the fresh vegetables and fruits sold in supermarkets have been genetically engineered. Exceptions include virus-resistant papaya, plum and squash, as well as pest-resistant sweet corn.
One reason that so few fresh fruits and veggies are GMOs is that, on the whole, they are far less profitable and less widely grown than the country’s biggest crops: corn, soybeans, hay, wheat, cotton and rice. When it comes to fruits, veggies and other so-called specialty crops, seed companies are not as motivated to deal with the burdensome and costly safety tests and federal regulatory procedures required to approve a GMO for sale.
The other big hurdle to GMO fruit and vegetables is public opposition. Genetic engineering is a technology—a specific way of modifying the plants we eat—and, like all technologies, it has both advantages and risks. Banishing all GMOs in one fell swoop solely because of the way they are made would be equivalent to, say, forbidding any object made by metalwork because some metal objects are dangerous. Instead, GMOs should be evaluated on a case-by-case basis. When not used responsibly, some GMO crops encourage overuse of certain weed-killers and insecticides, which can foster weeds and bugs that are very hard to kill. Yet researchers have also documented cases in which crops genetically engineered to battle pests have significantly decreased the use of toxic insecticides, benefitting both farmers and the overall ecosystem. GMO rice could save millions from the debilitating consequences of vitamin A deficiency and genetic engineering is likely the most effective way to rescue disease-ravaged orange trees in part because it is so much faster than traditional breeding. As for health concerns, the American Association for the Advancement of Science, the World Health Organization and the European Union agree that GMOs are just as safe as foods created via conventional breeding. Despite all this, seed companies know that introducing new GMOs to the produce aisle today could ignite a furor among a large segment of the U.S. population. Most shoppers remain oblivious to the genetically engineered fruits and veggies already in stores because they are usually not labeled as such.
In part to circumvent the controversy surrounding GMOs, fruit and vegetable breeders at both universities and private companies have been turning to an alternative way of modifying the food we eat: a sophisticated approach known as marker-assisted breeding that marries traditional plant breeding with rapidly improving tools for isolating and examining alleles and other sequences of DNA that serve as “markers” for specific traits. Although these tools are not brand-new, they are becoming faster, cheaper and more useful all the time. “The impact of genomics on plant breeding is almost beyond my comprehension,” says Shelley Jansky, a potato breeder who works for both the U.S. Department of Agriculture (USDA) and the University of Wisconsin–Madison. “To give an example: I had a grad student here five years ago who spent three years trying to identify DNA sequences associated with disease resistance. After hundreds of hours in the lab he ended up with 18 genetic markers. Now I have grad students who can get 8,000 markers for each of 200 individual plants within a matter of weeks. Progress has been exponential in last five years.”
Marker-assisted breeding is one of the engines pushing breeders to completely rethink their craft. Whereas the major GMOs and most conventionally created crops on the market were designed primarily to benefit farmers, many breeders are now shifting their attention to the consumer. “Asking what the consumer wants sounds really obvious, but it’s not,” says Harry Klee, a tomato breeder at the University of Florida. “Almost always you see the opposite: people breeding for what the grower wants and pretty much ignoring what the consumer wants. There has been a disconnect between commercial growers and consumers that has in my personal opinion led to the deterioration of flavor and other qualities of our food.”
The palate paradox
Over and over again plant breeders have run into the same dilemma: tailoring plants to the needs of growers and grocers—guaranteeing high yield and the ability to survive days or weeks of shipping and storage in dark, cool conditions—often means sacrificing flavor and texture. Perhaps no food better exemplifies this predicament than the classic supermarket tomato.
For decades, experts have regarded the balance of acids and sugars in a tomato as the primary factor that determines whether people enjoy its taste. In general, people like tomatoes on the sweet side (although focus groups almost always have a few people who want a tomato with a kick). But most breeders have not been primarily concerned with flavor. With large-scale commercial growers in mind, breeders have instead favored tomato plants producing lots and lots of smooth, hardy fruit that remained plump on the sometimes long journey to the supermarket. The more tomatoes a plant makes, however, the fewer sugars it can give to each one. Typical supermarket tomatoes may look pretty, but they simply do not have enough sugar to satisfy our taste buds.
Klee is determined to rescue the industrial tomato from its current gustatory doldrums. At this point, he has screened nearly 200 varieties of heirloom tomatoes in taste tests—older cultivars preserved by small groups of farmers and gardeners and sold at some grocers and farmers’ markets. Heirloom tomatoes are known for their vibrant colors and fantastic flavor, but their skin easily cracks and scars, they often go soft quickly and the plants they come from do not make enough fruit to meet the demands of large commercial farmers.
What Klee has learned from his research, however, is that many heirlooms are tastier than standard supermarket tomatoes not because they have more sugar, but rather because they are chock full of a much more elusive component of tomato flavor. In a 2012 study, for example, Klee and his colleagues discovered that people actually enjoy a tomato with moderate levels of sugar if it contains enough of a pungent compound called geranial. Klee suspects that geranial and other volatile compounds—molecules that waft off plants and into our nostrils (think: freshly cut grass or pine trees)—not only give a tomato its scent, but also magnify the fruit’s innate sweetness. In follow-up studies he created tomatoes that lacked geranial and other fragrant molecules. People did not like them. If a tomato had average to high sugar levels but no volatiles, volunteers did not perceive it as sweet.
Lately, Klee has been trying to make hybrid plants that give growers and consumers the best of both tomato worlds, old and new. In past three years he and his colleagues have mated the most delicious heirlooms they could find with modern conventional tomatoes to create crossbreeds that yield well, are firm and smooth-skinned and taste great. Klee routinely stocks up on cheap electric toothbrushes, which he and his team use to gently but thoroughly rattle tomato flowers, gathering the pollen that falls off in test tubes so they can play matchmaker. All the while the breeders have been using hole punches to collect bits of leaves and analyze the plants’ DNA, looking for genetic patterns that correspond to high levels of volatiles, for instance, or flawless skin. “Genetic analysis has definitely informed crossing decisions,” Klee says. “Our work has really accelerated in last couple of years with the emergence of the tomato genome sequence.”
The University of Florida has just released two of these hybrids—Garden Gem and Garden Treasure—that they would like to license to a seed company for mass distribution. Although the hybrids do not yield quite as much as commercial tomatoes, they produce more than three times the number of fruit as their heirloom parents, their flavor is tremendous and they can survive a good deal of shipping.
In some ways the cantaloupe is the tomato of the melon world. Many Americans—especially on the east coast—remain sadly unaware of the cantaloupe’s true epicurean delights because they have never eaten the melon within a few days of picking. The vast majority of cantaloupes harvested in the U.S. are grown in California and Arizona and distributed elsewhere from there. When winter arrives, everyone in the nation is out of luck. Cantaloupes are rarely harvested in the continental U.S. from December to April or so—it is simply not warm enough for a melon whose ancestors evolved in the Middle East. Instead, the U.S. imports all the cantaloupes it consumes during the colder months from Honduras, Guatemala and other much more tropical countries.
To make such international exchange possible, breeders had to create unique types of melons. On the vine cantaloupes ripen and soften rather quickly following a burst of a plant hormone known as ethylene. If you pick a melon at its peak ripeness and eat it right away, it’s firm and flavorful. This speedy ripening is problematic when transporting the fruits long distances, however. Even on ice, the melons become mushy by the voyage’s end. Just as tomato breeders have favored hardy tomatoes that could survive shipping, melon breeders were partial to cantaloupes that did not produce as much ethylene as usual, so that they stayed firm on the trip from field to produce aisle. But the chemical reactions responsible for all the volatile compounds that create the characteristic melon aroma and taste do not happen without that spurt of ethylene. The end result: during the winter, U.S. supermarkets sell exceptionally insipid cantaloupes.
Several years ago, a plant breeder named Dominique Chambeyron working for Monsanto in France created a new kind of small, sweet cantaloupe that—amazingly—retained its firmness for weeks after it was harvested. Some grocers in the U.S., such as Sam’s Club and Hy-Vee already sell this “Melorange” cantaloupe. Now, Monsanto’s Jeff Mills and his colleagues are mating Melorange with conventional long-distance shipping cantaloupes in an attempt to greatly improve the flavor of the latter. Although Mills cannot divulge proprietary details, he confirms that he and his colleagues have identified melon genes underlying several traits, such as resistance to common melon diseases and the overall quality of the fruit.
Mills can look for these markers in cantaloupe seeds before deciding which ones to plant thanks to a group of cooperative and largely autonomous robots, some of which are housed in Monsanto’s molecular breeding lab at its vegetable research and development headquarters in Woodland, Calif. First, a machine known as a seed chipper shaves off a small piece of a seed for DNA analysis, leaving the rest of the kernel unharmed and suitable for sowing in a greenhouse or field. Another robot extracts the DNA from that tiny bit of seed and adds the necessary molecules and enzymes to chemically glue fluorescent tags to the relevant genetic sequences, if they are there. Yet another machine amplifies the number of these glowing tags in order to measure the light they emit and determine whether a gene is present. Monsanto’s seed chippers can run 24 hours a day and the whole system can deliver results to breeders within two weeks.
Like cantaloupe, U.S.-grown sweet onions are not available to most Americans between late fall and spring. Different types of onions require different lengths of daylight to begin forming bulbs underground and, consequently, are harvested at different times of the year. Pungent “long-day” onions need at least 14 hours of sunlight and are harvested in the late summer and fall, whereas sweet “short-day” onions need only 10 to 13 hours and are harvested in spring and early summer. By the time September arrives, however, the U.S. turns south to Peru, Chile, Mexico and other countries for its sweet onions, importing them until homegrown crops are ready for harvest the following spring.
More than a decade ago, Scott Hendricks and his colleagues at Seminis Vegetable Seeds began a project to make U.S.-grown sweet onions available to consumers in the fall. They started by growing fields of pungent long-day yellow onions and saving seed only from those that were sweetest. Instead of tasting onion after onion—an impractical strategy for obvious reasons—Seminis, which was acquired by Monsanto, developed a laboratory test for pungency. Their assay detects a byproduct of the chemical reactions that make onion lachrymatory factor—the volatile gas responsible for tear-soaked chopping boards. When a wedge of onion is liquefied and mixed with certain molecules, that once transparent byproduct turns a shade of amber, explains Monsanto’s John Uhlig. He and his colleagues have similar chemical and mechanical tests for just about every vegetable they work with: probes that squish and prick melons and tomatoes to assess their firmness; a series of ice pick-like prongs that measure the crispness of lettuce; machines that distill scents and judge the intensity of pigments.
The final product of the breeding program initiated by Hendricks is known as the EverMild—a yellow long-day onion grown in the Pacific Northwest. Unlike many of its long-day white and yellow cousins, it contains low enough levels of onion lachrymatory factor to qualify as a sweet onion. Now, Jason Cavatorta, another Seminis onion breeder, is working on a mid-day variety of the EverMild to fill the current availability gap right smack in the middle of summer, which is a little too early for the EverMild and too late for typical sweet onion harvest. If he succeeds, the new onions will join two other foods that Monsanto recently created for the produce aisle: snack-size BellaFina bell peppers, which are one third as large as their more familiar cousins and are sold in plastic bags like baby carrots in WalMart and Safeway; and Frescada lettuce, a sweet crispy cross between iceberg and romaine available at Sam’s Club.
Seeding innovation
Along with tomatoes, onions and melons, another notable vegetative victim of distribution difficulties is broccoli. About 75 percent of broccoli harvested in the U.S. is grown in California. Broccoli adores cool weather and flourishes in the Salinas Valley’s occasional fog blankets. When forced to endure hot sticky summers in the Northeast, the vegetable produces gnarly heads with buds of mismatched sizes. Each of the small buds that, together, make up broccoli’s treetop dome is a flower that has not yet blossomed. Thomas Bjorkman of Cornell and his colleagues recently discovered that, during a critical period of its development, broccoli counts how many hours of cool temperatures it enjoys and produces a uniform flowering head only if the tally is high enough. That’s why broccoli grown on the east coast might end up with an unattractive mix of nice, plump flower buds and dinky, almost imperceptible ones.
Three and a half years ago, Bjorkman, Mark Farnham of the USDA and their many collaborators decided to breed a new kind of broccoli that would thrive in the eastern part of the country. In their lab’s growth chamber Bjorkman and his team have been subjecting broccoli to east coast levels of heat and humidity, keeping seeds only from the plants that grow the most attractive flowering heads under these conditions. Although they have a lot of work ahead of them, they have already bred broccoli that can deal with a few more weeks of summer heat than the cultivars currently grown in the east. Meanwhile, the researchers are searching the genomes of the various plants they grow, looking for genes that explain why some broccoli fares better than others. Finding them could shave years off the journey toward their ideal plant.
Creating broccoli that stays beautiful in the heat is not just an exercise in aesthetics—it’s also about getting tastier and more nutritious broccoli to farmer’s markets and grocers. Fresh broccoli consumed the same day it was harvested is completely different from typical supermarket fare, Bjorkman says—it’s tender, with a mellow vegetative flavor, a hint of honeysuckle and no sharp aftertaste. Trucking broccoli from California to other parts of the country requires storing the vegetable on ice in the dark for days. With no light, photosynthesis halts, which means that cells stop making sugars. Rapidly dropping temperatures rupture cell walls, irrevocably weakening the plant’s structure and diminishing its firmness. When the broccoli is thawed, various enzymes and molecules that escaped their cells bump into one another and trigger a sequence of chemical reactions, some of which degrade both nutritional and flavorful compounds. Giving farmers in the east broccoli they can grow and sell locally solves all these problems. In a separate effort to boost the nutritional value of broccoli, Monsanto released Beneforte broccoli, which has been bred to contain extra high levels of glucoraphanin, a compound that some evidence indicates may fight bacteria and cancer. You can find the florets at some Whole Foods and States Bros.
In order to get the initial grant that kicked off the Eastern Broccoli Project, Bjorkman and Farnham had to assure the USDA that seed companies were genuinely interested in this potential new regional market for broccoli by securing funding from the private sector. Although they are technically competitors, Monsanto, Syngenta and Bejo Seeds are all contributing. In theory, both seed companies and university researchers can benefit from such collaborations. During the research and development phase, they all share information and even exchange seeds. Eventually, however, it is time for negotiations. As is the case for Mazourek and his habanada, as well as Klee and his tasty tomatoes, Bjorkman hopes that once he and his colleagues get closer to their beauteous broccoli, a private company will license those seeds and produce them on a massive scale for commercial growers. Bjorkman and his team simply do not have the capital to do so themselves. Sequencing the genomes of individual plants may be getting cheaper all the time, but generating enormous quantities of seed and marketing it to farmers is still a very costly endeavor.
Some plant breeders worry that because giant seed companies have far more financial and technological resources than do smaller firms and universities, true innovation will wither. “There’s been a rather large decline in public sector breeding programs as the technology has transferred into the private sector,” says Irwin Goldman of the U.W.–Madison, who recently debuted flame orange table beets with concentric gold stripes. “Some people argue that this transfer is a success for this country, but public breeding will do things that private sector won’t do—things that take too long or are too high risk.”
Jack Juvik, who is director of the plant breeding center at the University of Illinois at Urbana–Champaign and first got into breeding in the 1970s, remembers when big companies were not nearly as dominant as they are today. “When I first started, there were a lot of smaller companies selling a lot of seeds, but they have all been basically bought out or driven out of the market by the mega-companies. That has changed the whole texture of the industry,” he says. “Instead of having people at public institutions developing finished varieties, most of us design germplasm [seeds and cultivars] for big companies to work with. These large companies have the resources to do some good testing and make some really good varieties, but they end up controlling most of the germplasm and technology used to make it.”
Goldman and his University of Wisconsin-Madison colleague Jack Kloppenburg belong to a group of 20 breeders and farmers from around the country who are interested in creating the equivalent of open-source software for seeds—nonpatentable varieties that anyone can use. There’s really no strong precedent for how to go about this in the 21st-century commercial seedscape, though. One potentially expensive option is for plant breeders to hire lawyers and obtain standard patents or copyright on their seeds with the intent of letting just about anyone use them (excluding mammoth private companies, of course). Alternatively, they could try to create a kind of open source license that allows people to use seeds only if they, too, agree to freely share them and anything they make with them. Goldman has also proposed a compromise in which breeders license some seeds to the private sector to make a profit, but give others away.
Klee also wonders whether a certain degree of conciliation is the best way forward. “The reality is we in academia cannot compete with the Monsantos or other big seed companies,” he says. “Breeders at universities are pushed out of big crops and into niche crops. In my department we have a peach breeder, a blueberry breeder and a strawberry breeder. I know a lot of people at Monsanto who have dropped these kinds of crops that are marginal for them.” Such dichotomy, he hopes, can be complementary, with the public and private sector relying on one another for distinct specialties.
Ultimately, what Klee cares about more than anything is the same prospect tantalizing more and more modern plant breeders: bridging the gulf between what growers need to make a living and what consumers want on their plates. “Marker-assisted breeding makes it possible to go back and fix things like flavor and texture,” Klee says. “In the end, it’s really very simple: Let’s give people stuff they like.”
