Monsanto tomato breeder Alan Krivanek checks on tomato plants he’s breeding in one of the agriculture company’s greenhouses in Woodland, Calif. Krivanek, 42, is part of a new generation of plant breeders who use a novel technology that screens DNA to create elite crops, transforming the 10,000-year history of plant selection.

March 11, 2014 Monsanto tomato breeder Alan Krivanek checks on tomato plants he’s breeding in one of the agriculture company’s greenhouses in Woodland, Calif. Krivanek, 42, is part of a new generation of plant breeders who use a novel technology that screens DNA to create elite crops, transforming the 10,000-year history of plant selection. Max Whittaker/Prime/For The Washington Post

Scientists at Monsanto are using a novel technology that screens DNA to create elite crops, transforming the 10,000-year history of plant selection.

Scientists at Monsanto are using a novel technology that screens DNA to create elite crops, transforming the 10,000-year history of plant selection.

Scientists at Monsanto are using a novel technology that screens DNA to create elite crops, transforming the 10,000-year history of plant selection.

Alan Krivanek, a tomato breeder for Monsanto, dons a white protective suit, wipes his feet on a mat of disinfectant and enters a greenhouse to survey 80,000 seedlings. He is armed with a spreadsheet that will tell him which ones are likely to resist a slew of diseases. The rest he will discard.

Krivanek, 42, is part of a new generation of plant breeders who are transforming the 10,000-year history of plant selection. And their work has quietly become the cutting-edge technology among today’s major plant biotech companies. Instead of spending decades physically identifying plants that will bear fruits of the desired color and firmness, stand up to drought, and more, breeders are able to speed the process through DNA screening.

When his tomato plants were just a week old, technicians manually punched a hole in each seedling to get leaf tissue that was taken to a nearby lab, converted into a chemical soup and then scanned for genetic markers linked to desired traits.

Krivanek uses the information to keep just 3 percent of the seedlings and grow them until they fruit this spring, when he can evaluate fully grown plants, keep a few hundred, sow their seeds and then screen those plants.

“I’m improving my odds. Maybe I can introduce to market a real super-hybrid in five years,” Krivanek said. “A predecessor might take a whole career.”

View Graphic Marker-assisted selection speeds development of new varieties

The technology — called marker-assisted or molecular breeding — is far removed from the better-known and more controversial field of genetic engineering, in which a plant or animal can receive genes from a different organism.

Marker-assisted breeding, by contrast, lays bare the inherent genetic potential of an individual plant to allow breeders to find the most promising seedling among thousands for further breeding. Because the plant’s natural genetic boundaries are not crossed, the resulting commercial hybrid is spared the regulatory gantlet and the public opposition focused on such plants as genetically modified Roundup Ready corn or soybeans, which are engineered to withstand herbicide sprays.

Marker-assisted breeding has been embraced not only by the multinational biotech companies here in California’s Central Valley but also by plant scientists in government, research universities and nongovernmental organizations fervently seeking new, overachieving crops. The goal is to sustainably feed an expanding global population while dealing with the extremes of climate change.

But critics of Big Agriculture worry about the needs of small-scale farmers and breeders. Low-tech conventional breeding — judging plants by how they look and perform, not by their DNA — has been the lifeblood of small seed companies and local growers, often in conjunction with breeding programs at land-grant universities. But those programs have shrunk by a third in recent years, and the remaining ones are increasingly gravitating to the trendy sphere of molecular breeding.

Organic farmers, who need crop varieties designed for specific regions and less-intensive growing methods, are not being served by the new applied science, said John Navazio, a senior scientist with the Organic Seed Alliance.

“There used to be a significant winter spinach production area in southern Virginia and Delmarva, and that’s completely gone,” he said. The spinach-growing industry has moved to megagrowers in California and Arizona.

Progress comes sooner

Few observers, though, expect plant scientists to abandon a technology that has already yielded significant results. One of the earliest validations of ­marker-assisted breeding came in 2009 with the introduction of a rice variety in India that could survive complete submersion after monsoons, which earned it the nickname “scuba rice.” Once the genetic marker was identified, the variety was developed in just three years by scientists at the International Rice Research Institute in Los Banos, the Philippines.

The key was to create rice that looked and performed like the existing one favored by Indian farmers — so that it would be accepted — but with the flood-tolerant gene, said Glenn Gre­gorio, a senior rice breeder with the institute. The organization has since released more than 10 additional monsoon-resistant varieties to flood-prone areas of India, Bangladesh, Indonesia and the Philippines.

The varieties would have been extremely difficult to create with conventional breeding, he said, and taken decades to achieve.

The big multinational companies, including Monsanto, Syn­genta, DuPont Pioneer, Bayer CropScience and Dow AgroSciences, have invested heavily in the new plant-breeding programs, which will increasingly require colossal data-processing abilities.

“In many ways, the company has gone beyond” genetic engineering, said Robert T. Fraley, Monsanto’s chief scientist. “The breeding technology has changed dramatically in the last few years.”

Marker-assisted breeding won’t bring an end to GMOs, scientists say, because genetically engineered crops can achieve highly specific tasks now unobtainable through even marker-assisted breeding. But given the obstacles to GMO development — $100 million to create one variety, at least 10 years for regulatory approval and widespread public opposition — marker-assisted breeding has become alluring to such companies as Monsanto.

It is attractive because it is a powerful tool to assemble an array of desirable traits in a plant. A GMO plant, by contrast, has been engineered for a specific task — such as containing a bacterium that would kill a certain pest.

“GM really hasn’t delivered on its promises,” said Janet Cotter, a scientist with Greenpeace’s international science unit in Exeter, England. “For more-complex traits, I think people are seeing marker-assisted selection as a lot more valuable.”

The rice institute’s Gregorio said that about 5 percent of its breeding programs involve genetically engineered varieties, while marker-assisted varieties account for as much as 15 percent.

In a decade, probably two-thirds of its introductions will be developed through next-generation advanced molecular breeding, he said.

A matter of taste

For developing nations, the technology promises to avert certain crop disasters; for the supermarket shopper in the West, it might bring a whole new experience: flavor.

Seed companies acknowledge that in their quest to improve yield and shelf life, the taste has suffered, but they say that advanced breeding is bringing heirloom flavors back to industrialized varieties.

“This is one area where [marker-assisted] breeding begins to make an impact,” said Alexander Tokarz, head of vegetables for Syngenta, the Swiss biotech ­giant. “Early on, we brought shelf life into tomatoes and lost the flavor.”

The technology has been around for about 20 years but has become much easier and less expensive to use in the past few years, and consumers are only now seeing the results. Precision-bred cucumbers, peppers and other vegetables are showing up in supermarkets, but the unlabeled and brandless nature of loose produce makes it difficult to distinguish them, said Carly Scaduto, a spokeswoman for Monsanto.

Some varieties of Monsanto’s improved-nutrition broccoli — branded as Beneforté — became widely available in 2012. Last year, the company introduced Debut, an advanced hybrid tomato for growers and home gardeners. A group of blight-resistant peppers are in the final stage of testing before their commercial introduction, she said.

Felix Serquen, who heads Syngenta’s tomato-breeding research in Woodland, this year is introducing a beefsteak for California growers that resists the nematode, a root pest.

He is launching another variety — SevenTY III — that resists a strain of fusarium that is a major bane to growers in Florida.

Scientists acknowledge that the technology has evolved with little effort to inform the public about it. Sekhar Boddupalli, head of Monsanto’s consumer research for vegetables, wonders whether people even want to know. He pulls out his smartphone and places it on the table in front of him. “Are they asking how the iPhone really works? ‘Is it safe for me?’ ” he said. “No. But what they’re seeing is the benefit of this.”

Fast-paced testing

Monsanto, Syngenta and other multinational biotech companies conduct much of their vegetable research and development in the rich, loamy soils just outside Woodland, a few miles west of Sacramento, in ranges of greenhouses and, increasingly, laboratories on site and around the globe.

Krivanek’s leaf samples had gone to a testing lab within Monsanto’s new office complex in Woodland. The laboratory is starkly bright, clean and silent except for the hum of an automated machine encased in a cube of glass the size of an office cubicle. Inside of it, two robotic arms perform a frenzied dance with plastic plates, each containing almost 100 leaf samples.

The machine, called the Biocell, does the work of 30 lab technicians and can process tens of thousands of tissue samples daily, said Jeff Touchman, Monsanto’s head of molecular breeding in Woodland. The samples are liquefied, clarified and eventually injected into tiny indentations on a clear plastic ribbon.

The ribbon is spooled onto a scanner that uses light to trigger a chemical fluorescence, which reveals the presence of any desired genetic markers. A blue Internet cable threads upward, carrying the data to Monsanto’s headquarters in St. Louis, where the company’s vegetable breeders around the globe can download their results.

“If plants were people, we could test the entire population of Los Angeles for breast cancer susceptibility in a month and a half,” Touchman said. “We think this is the highest throughput of genetic testing in the world, of any industry.”

It is about to get higher.

For plants with larger seeds, breeders can clip off a piece of the seed and test its DNA without waiting for it to grow into a seedling. Later this year, Monsanto plans to add to Touchman’s lab a robotic machine that will clip melon seeds. The process, called seed chipping, isn’t as easy at it might seem: The robot must be able to examine and orient the seed before chipping it to make sure the sampling doesn’t damage the plant embryo so a sampled seed can grow. The company has also developed chippers for corn, soy, cotton and wheat, whose seeds are relatively large and easier to chip than, say, those of a tomato or lettuce.

The machine can chip thousands of seeds a day. The breeder must still grow out selections and evaluate them, and prospective hybrids are typically field-tested in farms in different regions and climates before final commercial introduction. Still, the chippers will take advanced breeding to the next level. “If you are looking at [breeding for] five, six, seven traits, you would have to sow about a million plants,” Touchman said. With seed chipping, “space is no longer a limitation.”

Loss of diversity feared

As young as it is, marker-assisted breeding has already evolved. Some traits are the product of a single gene, making their incorporation relatively straightforward. But some crop attributes — resistance to some diseases, yield, quality and nutritional value, for example — are linked to a whole series of dis­parate genes.

To reach those, the scientists now are able to statistically predict if an individual plant has all the genes needed to provide the desired trait.

“The prediction model tells us the overall value of an individual” to a breeding program, said Mark E. Sorrells, chairman of plant breeding and genetics at Cornell University. The technique, called genomic selection, is about five years old and is used increasingly in such economic crops as corn and soy, although scientists expect its use to spread to important vegetable crops as their genomes are fully sequenced.

Major Goodman, a leading corn expert and geneticist at North Carolina State University, worries that the new technology is so precise in finding desired genes that the genetic diversity of the discarded material will be lost. “In the long term,” he said, “it may have a detrimental effect. We are getting advances now that may cost us in the future.”

Ralph Scorza, a peach breeder at the Agriculture Department’s Appalachian Fruit Research Station in Kearneysville, W.Va., believes, however, that “well-trained breeders will understand the balance between going headlong for a particular trait and also maintaining a population with diversity.”

Scorza works for the Agricultural Research Service, which with land-grant university researchers is making genomic data and methodologies public so that breeders outside the proprietary universe of the biotech companies can work on developing new hybrids.

“The federal government has led the world in releasing all the DNA sequencing information we have,” said Kay Simmons, deputy administrator of the research service.

But many small seed companies and breeders may not find that helpful, critics say. “It’s hard for small companies not only to access germ plasm, but also, many of them don’t have the wherewithal to use this new technology,” said Bill Tracy, a professor of agronomy at the University of Wisconsin. “So in a sense, it puts them at a double disadvantage.”

For those in on this science, the work has shifted in large part from the gritty, earthy environment of the greenhouse and test-field to the cold sterility of the lab.

And yet the high-tech breeders of Woodland still perform the ageless rituals of those who came before them. They must still take the pollen from one plant and fertilize another, and grow out candidates in the field, and see how they look, taste and feel. They must still select the parents and the crosses of their offspring. They must still walk the fields around their research farms and see if the genetic soothsayers were right.

“You have to have the feeling for the organism,” said Serquen, of Syngenta. “Otherwise you become computational, molecular.”