Genetic markers identify naturally occurring genes that scientists use to develop desirable traits in plants that can help them to resist droughts and pests while increasing fruit or grain output

By Virginia Baldwin Gilbert
Of the Post-Dispatch

July 23, 2001
Suppose you could develop new varieties of corn or wheat in six or seven years instead of 10 or 12 years.

Suppose you could analyze soybean seedlings that are only a few days old, rather than waiting until the beans are ready to harvest, and could t ell which plants would grow beans with lower fat content.

Suppose when you crossed a high-yield variety of a cash crop with a drought-resistant wild cousin, you could transfer only the drought-resistance trait, leaving behind the weedlike traits in two plant generations instead of four or six.

Suppose you could do all that now without modifying the genes of plants and arousing consumer wariness or unsettling export markets.

Researchers are doing so with techniques that use genetic markers, which are strands of synthetic DNA that they mix with plant material in the lab to identify a part of the plant's genetic structure, or DNA, without changing it. It's a technique that uses chemistry to guide agriculture.

"Markers have become profoundly important tools over the last two decades," said Marlin Edwards, the global lead scientist for the molecular breeding program at Monsanto Co.

Markers work at the cellular or molecular level, acting as signposts to DNA, he said. "They allow us to recognize unique stretches of DNA and thus allow us to characterize one individual versus another and determine whether they're similar or dissimilar for that particular stretch of DNA," he said.

In general, it's the same technology used in court cases to determine pa ternity or to identify crime suspects from a strand of hair or a drop of blood.

The techniques are being used by researchers in large corporations like Monsanto, in research centers like the Danforth Plant Science Center, in academic labs sponsored by the U.S. Department of Agriculture or the United Soybean Board and in small startups such as Orion Genomics at the Center for Emerging Technologies in St. Louis.

It's a marriage of technology and nature, using the latest in genetic research and the fastest computer technology to bring out the best that resides in plants.

Researchers are working with "naturally variable traits," Edwards said, specifically those that increase yield, resist disease or improve the quality of grain. "We're using markers to identify existing native, natural genes and then controlling those traits" with conventional breeding in most cases, he said.

Prakash Arelli, a professor of agronomy at the University of Missouri, believes technology that works with plants at the genetic or molecular level offers great promise.

"Traditional technology depends mostly on gambling and guessing games," Arelli said. "Molecular technology is pinpoint accurate and sharp." Researchers using markers "can do in the lab within two or three weeks the same kind of identification that might take a year or two using traditional techniques."

Researchers use genetic markers for a variety of tasks:

* Mapping and sequencing plant genomes. Late last year, they completed the genome of arabidopsis. The small, weedy plant is being used as a model for genomic study of all plants, said Karel Schubert, the director of science administration for the Danforth Center.

* Finding genes that could produce improved traits. Scientists are concentrating on areas in the genome that affect important processes like a plant's fruit or grain yield, disease resistance, or development of specific proteins or fats in the food product.

* Getting desirable genes into a plant without introducing undesirable ones. For example, getting a drought-resistant gene into a plant without affecting yield or the taste of the fruit.

* Speeding up the breeding-selection process.

Sifting through junk

Plenty of material that could improve plants is hiding in plain sight, said Nathan Lakey, the chief executive of Orion Genomics in St. Louis.

"Half the genome of a particular species is junk," Lakey said. In plant research, as in medical research for people, "The question is how to find what's valuable in that huge space of junk," he said.

Scientists know where to look, he said. For example, they know the approximate location of genes that regulate the water intake or the seed growth of most plants.

Orion struck a deal recently with a subsidiary of the New Zealand Dairy Board to sequence the genome of forage plants eaten by dairy cows. Orion's scientists will work with scientists based in Auckland. They'll share discoveries and technologies. Orion will use the information for row crops grown in the United States, and the New Zealand company, ViaLactia Biosciences, will use the information for forage plants.

Researchers are working to identify the best genes in a type of crop or within a variety and then to breed the genes into other plants. Also, they're looking for beneficial mutations -- new genetic variations -- that could improve plants.

"It's possible within a species there are mutations that are silent in their current form," Lakey said, meaning that they don't influence the plant's development or function. "But if they're combined with other genes, we could enable them to be recognized."

Staying simple

David Shleper, a professor of agronomy at the University of Missouri, said breeding researchers "try the simplest approach first."

"We put pollen from plant A onto the stigma of plant B."

Though the method of crossing plants remains the same, "We've gone from the whole-plant level to the molecular level," Shleper said. "That's what has changed" in the 27 years he has been researching new crop breeds.

"We used to depend on cruder means to evaluate" plant reproductive cells, he said. Now, computerized databases enable scientists to keep track of the possible combinations, and genetic markers enable them to choose only the best plants for further breeding.

Once the genes are identified, marker technology can help researchers se lect plants with the good genes and screen out the undesirable ones.

Researchers can test subsequent generations of cross-bred plants in the lab for the presence of the gene. If it's there, the plants are grown for seed. If it's not, the seedlings are discarded.

Such lab tests "replace a greenhouse process that takes a couple of months," said Edwards, the Monsanto scientist. "It saves a year or more of testing varieties you'd later abandon."

Grover Shannon, another Mizzou agronomy professor, directs field trials in Portageville, Mo., for a project to develop soybeans that are resistant to the cyst nematode.

Shleper and Arelli, the counterparts of Shannon's in the university's labs, "might find a new source of resistance and incorporate that in a gene," Shannon said. "My job in the field is to get that gene into something the farmer can use."

Whether through conventional breeding or genetic engineering, "You can put a gene into anything," Shannon said. "But will it yield? Is it well-adapted to different soil types? A farmer's not going to plant something that won't yield well."



* DNA: Deoxyribonucleic acid, the huge molecules that make up genes and contain the operating instructions for all living things.

* Genome: The sum of all genetic information contained in an organism.

* Genomic sequence: The order of the building blocks that make up DNA sections.

* Stigma: The part of a plant on which pollen grains fall, beginning the process of becoming seeds.


(1) Color PHOTO BY LARRY WILLIAMS / Post-Dispatch - Orion Genomics employees Muhammad Arief Budiman (left) and Betsy Flick insert plant DNA into bacteria Tuesday to duplicate, or clone, the DNA for use as genetic markers. They are helping to develop ways to identify plant genes that promote plant development and growth.

(2) Color PHOTO - Tim Leland, a project leader at the Monsanto Technical Research Station, takes samples of a corn leaf to mix with genetic markers that can tag the gene that he wants to check.

(NOTE: The following related photo appeared on the COVER:)

3) Color Photo by Larry Williams / Post-Dispatch - Field scientist Becki Siefert pollinates corn Wednesday at the Monsanto Technical Research Station near Jerseyville. Breeding is done "the old-fashioned way," in the field, Monsanto scientist Marlin Edwards says. But genetics helps in choosing which plants to breed.