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From Mendel to Molecules

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Posted Sep. 9, 2009

Molecular breeding program fast forwards development of new forage varieties
Malay Saha, Ph.D.
Malay Saha, Ph.D., checks data during a visit to test plots that hold new forage varieties developed using molecular markers.
Maria Monteros, Ph.D.
Maria Monteros, Ph.D., examines white clover being studied in the Noble Research Institute's greenhouse facility.

The 19th century friar Gregor Mendel made one of the greatest discoveries in all biology and never knew it. Before Mendel, the laws of heredity were assigned a variety of creative explanations, including one theory that each plant and animal contained its own descendants in miniature, like Russian nesting dolls.

In 1865, Mendel embarked on a now famous set of experiments. Over the next few years, he bred pea plants (he had the peas and the time), making detailed notes of various characteristics: whether stems were tall or short, whether flowers were purple or white, whether seeds were smooth or wrinkled. He discovered that the next generation inherited each trait in mathematically predictable patterns. Not until decades after Mendel's death did scientists figure out the reason - the instructions for each plant were passed down through its genes.

Scientists are still breeding plants in Mendelian fashion, selecting plants with the most desired characteristics and crossing them to improve the next generation. But Mendel and decades of plant breeders following him had to wait for a plant to grow before they knew what they had. Improving complex characteristics that involve many genes, like yield, proved frustratingly difficult. And there were logistical problems trying to enhance traits that were difficult to see and measure, such as digestibility.

Today, scientists don't need whole plants. They don't even have to wait for plants to mature. They can breed the genetic material, take a look at the genes themselves and select the best candidates for the next generation. Instead of plant breeders, they are more like gene breeders. "I was a traditional breeder originally," said Malay Saha, principal investigator of the Noble Research Institute's Forage Improvement Division. "When I saw this advancement early in my career, I thought this is the future."

It is also the present. Molecular breeding is to crop improvement what the Concorde was to air travel in the mid-70s - it can get you to the same place faster and more efficiently. The technique is particularly useful for traits involving several genes - traits much more complicated than Mendel's flower color and wrinkled seeds. When trying to enhance a complex trait such as drought tolerance, "it would normally take 10 or 11 years to get to the progeny you want," said Maria Monteros, assistant professor, leader of one of the Noble Research Institute's legume breeding laboratories. Even crossbreeding the best of the lot, each generation may come with a lot of clutter you don't want, along with the traits you do. "You would have to do multiple years of field testing," she said. "With molecular breeding, you can develop a better plant with the traits you want in about five to seven years."

It was, in fact, the idea of more efficient breeding in a laboratory that got her interested in the process. As an undergraduate student in Guatemala, she spent her time propagating plants the old-fashioned way, in test fields. "You would have to get up early in the morning and be out in the heat," she says. When she learned that desirable plants could be identified in a laboratory with more precision, she was sold.

Not that molecular breeding isn't difficult, meticulous work, even in air-conditioned comfort. Scientists first have to identify which genetic instructions are important to the trait - a process that can take years. Those genes are then tagged with molecular markers. Molecular markers are like road signs for the genome, allowing you to easily spot whether the plant has the gene. (In the same way an exit for Indian Nation Turnpike lets you know, even without looking at a map, you're in eastern Oklahoma.) By identifying the telltale signposts of inherited traits - usually these are distinct patterns in the building blocks of the genes - scientists can follow a plant's makeup through generations of progeny without having to see how the plants look and behave.

Take, for example, developing disease resistance. The traditional approach is to expose plants to something that causes disease, such as fungal spores. Some of the plants exposed to the fungus will die, but some will survive. If you breed only the plants that remain, the next generation has a greater ability to withstand the fungus. Then you breed the hardiest of those. And the best of the next crop. But selecting for disease resistance this way not only takes time, it can be imprecise. For one thing, you can't tell by looking at the plant if it was truly resistant or just lucky. It may have survived simply because no spores happened to find it. "Whether it escaped or whether it was resistant, you don't have any way of knowing," said Saha. "You may select a susceptible plant as resistant."

But let's say you know genes that help confer disease resistance - maybe they enable a plant to produce a certain chemical that protects it or gives it the ability to resist any damage - and you flag them with molecular markers. You don't have to expose the plants to know which ones have kept their resistance from generation to generation. The markers will tell you. Also, you can experiment with many more plants in a batch. "In three months, you can evaluate 1,000 plants," Saha said.

Once the genes become concentrated in a particular generation, you can then grow them the old-fashioned way for testing. "Molecular breeding does not override traditional breeding," Saha said. "It's a tool to facilitate the breeding process."

"Molecular breeding can better concentrate the quality you're looking for," said Stephen Moose of the University of Illinois, Urbana-Champaign. "It doesn't always speed things up," he said, "but you can achieve more progress in the same amount of time. The end result can be more dramatic." Molecular breeding has already assisted the development of soybean varieties that are resistant to certain diseases and corn plants that are able to grow with less thirst for water.

Scientists in Monteros' group at the Noble Research Institute are using molecular breeding to try to improve traits that involve multiple genes, including biomass production under drought conditions and the ability to grow in soils with aluminum toxicity problems. The identification of markers - identifying the signposts - can be the first and most labor intensive step in molecular breeding. Recently, Monteros' group has made significant progress in identifying markers with the potential to enhance biomass yield in alfalfa under limited water availability. "Alfalfa plays a significant role in the agricultural industry, contributing more than $9 billion to the national economy each year," Monteros said. "Increased biomass, especially with limited water, could have a substantial impact on an already valuable crop."

Among other projects, Saha's laboratory is trying to identify genes that make tall fescue more digestible to livestock. "Digestibility has a really huge impact on animal gain," Saha said. "If we can increase digestibility by 1 percent, it leads to a 3.2 percent increase in daily life weight gain." Through molecular breeding, he has developed three new varieties of tall fescue that are now undergoing field tests.

More projects are underway, at Noble and elsewhere. Eventually, molecular breeding will become the standard for plant improvement efforts, Monteros predicts. "With molecular tools, you can make breeding more efficient and faster," she said. "We're still using the principles of Mendel, but in a modern way."