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Feature: Life Sciences

Genomic Explorers Go Deep into Plants

Cornell scientists use genomics to improve global food security.
By Amanda Garris


Whether it’s a local crop failure, chronic malnutrition, or regional famine, unpredictable food production is a barrier to prosperity. While many factors play a role in food security, the foremost factor is agricultural production itself, which is based on plant varieties that thrive—or at least survive—even in difficult seasons. It’s a tough world for plants, with unpredictable weather, pressure from insects and diseases, and no means to retreat from challenges.

How do you build a robust wheat plant or a tolerant apple tree? For plant breeders, the answer lies in harnessing the diversity in crops and their wild relatives. Contained in each and every cell of a plant is DNA, which until recently was as cryptic as creatures on the bottom of the sea. However, with breakthroughs in technology, Cornell scientists are turning the promise of genomics into the reality of food security by using genetic markers to breed crops for disease resistance and other traits.

Genetic markers are tools for targeting differences in DNA, such as a change in size or coding on a particular chromosome. They become useful to breeders when they are near an important gene, such as those for yield and disease resistance. Once a link between a specific marker and a specific trait has been established, breeders can rapidly use that marker to predict a seedling’s potential for traits like yield, disease resistance, or drought tolerance. By comparison, classic breeding would require testing plants for weeks, months, or years in the field or greenhouse. Molecular markers allow breeders to track their most important genes, decreasing guesswork and improving efficiency.

Cornell researchers are working to improve food security both locally and globally with new and disease-resistant varieties of apples, potatoes, maize, and wheat. With the genomics tools on hand, the next generation of solutions for disease may not emerge from the nozzle of a sprayer but from unleashing the potential encoded in the plants’ own DNA.

Mark Sorrells
Linda McCandless

Mark Sorrells

Global Wheat Threat

In a Ugandan wheat field in 1999, a scourge of the 1950s reinvented itself. Brick-red pustules on wheat stems in a plant-breeding nursery signaled the return of wheat stem rust. Wheat breeders around the world thought the problem of stem rust had been solved through aggressive breeding for resistance, but this new strain—named Ug99 for Uganda 1999—trumped previously rust-hardy varieties.

Since its first sighting, Ug99 has spread from Africa eastward to Iran, resulting in severe crop losses and raising concerns for the wheat fields of China, India, America, and Russia. Plant breeders around the world are in a race against the fungus to generate new, resistant varieties, and Cornell small grains breeder Mark Sorrells is using genomics to speed the pace.

Because large-scale wheat failure could jeopardize the global food supply, the response by the wheat-breeding community has been rapid and well-coordinated. Sorrells credits the Bill and Melinda Gates Foundation with keen foresight for funding the Durable Rust Resistance in Wheat Project led by Cornell. “Without their support, this ambitious, urgent project would have been difficult to fund,” he says.

“Our role in the project is not the variety development itself, but rather to provide tools, materials, and strategies to breeders in Africa, Canada, Mexico, Syria, and other countries,” explains Sorrells, chair of the Department of Plant Breeding and Genetics. Sorrells has already contributed his own breeding lines, reinforced with three and four different resistance genes.

In addition, they are providing strategic support to the international breeding programs. One strategy is to assist breeders in “pyramiding” genes—incorporating several resistance genes into a single variety—which is feasible using molecular markers. To start, Sorrells’s group tested and verified all known molecular markers for Ug99 resistance genes, putting over 20 tools in the hands of wheat breeders. If they can build several resistance genes into their varieties, this will be a greater challenge to the fungus and buy time for growers in high-risk regions of Africa.

The second approach is called genomic selection—a technique new to plants but already used commercially in the dairy industry to identify the best breeding animals. A similar application is in the DNA testing kits for people, to predict disease risk.

Researchers probe the DNA of seedlings at thousands of sites, compare the results with DNA from plants known to be resistant, and confidently predict which seedlings will be resistant, but with a key improvement. This high-tech approach allows them to track for the first time genes with small but significant roles in fighting disease. With enough of these genes in a variety, breeders can expect resistance that is more durable. Sorrells’s goal is to put this emerging, powerful method into the hands of breeders around the world.

Although the situation is dire, Sorrells admits it is an exciting opportunity to make a significant difference in global food security using the latest genomics technologies. He says, “This was simply not possible before, but now advances in genomics have caught up with needs of breeders and farmers.”

Walter DeJong
Jason Koski/University Photography

Walter De Jong

Progress in Potato Genomics

For such a diminutive worm, the golden potato cyst nematode has a knack for longevity. Microscopic females produce cysts with hundreds of eggs, which are viable for up to 30 years in the soil. Feeding on potato roots by the females causes massive decreases in yield, and benefits from soil fumigation are short-lived. For associate professor of plant breeding and potato breeder Walter De Jong, genomics is key to the future of managing this pest.

“The only real solution we have is breeding for resistance,” he says. “But to fight the nematode we have to move genes from wild species from the Andes of South America into our domesticated potatoes without displacing their desirable traits.”

In New York State, potatoes are an important commodity for the potato chipping and fresh market niches. Two races of golden nematode are found in New York, yet they are distinct enough that different genes are required for resistance in the field. Race 1 was found on Long Island in the 1940s, possibly introduced from contaminated European soil on military equipment after World War I. To guarantee resistance in his varieties, De Jong developed a simple marker for a gene—called H1—that confers resistance to Race 1. Each year, he and other breeders around the world use this marker to select Race 1 resistant varieties.

However, a second race has recently been found in New York, and breeding for this is not as simple as screening with one molecular marker. De Jong explains, “It takes several genes to provide resistance to this pathogen. Our research suggests it requires two or three genes. And we are still looking for markers for them.” Although Race 2 is not yet widespread, the fact that it takes 12 to 15 years to release a new potato variety gives urgency to the task of finding markers.

He concedes that, at the moment, the use of molecular markers is the exception rather than the rule in potato breeding, though it’s not from lack of interest. “Potato genetics have been stymied by the fact that potatoes are autotetraploids—they have four copies of each chromosome rather than the two copies that are the norm in many organisms, including humans,” De Jong says.

Potato genomics is on the brink of change, though. De Jong is a leader on a project which has already developed more than 8,000 new markers for cultivated potato. The markers—called SNPs for single nucleotide polymorphisms—will finally provide the genomic coverage they need to connect markers to traits. His first target is finding markers for resistance to golden nematode Race 2. That, in addition to markers for the traits that produce quality chipping potatoes, such as high starch and low sugars, will allow De Jong and other breeders to select only the most promising seedlings in their breeding program.

“The potato community is excited—we anticipate much more rapid progress in finding markers for key traits in the next five to 10 years,” De Jong says.

Susan Brown
Joe Ogrodnick

Susan Brown

Improvements for Apples

An apple farmer plants an orchard to last for decades, through winter cold, variable summers, and persistent diseases. Apple breeders aim to develop apples worthy of generations, but can they do so in less than a generation themselves? With more than 50 acres of apples under evaluation, Cornell horticulture professor Susan Brown’s apple breeding program is one of the largest in the world. (Brown is the Herman M. Cohn Professor of Horticulture.) While breeding new apple varieties may never be as rapid as breeding annual crops, Brown is using genomics to take the guesswork out of choosing the best parents for breeding.

“We use markers routinely to screen potential parents before making crosses, to ensure that they have resistance to our most pressing diseases—apple scab, fire blight, and powdery mildew,” Brown says. “The markers allow us to test their genomes for strengths and weaknesses before committing their genes to the next generation of apples.” She now tracks seven different scab resistance genes in her breeding program, as well as genes that affect fruitfulness and yield.

A good apple variety demands a lot from its genetics: the buds, branches, and trunk must survive cold winters and spring frosts; the flowers, leaves, and roots need resistance to multiple pests and diseases; and the abundant fruit should appeal to consumers even after months of storage. Since its inception in the 1890s, the Cornell apple breeding program has released 68 varieties to address these challenges, but recent developments in apple genomics promise major breakthroughs in combining the best of traits in new varieties.

Brown credits two significant developments in genomics with feeding the momentum. In August 2010, the sequence of the apple genome was published, giving apple researchers a complete roster of the genes in the apple genome. In addition, Brown is part of the RosBREED project, an international alliance of researchers committed to increasing the rate at which genomics research is translated into supermarket-worthy varieties.

The link between genomics and new varieties is marker-assisted selection, which requires researchers to identify markers that can reliably predict from an apple seedling’s DNA the kind of tree and fruit that it would produce when mature.

With her RosBREED collaborators, Brown has set her sights on key traits that lack markers, shifting focus away from disease resistance and onto the fruit itself. Her students are currently tracking genes that affect fruit quality—fruit texture, acidity, and sugar accumulation—as well as the genes that keep these stable during storage.

“When I started breeding apples 20 years ago, molecular genetics didn’t have an immediate, practical application,” Brown says. “Now it is the bridge from imagining the next great new apple to delivering it.”

Rebecca Nelson

Rebecca Nelson

Durable Resistance in Maize

To survive in sub-Saharan Africa, corn must weather both drought and chronic disease infestations. Breeders have responded to specific threats by breeding in resistance to one disease, only to find their varieties susceptible to a new pathogen strain or emerging disease.

Professor of plant pathology and plant-microbe biology Rebecca Nelson is searching for a different kind of resistance, one based on more modest but reliable genes.

She explains that in the past, breeders relied on “major genes” or “qualitative resistance”—individual genes that strongly and specifically target a particular pathogen strain. However, given sufficient time, these genes are eventually outwitted by the pathogen and cease to protect. Their complement is “quantitative resistance,” which relies on genes that build tolerance to pathogens, rather than immunity to one.

“Quantitative resistance is a big, practical issue in agriculture, but most genomics research has been on qualitative resistance,” Nelson says. “There are only a few ways to completely shut down an infection through qualitative resistance, but there are more ways to slow down or impede pathogens. This is our goal for longer-term, durable resistance.”

Nelson’s tactic is to seek the genes in corn’s general defense plan, regardless of which pathogen is attacking. In reality, farmers here and abroad face several diseases, including grey leaf spot and northern leaf blight, which can cause annual yield losses and intermittent crop failure. Sub-Saharan Africa has the additional threat of aflatoxin, a carcinogen, liver toxin, and anti-nutritional that is produced in grain contaminated with the fungus Aspergillus.

In collaborative work with Ed Buckler, a research geneticist with the USDA in Ithaca, N.Y., Nelson’s lab is targeting genes for quantitative disease resistance. High-throughput genomics combined with field screening for disease resistance quickly led them to a molecular marker for resistance. It boosts resistance to three pathogens: northern leaf blight, Stewart’s wilt, and common rust—the broad-spectrum resistance they were seeking.

“It’s gratifying that we are beginning to understand the mechanics of how plants fight back—finding genes that work at different stages,” she says.

For example, she now has a marker linked to early defense, when the fungus is initially puncturing through the leaf. Another marker predicts which plants effectively deploy chemical deterrents once the fungus had breached the cell wall, like sandbags piled against a leak.

Nelson’s enthusiasm for the molecular mechanics is matched by her determination to make real progress toward African food security though collaboration with James Gethi, PhD ’03, a maize breeder with the Kenyan Agricultural Research Institute and an alumnus of the Cornell plant breeding and genetics program.