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Going in Crop Circles


The battle against plant pathogens lacks sequence data, a consensus priority list, and clear supervision. TIGR’s Claire Fraser wants to change that.


By Diana Jong


Compared to finding a cure for cancer, preventing potato blight is about as glamorous as, well, a field of potatoes. But the heightened awareness of US security issues since September 11 and the subsequent anthrax attacks has put potato blight and other plant pathogens in a different light — as possible bioterror agents. Armed with their expertise and allied with TIGR president Claire Fraser, scientists from the American Phytopathological Society descended on Capitol Hill recently to brief lawmakers on the vulnerabilities of our nation’s crops and how genomics might help.

As unnoticed as the anthrax letters were when they were first mailed, the release of a plant pathogen such as wheat leaf rust would be nearly impossible to detect. Even naturally occurring episodes have proven devastating: Citrus canker first appeared in Florida in 1995, was unreported for three years, and has destroyed more than two million trees to date. In Minnesota, a bout of wheat scab that started in 1993 ruined the farmers and the communities built around them, resulting in about $2 billion of loss in crops alone. A widespread attack could have an even more serious impact.

On average, naturally occurring crop diseases cause $30 billion worth of damage a year. Over barbecue sandwiches in a Rayburn Building conference room decorated with NASA images, Fraser and the APS scientists presented their suggestions for a coordinated national effort to protect crops.

The most pressing problem, according to the scientists, is the lack of complete sequences of plant pathogens. Of the 60 completed bacterial genomes published in the literature, only three of them infect plants, despite plant bacteria far outnumbering human strains. That two of the three were sequenced by foreign teams is “even more disturbing” to Fraser. “This is an embarrassment for all of us given our technology and resources,” she says.

For between $150 million and $200 million, Fraser believes an extensive database — including, in one example, nine bacteria, 26 fungi, and 20 viruses — could be compiled. To make it a “fabulous forensic database,” three strains of each pathogen would be completely sequenced, in addition to high-coverage screening of 10 to 20 related strains. As an initial investment, APS president-elect Jacqueline Fletcher requested $25 million to begin the sequencing.

With the sequences in place, the door to other advances would be opened. “Having the genome sequenced really energizes a field. That information really attracts investigators where they wouldn’t be otherwise,” Fraser says.

Another fundamental problem is the lack of a nationally agreed upon list of the most dangerous pathogens. Different lists have been compiled by independent groups of researchers and agencies, including the CDC, DARPA, and the General Accounting Office, but creating a single list could help prioritize research and funding, the scientists say.

The absence of a consensus pathogen list reflects the lack of an organizing body for the defense against plant pathogens. Larry Madden of Ohio State University proposes a national laboratory modeled after the CDC but dedicated to plant diseases. It could also coordinate with other agencies to develop strategies to eradicate diseases and respond to emergencies.

The scientists hope technological advances can protect crops before an attack even occurs. They envision the development of a rapid, reliable pathogen detection system, perhaps a type of microarray sensor, that could be produced cheaply enough to place throughout fields. Genetic information could also help breeders create hardier plants that are resistant to multiple pathogens. “Preemptive control is a deterrent to attack,” says O. W. Barnett, a past APS president.

For the members of APS, these concerns aren’t new. “We’ve been working on this a long time, but there’s so much renewed interest outside of APS now that we see it as an opportunity not only to respond to a national need at this moment, but to help achieve the things that we’ve needed to achieve,” Fletcher says. “Even if we never have [a] bioterrorist attack, the things we’re asking for will allow our agricultural system to work much more effectively.”

The Scan

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Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.