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Cacao, Innovative Diagnostics, Tracking Sustainability

Posted by | October 6, 2010
WSU bioinformaticist Dorrie Main
WSU bioinformaticist Dorrie Main

WSU Researcher Sinks Teeth into Chocolate Genomics Tools

Since its public release a couple weeks ago, the database housing the cacao genome has had more than 6,000 visitors, said WSU bioinformaticist Dorrie Main.

That’s a lot more traffic than most draft genome sequences get, Main observed. “There’s a lot of public interest in cacao because it’s the source of chocolate,” she said.

The 6.5 million farmers in Africa, Asia and South America raising cacao can’t keep up with the growing global demand for chocolate. “Diseases greatly reduce production in those countries,” said Main, who is based in WSU’s Department of Horticulture and Landscape Architecture, home to the Cacao Genome Database.

Creating disease resistance in cacao and improving yields are primary reasons candy-maker Mars, Inc. funded the genome research–and then made the results publicly available via the database portal.

“Mars wants to sustain chocolate production and the livelihood of cacao farmers,” Main said, “and the best way to do that is to make the genome data public so lots of people can work with the data to produce superior cultivars.

“I love chocolate,” Main affirmed, though that’s not the reason she got involved with the U.S. team of scientists working together to sequence the cacao genome.

Main’s bioinformatics lab contributed to the project by helping to analyze the assembled genome and making the results of annotation available through the database portal. Main works primarily with genomic data for tree fruit–apples, cherries, peaches–and other crops grown in Washington.

Chocolate -- need we say more?
Chocolate -- need we say more?

“But all our projects merge together,” Main said, “as our role is to enable communities of scientists to have access to this information and the tools to interrogate it.”

Main and her colleagues develop software tools and interfaces that allow researchers to compare genomes across cultivars within crops as well as the genomes of different species.

By itself, a genome sequence is not particularly useful. Its value is tapped when we know what particular genes do, where they are, and how they interact with other genes. The function of genes in a large number of crops is now the focus of intense research by WSU’s horticultural genomics team.

As plants are all related, at least distantly, it’s no surprise that they share many genes and that the function of those genes is similar across a vast swath of crops found all over the world. Genes for fruit ripening, many kinds of disease resistance (or susceptibility), yield, plant size and more are all shared by many kinds of plants.

“We’re building a suite of tools all developed using a standard infrastructure,” Main explained. “There’re lots of tools out there, but they’re written for programmers, not scientists. We’re working to change that situation.”

Main and her team develop the tools using freely available and easy-to-use components which they then customize and deploy with user-friendly web-based interfaces. Gone are the days, Main said, of expensive and proprietary software systems that require specialized training. Main wants to empower scientists to do science instead of spending their time learning to use the latest version of a software package.

“You can’t be a plant breeder these days without using these sorts of database tools,” Main said, raising one of the primary reasons she is involved with sequencing projects involving crops not grown locally.

“Plant breeding translates across crops,” she pointed out, because plants share so much genetic information. “And at WSU, we are training the next generation of plant breeders. That means students are really cross-trained–in breeding, in genomics, in bioinformatics–they get trained in all the components required for building a truly modern breeding program that is both efficient and effective.”

Need a chocolate fix? Visit the cacao genome database and get the full-meal deal: Check out Main’s bioinformatics lab on the web by visiting

Ingenious Diagnostics Combat Global Plant Disease

Graduate student Sudarsana Poojari with mentor Rayapati (back) in their plant diagnostic laboratory
Graduate student Sudarsana Poojari with mentor Rayapati (back) in their plant diagnostic laboratory

Humble yet ingenious. A scrap of heavy-gauge paper the size of a postcard is being used by WSU scientists to help eradicate crop diseases in developing countries around the world.

In an age of globalization, developing nations often benefit from new ideas. But, in some cases, changes to traditional agricultural practices have unleashed new problems for subsistence farmers in Africa, Asia and South America. Unforeseen consequences, such as rampant spread of viral diseases, can be deadly, decimating crops and wreaking economic ruin for families and communities already living on the edge.

“Many farmers are unaware of plant viruses, knowing only that plants are dying or that fruits appear irregular. This makes management of viral diseases in plants especially difficult,” said WSU plant virologist Naidu Rayapati.

Diagnosing those diseases is also a problem, particularly for countries with scarce resources and poor infrastructure. In addition, U.S. scientists hoping to bring samples back to their laboratories for testing face stiff federal regulations prohibiting the transport of live plant material into the country.

But Rayapati, an assistant professor in the Department of Plant Pathology based at WSU’s Irrigated Agriculture Research and Extension Center in Prosser, puts his faith in creative thinking and bringing people together to solve common problems.

Rayapati discovered that many medical scientists were using FTA Classic Card technology to test for HIV/AIDS, malaria and other diseases in developing countries. Blood samples are collected from villages and stored on small cards, then easily transported to a central location for testing. Even better, the cards are stable at room temperature and can be shipped in the mail.

Rayapati thought a similar process could be used to diagnose plant diseases. The leaves or other tissues of an infected plant could be rubbed on the card, capturing sap instead of blood.

“With the cards, only harmless nucleic acids (DNA or RNA) are brought into the country,” he said. “Any pathogens that may be present — bacterial, viral or parasitic — are inactivated and no longer infectious.”

Backed with funding by the U.S. Agency for International Development, Rayapati and his team members in the Integrated Pest Management-Collaborative Research Support Program began using the FTA cards for plant diagnostics in 2005.

Five years later, Rayapati boasts a string of success stories as well as international awards for his work with the FTA cards. Although the technology has been used on a limited basis, he believes there is much broader potential for this type of program. In fact, his lab has begun using the cards to detect not only crop viruses, but also the insect vectors that spread the diseases.

In 2008, for instance, farmers in Java lost more than 80 percent of their crop of yard-long beans — a popular legume extensively cultivated in Indonesia — to an unknown viral epidemic. Using FTA cards, Rayapati and his colleagues were able to identify the virus as a strain of the bean common mosaic virus, which has been documented in many countries, including the U.S.

Because Indonesian farmers had been using yard-long bean seed imported from China, Taiwan and Thailand. Rayapati speculates that the virus was introduced through the seed and then spread throughout the region by aphids.

“By providing an accurate diagnosis of a plant virus problem, scientists educate farmers about contaminated seed and convince them stop using it,” he said. “We also provide information to seed companies to ensure they provide quality seed to farmers, which helps stop the spread of viruses to other countries.”

By 2009, Java farmers were able to grow enough healthy yard-long beans to overcome their previous losses.

“Now it is easy for them to manage any problems,” Rayapati said with a smile. “The beauty is that people who are not familiar with the FTA card technology can use it, as it’s so simple; we just send the card to them with instructions and they send it back for analysis.”

–Becky Phillips

Read a longer, more detailed version of this story at Check out the related video by visiting

Research Tracks Organic Farmers’ Sustainability

Lynne Carpenter-Boggs
Lynne Carpenter-Boggs

WSU researchers have received a $1.5 million federal grant to help organic farmers keep a better account of their ecological footprint.

Seven researchers in the WSU Center for Sustaining Agriculture and Natural Resources, Biological Systems Engineering, and USDA Agricultural Research Service will focus in particular on carbon and nitrogen–two elements central to farming and out of balance with the planet’s biological boundaries.

The researchers will conduct both laboratory and on-farm research to model how carbon and nutrients are cycled through organic farming systems. They will concentrate on five commercial organic farms covering a range of vegetables, livestock, grains, rainfall and irrigated systems. Ultimately, they will develop a tool for other farms, both organic and conventional, to estimate their greenhouse gas emissions and the overall impact, or life-cycle analysis, of different farm inputs and systems.

“This research and this tool will let farms analyze what they’re doing–their crops, their soil management, and their exact place on earth,” said Lynne Carpenter-Boggs, a research leader for WSU’s Biologically Intensive Agriculture and Organic Farming program and director of the university’s graduate certificate in sustainable agriculture. “They can ask, ‘How much carbon am I bringing in? How much carbon am I releasing and storing?’ And they can ask the same with nitrogen.”

Levels of carbon in the atmosphere and reactive nitrogen in the earth’s land, air and water are generally considered to be too high for the earth’s life-support systems. Rising carbon dioxide levels are warming the earth, while byproducts of reactive nitrogen used as fertilizer are both contributing to global warming and marine “dead zones.”

“Agriculture has been a contributor to these problems, but can also be part of the solution,” said Carpenter-Boggs.

Meanwhile, consumer groups and large buyers like Walmart and McDonald’s are asking suppliers to account for the ecological sustainability of their practices.

“Carbon and nitrogen impacts could very well be decreed,” said Carpenter-Boggs. “I know they’re being looked at by these big purchasers.”

Funding for the research comes from the Organic Agriculture Research and Extension Initiative of the National Institute of Food and Agriculture, an arm of the USDA.

–Eric Sorensen

Learn more about the Center for Sustaining Agriculture and Natural Resources and BioAg by visiting