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WSU Researcher Sinks Teeth into Chocolate Genomics Tools

Posted by struscott | October 10, 2010

Since its public release last week, the database housing the cacao genome has had more than 6,000 visitors, said Washington State University 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 global and growing demand for chocolate. “Diseases greatly reduce production in those countries,” said Main, who is based in WSU’s Department of Horticulture and Landscape Architecture which houses 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 the 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.”

Ripe cacao pods

Ripe cacao pods. Photo courtesy Wikimedia Commons/Rigues/Creative Commons.

“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.

The Main 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.

“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.

“But we can’t do the one-gene-at-a-time thing anymore,” Main pointed out — it just isn’t time and cost efficient.

Instead, Main and her team develop tools that allow researchers to analyze large numbers of genes very rapidly and to quickly make an impact on horticultural production systems.

“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 correct 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.”

As Main pointed out, the cacao project contributes directly to the improvement of Washington crops.

“We can take the tools we honed in this project and customize them for our breeders working on new varieties of apple, cherry, peach, pear and so on. That’ll give Washington producers a competitive edge in the global market place,” Main said.

Mars was the primary funder of the project, investing millions into the research. Other partners in addition to WSU, the USDA-ARS Subtropical Horticulture Research Station in Miami, the Jamie Whitten Research Center in Stoneville, Miss., and IBM, include Clemson University Genomics Institute; Public Intellectual Property Resource for Agriculture at the University of California-Davis; National Center for Genome Resources; Center for Genomics and Bioinformatics at Indiana University; AlphaHudson Institute for Biotechnology; and Washington State University. Moving forward, the collaboration will continue to analyze and characterize the cacao genome in preparation for submission to peer-reviewed journals.