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Mars, USDA, IBM-Led Team Sequence Cacao Genome

By Andrea Anderson

NEW YORK (GenomeWeb News) – A research team led by investigators at Mars, Inc., the US Department of Agriculture's Agriculture Research Service, and IBM announced today that it has sequenced a draft version of the cacao genome and is making the data publicly available.

"Traditional [cacao] breeding has more and more tools than it's ever had before to deliver the value of high yielding, pest and disease resistant trees," Howard Shapiro, global staff officer in plant science at Mars, told GenomeWeb Daily News.

Shapiro, who also is an adjunct professor of plant sciences at the University of California at Davis, explained that the cacao genome sequencing project was done as a public-private partnership largely funded by Mars.

Those involved in the collaboration initially announced the undertaking in the spring of 2009. At that time, the effort was expected take about five years. Researchers were able to deliver the genome sequence earlier than anticipated, in part, because of advances in high-throughput sequencing technology, Juan Carlos Motamayor, leader of cacao research for Mars, told GWDN.

The team used several complementary strategies to sequence the cacao genome, he explained, including physical mapping of the genome, a paired-end library, high-throughput sequencing using Roche 454 and Illumina platforms, and BAC end sequencing using the Sanger method.

The Matina 1-6 cacao cultivar was selected for the project because it was highly homozygotic and represents the cultivar from which most cocoa in the world is cultivated, Shapiro explained.

"We determined that to have something that has this much influence on the cocoa world would give us the best basis to make decisions going forward," he said.

The researchers generated enough raw sequence to cover the cacao genome about 200 times, though not all of this data has been included in the existing genome assembly.

Preliminary analysis suggests the cacao genome contains an estimated 35,000 gene models, though the team is continuing to scrutinize the genome and run additional predictions based on additional EST evidence, Motamayor explained.

"Within the next few months we'll have a definitive annotation of the genome," he added.

The sequence is expected to provide insights and tools that can be applied by breeders to improve cacao crops and benefit cocoa farmers, such as increased yield and drought and disease resistance.

For instance, researchers from Mars and the USDA have been collaborating on a large, international breeding network for about a decade, Motamayor noted, and information and expertise from the cacao genome project is being passed on to scientists involved in this network.

"We have trained scientists working in cacao genetics to use the technologies and the tools derived from the genome sequence," he said.

Shapiro also emphasized the importance of having the cacao genome in hand as a way to spur additional research into the commercially important plant.

"We needed to catch the science up to attract young West African, East Asian, South American, Latin American, and American scientists to work on this crop," Shapiro said. "It's one of the 10 largest traded commodities in the world."

"By generating so much genomic data, we are also attracting research institutions that have not traditionally worked in cacao — that have been working in more modern or more scientifically attractive crops like corn or rice," Motamayor agreed.

In addition to their ongoing annotation and analyses of the cacao genome, he said the team is starting to re-sequence cacao plants from other populations as well.

A few papers stemming from the cacao genome sequencing effort have already been submitted for publication, Shapiro said, and the researchers will likely submit several more in the future.

Data from the genome is being made available for use by other researchers through the Cacao Genome Database through an agreement that does not allow patenting based on the data.

Another team of researchers from France, Pennsylvania State University, and elsewhere is involved in an independent effort – partly funded by Hershey — to sequence the cacao genome as well, according to a report today in The New York Times.

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