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Bringing Home the Apple (Genome) Cup: WSU, UW Spearhead International Project to Sequence Rosaceae DNA

PULLMAN, Wash. – Scientists at Washington State University and the University of Washington are spearheading a public, international effort to map and unlock the secrets of the apple genome to develop better tree fruit faster.

“The Washington apple is an icon of quality around the globe,” said Dan Bernardo, dean of the WSU College of Agricultural, Human, and Natural Resource Sciences. “This is a natural home for the advanced science necessary to map the tree fruit genome and actively study how it functions.”

WSU’s Agricultural Research Center is providing seed money for the project as part of its larger investment in basic and applied plant science programs. “Investing in this program is a matter of building on our strengths in horticulture to leverage bottom-line results for industry,” said Ralph Cavalieri, associate dean and ARC director.

Another primary supporter of the initiative is the Washington Tree Fruit Research Commission. “This is one more step forward in the partnership between WSU and specialty crops in Washington,” said Jim McFerson, the commission’s executive director. “This effort not only builds a knowledge base for apples, but for all crops within the Rosaceae. It’s a pleasure to see the partnership expand to include the scientific expertise at the University of Washington.”

WSU scientists Amit Dhingra, Dorrie Main and Ananth Kalyanaraman, along with UW researcher Roger Bumgarner, already are working to finalize a consortium of partners from Italy and France to New Zealand and South Africa.

“This initiative will establish Washington as the worldwide hub for Rosaceae functional genomics and is attracting internationally renowned scientists, as well as quality graduate and undergraduate students to Rosaceae research at WSU,” Dhingra said.

The Rosaceae family includes Washington’s largest crop—apples–and other tree fruit as well as cherries, peaches, strawberries, raspberries, roses, and nuts. In terms of economic volume, Rosaceae is the third most important family in the U.S. and other temperate regions of the world. Its aggregate wholesale value in the United States is more than $8 billion, representing 8.5 percent of total crop production value in the United States in 2006.

WSU is already home to the international databank for the Rosaceae family, an online database which received 3.9 million hits in 2007. “The integration of this apple genome sequence data with other peach and strawberry genome sequence data will maximize the utility of this data to the world-wide plant research community and further enhance WSU’s reputation as a leader in plant science,” Main said.

The WSU/UW consortium is the only initiative of its kind in the world that aims to sequence a genetically unique, double-haploid Golden Delicious apple.

Bumgarner’s lab at the University of Washington is providing the sequencing expertise and capability to the project. His laboratory recently obtained a new DNA sequencing instrument from Roche Applied Science that provides sequence data approximately 1000-fold faster than instruments that were available just a few years ago.

“There is tremendous opportunity for crop improvement when it’s guided by a detailed understanding of plant genomes. Sequencing the apple genome will allow us to identify all the genes, to understand which genes drive which traits and to better select for desirable genes and traits. The advent of ultra-high throughput DNA sequencing instrumentation makes such a project feasible at reasonable cost,” said Bumgarner, associate professor in the department of microbiology at UW.

The goal of the project is to obtain a draft genome sequence of apple and then augment that information with scientific contributions from international collaborators. The vision is to create a knowledge base in Rosaceae genomics at WSU that will translate to improved and innovative varieties for growers in Washington and worldwide.

“Bioinformatic prediction of the function of the genes deciphered from this sequence will speed up development of functional markers that we can use for innovative crop improvement through apple and other tree-fruit breeding programs,” said Main. “Pear, sweet cherry and raspberry are some other Washington fruit crops closely related to apples, so the benefits of this work will also accrue to improvement in those commodities.”

Dhingra agreed. “Validating how the genes function in a rapid-cycling apple–that is, those that flower in a few weeks rather than years–will enable us to generate reliable markers for genomics-assisted crop improvement,” he said. “That represents one of the immediate tangible outcomes of this initiative that will be of great benefit to the industry worldwide.”

The activity is also providing a platform for interdisciplinary training of graduate and undergraduate students. “Besides nurturing a fresh inter-disciplinary synergy, the genome discovery project is exposing computer science students to new frontiers in biology and catalyzing the development of novel computational methods for distilling large amounts of genomic information,” Kalyanaraman said.

Main agreed. “This project further enables us to train students in sequence analysis methods providing them with highly sought after bioinformatic skills.”

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