Bringing Home the Apple (Genome) Cup
Scientists at WSU 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 State Tree Fruit Research Commission.
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, 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.
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.”
The activity is also providing a platform for interdisciplinary training of graduate and undergraduate students. “Besides nurturing a fresh interdisciplinary 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.”
WSU and UW are partnering to sequence the genome of the Golden Delicious apple.
The Genome Database of Rosaceae is located at http://www.bioinfo.wsu.edu/gdr/.
Learn more about WSU’s program in Molecular Plant Sciences: http://www.wsu.edu/molecular-plants/.
Learn more about tree fruit research at WSU: http://treefruit.wsu.edu/ and http://www.tfrec.wsu.edu/.
Good Goober Growing
Growing peanuts in Washington may sound nutty, but for Basin City farmer Steve Price the results are both surprising—and surprisingly tasty.
As we reported back in December, Price first planted peanuts “just to see if he could grow them.” Collaborating with WSU Extension educator Tim Waters on refining growing regimens and purchasing harvesting equipment, Price and Waters have been surprised by the yields their experiments have produced, which have been equal to or above the national average.
Price figured he could grow the oily crop for the region’s nascent biofuel industry. In 2006, though, Price and Waters each planted test acreage. After harvest, they sent the peanuts out for grading, according to the Tri-City Herald. Two of the varieties they grew came back as Class A, the highest food quality.
The pair has already been approached by Clark Bowan, owner of CB’s Nuts in Kingston. “I already have told them I’d take 40,000 pounds of organic peanuts if they would grow them,” Bowan told the Herald. Bowan said he knows what customers want: “They want locally grown peanuts, and they want organic. But local trumps organic.”
The only other grower producing peanuts in Washington is another Extension-connected farmer, Hilario Alvarez, who grows organic peanuts in his Mabton greenhouse and sells them at West Side farmers’ markets.
Meanwhile, Price is looking for more research collaborators. “I can’t afford to do more than I have been doing,” Price told the Herald. “There’s so many things they can be used for–the oil for biofuels, the shells can be used in plywood, and there’s even value to the peanut hay.” And heck, they’re good to eat, too.
For more information on Extension and small farmers, check out this short video interview with Hilario Alvarez: http://tinyurl.com/2yc8y3.
Peanuts in Washington: not as crazy as it sounds.
eXtension Web Site Launches
eXtension, a national Web resource that brings the knowledge and resources of the nation’s land-grant universities to one site, will be formally launched Feb. 21 as part of the 2008 Agricultural Outlook Forum in Washington, D.C.
Secretary of Agriculture Ed Shafer is scheduled to “cut the ribbon” during a ceremony, scheduled for noon Pacific Standard Time.
eXtension provides space where content providers from across the nation’s Extension system can join together to produce new information and educational resources on a wide range of topics.
“Users will be able to tap into the knowledge and expertise of 75 Extension organizations across the country 24 hours a day, seven days a week, to get credible, research-based answers to questions they have and dynamic learning modules,” said Linda Kirk Fox, associate vice president and dean of WSU Extension.
The site features customized answers to meet specific needs; a searchable knowledge base and “Ask the Experts” options; contact with more than 3,000 local county extension offices across the nation; as well as community building features, including blogs, online chats, content evaluation, rating and more.
Visit the new eXtension Web site at: http://www.extension.org/.
