It takes the new science of bioinformatics to find the needle of knowledge in the haystack of information created by a genome map.
In search of the needles that will guide tree-fruit breeders, WSU bioinformaticist Dorrie Main is combing through the haystack of the rosaceae family. Rosaceae includes the rose but, more important, Washington’s largest crop apples – as well as others important to the state, like cherries, peaches, berries 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 approximately $7 billion.
Mining the database
“We take all of the known genes in the public gene bank and analyze them based on function,” said Main, associate professor of horticulture and a scientist in the WSU Agricultural Research Center. “We are looking at 250,000 gene fragments and pulling out what’s meaningful.”
“We take all of the known genes in the public gene bank and analyze them based on function,” said Main, associate professor of horticulture and a scientist in the WSU Agricultural Research Center. “We are looking at 250,000 gene fragments and pulling out what’s meaningful.”
A self-identified “data miner,” Main uses a 128-processor computer to store and evaluate the international genome database for rosaceae, the repository for the rapidly growing haystack of genetic information about the family.
The meaningful needles pulled from the haystack are then turned over to horticultural genomicists Amit Dhingra and Cameron Peace, both assistant professors and scientists in the WSU department of horticulture.
Finding desirable traits
“Tree-fruit genomics,” said Dhingra, “is dedicated to the task of developing useful new varieties based on a large body of knowledge. It’s so large that we need bioinformaticists like Dorrie and her computers to narrow the search.”
“Tree-fruit genomics,” said Dhingra, “is dedicated to the task of developing useful new varieties based on a large body of knowledge. It’s so large that we need bioinformaticists like Dorrie and her computers to narrow the search.”
The two genomicists work with growers to identify desirable traits.
“Growers are the real scientists,” said Dhingra. “They have all sorts of knowledge gained in the fields and orchards that guide us in our research.
Basically, though, what we’re all looking for are new varieties that can resist stress – the stress from pests, diseases, climate and so on. The growers know what they want. We want to help them get there.”
