Searching the Genetic Landscape of Tree Fruit
“Apple breeding is like looking for a needle in a haystack,” says Bruce Barritt, the scientist who leads WSU’s apple breeding program.
“We work with huge populations of seedlings,” Barritt says, looking for desirable traits: the apple that is crisp, tart yet sweet, and pleasing to the eye. “It’s all about the consumer,” he adds. “We use the molecular tools available to make the selection process more efficient.”
Barritt’s “haystack” is the thousands of trees he sorts through in the search for new varieties. Meanwhile, some of his colleagues are searching through a very different kind of haystack: the genomes of members of the plant family rosaceae.
Rosaceae includes Washington’s largest crop—apples—as well as cherries, peaches, berries, almonds, roses and some 4,000 other species. In terms of economic value, rosaceae is the third most important family in temperate regions of the world, including the U.S., where its aggregate wholesale value is approximately $7 billion. “Apples are a $1 billion crop in Washington alone,” says Barritt.
A team effort
“We are looking at 250,000 gene fragments and pulling out what’s meaningful,” says WSU bioinformaticist Dorrie Main. Bioinformatics is a relatively new science that employs computer databases to manage huge amounts of biological information.
The meaningful gene fragments pulled from the haystack are then turned over to horticultural genomicists Amit Dhingra and Cameron Peace, both assistant professors and scientists in WSU’s Department of Horticulture and Landscape Architecture.
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 their fields and orchards that guide us in our research.”
The scientists are able to zero in on desirable traits using a technique called marker-assisted selection. A marker is simply a recognizable feature of the genetic landscape that is associated with a trait of interest.
The texture of an apple—how firm, crisp and juicy it is—is indicated by genes that code for a plant hormone called ethylene. The tartness of an apple is produced by malic acid, which also is correlated with a specific gene. Some characteristics, though, such as sweetness or size, are not so easy to locate on the genetic landscape.
Genetic markers for sweetness have to be “teased out of the genome,” says Barritt.
Traditional variety breeding requires scientists to wait up to ten years to see the fruit a selected tree bears. The process is not only painfully slow but expensive, too. Marker-assisted selection speeds up the process, greatly increasing the efficiency of the breeding program. “It’s still a work in process,” Barritt says, “but we have
an incredible team.” -Brian Clark
There's a haystack in there: mapping of the apple genome
was scheduled to be completed this summer. The human genome is made up of more than 3 billion base pairs, while the apple's is a mere 750 million pairs in length. (A base pair is a rung on the ladder of the DNA molecule.) But if you think size matters, consider this: at 6 billion base pairs, the tiny amoeba's genome is twice the size of ours.
(Photo courtesy of Wikimedia/Creative Commons.)
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