Berry pinch-hits as genome surrogate

U. ILLINOIS (US) — The completed genome sequence of the woodland strawberry is being used to speed up research on more complex fruits, including apples and peaches.

“The woodland strawberry is a good surrogate system for genetic studies of other fruits in the same Rosaceae family,” says Schuyler Korban, professor of molecular genetics and biotechnology at the University of Illinois.

“With the complete genome sequence of the woodland strawberry in hand, we can use the strategy of comparative genomics to investigate  similarities and differences between strawberry and apple or strawberry and peach, among others, to learn more about genes involved in various traits, such as fruiting and fruit quality.

“We can also use the strawberry to do functional genomic studies.  It also provides us with a larger tool box to do more targeted breeding and can be compared side-by-side with the already sequenced genome of the apple to identify genes that control certain traits such as flavor, nutritional composition, and flowering time.”

The research is published in journal Nature Genetics.

The woodland strawberry, Fragaria vesca, or F. vesca, is the second smallest plant genome to be sequenced. The smallest plant genome sequenced is that of Arabidopsis.

“Arabidopsis is used a lot as a model plant species for pursuing genetic and physiological studies because you can get results very quickly, but it produces pods, called siliques, rather than fruit,” Korban says.

“I wanted a fruit model system so that I can evaluate the function of apple genes that control various fruit traits such as those for flavor, texture, aroma, and other characteristics in a short period of time, and strawberry is a great model to pursue such studies.”

The cultivated variety of the strawberry has not been sequenced yet. “The reason we chose the woodland strawberry is because it is a diploid, that is, it has two sets of chromosomes, whereas the garden or cultivated strawberry is an octoploid with eight sets of chromosomes so it’s much more difficult to sequence.”

The strawberry sequencing was done using short-reads, short fragments of the strawberry genome.

“We actually used three different technologies that all produced short-reads of the sequence,” Korban says. The short-reads are difficult to assemble—like stitching together a series of photos to create one panoramic view.

“After the fragments are strung together, you anchor them against the chromosomes—the genetic map of the strawberry—to make sure that that they are in the correct order.”

By knowing genes, their structure and function, researchers can control and/or regulate how they are expressed in a plant.

“If one fruit has a higher sugar-acid ratio, for example, we can focus on the gene(s) that produce this variation.”

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