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Atlas maps 90,000 gene switches in plants

U. TORONTO (CAN) — A new genomic map may help explain why some plants can survive a freeze and others are sensitive to even the slightest drop in temperature.

Those that flourish activate specific genes at just the right time—but the way gene activation is controlled remains poorly understood.

The map, which is the first of its kind in plants, will help scientists localize regulatory regions in the genomes of crop species such as canola, a major crop in Canada.


“Amazingly, similar organization of switches was found for the genes that control early human development from an embryo—an example of convergent evolution,” says Robert Williamson. (Credit: onigiri-kun/Flickr)

The team has sequenced the genomes of several crucifers (a large plant family that includes a number of other food crops) and analyzed them along with previously published genomes to map more than 90,000 genomic regions that have been highly conserved but that don’t appear to encode proteins.

“Plants are complicated organisms, and they have many types of cells and structures,” says Annabelle Haudry, a former postdoctoral fellow at the University of Toronto and a lead author of a the study published in Nature Genetics.

“We found that genes involved in defining how these cells and structures grow as the plant develops from a seed and how it responds to environment’s stimuli are surrounded by many of these switches.”

“Amazingly, similar organization of switches was found for the genes that control early human development from an embryo—an example of convergent evolution,” says Robert Williamson, PhD student and study coauthor.

Convergent evolution is the scientific term for biological traits that arrive through different evolutionary lineages. Work is currently under way to identify which of those regions may be involved in controlling traits of particular importance to farmers.

“The study also weighs in on a major debate among biologists, concerning how much of an organism’s genome has important functions in a cell, and how much is ‘junk DNA,’ merely along for the ride,” says Professor Alan Moses, also involved in the study.

While stretches of the genome that code for proteins are relatively easy to identify, many other ‘noncoding‘ regions may be important for regulating genes, activating them in the right tissue and under the right conditions.

While humans and plants have very similar numbers of protein-coding genes, the map  further suggests that the regulatory sequences controlling plant genes are far simpler, with a level of complexity between that of fungi and microscopic worms.

“Plants seem to have a large fraction of their genome that is junk DNA,” says Professor Stephen Wright. “But our analysis allows for identification of the tens of thousands of ‘needles in the haystack’ that are important for gene regulation.”

Genome Canada and Génome Québec supported the project, along with the European Regional Development Fund, the Czech Science Foundation, and the National Science Foundation.

Source: University of Toronto

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