Creating a comprehensive functional genomic map for plants

What allows certain plants to survive freezing and thrive in the Canadian climate, while others are sensitive to 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.

A major step forward in understanding this process lies in a genomic map produced by an international consortium led by scientists from the University of Toronto and McGill University published online June 30 in the journal Nature Genetics.

The map, which is the first of its kind in plants, will help scientists to localize regulatory regions in the genomes of crop species such as canola, a major crop in Canada, say researchers who worked on the project. 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 do not appear to encode proteins.

“Plants are complicated organisms, and they have many types of cells and structures,” said Annabelle Haudry, one of the study’s lead authors and former U of T postdoctoral fellow. “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,” said Robert Williamson, U of T PhD student and study co-author. (Convergent evolution is the scientific term for biological traits that arrive through different evolutionary lineages.) Work is underway 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,” said Assistant Professor Alan Moses of U of T 's Department of Cell and Systems Biology, who was 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 published in Nature Genetics 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,” said Associate Professor Stephen Wright of U of T's Department of Ecology & Evolutionary Biology, another leader of the study. “But our analysis allows for identification of the tens of thousands of ‘needles in the haystack’ that are important for gene regulation.”

Funding for the research was provided by Genome Canada and Génome Québec, along with the European Regional Development Fund, the Czech Science Foundation and the National Science Foundation.