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Home > iSGTW 09 April 2008 > iSGTW Feature - Wonderful wheats: automating the search for new genes

 

Feature - Wonderful wheats: automating the search for new genes


How will growers meet the increasing demands for high quality food and feed produced in an environmentally sensitive, sustainable, and profitable manner? Engineering new wheat variety will allow for wheat cultivation to be transformed in the same way as maize, rice and soyabeans cultivation.
Stock images from sxc.hu

Providing vital food for billions of people, wheat cannot afford a sick-day off. It must resist new diseases, adapt to environmental change and flourish in the face of viruses, bacteria, insects and fungi.

Cultivated since the dawn of civilization, wheat must now enter the 21st century.

The race for survival

The keys to flourishing wheat fields are diverse and effective genes, found in wheat’s gargantuan genetic toolbox: a DNA collection containing an astounding 17 billion base pairs.

“If you can find the right genes and the right alleles for a given genome, you can select the qualities you want in a new wheat variety,” says Philippe Leroy of Génétique Diversité & Ecophysiologie des Céréales in Clermont-Ferrand, France.

“You don’t cultivate the same type of wheat in the North of Europe as the South of Europe or as in China,” Leroy explains. “Each area has its own strains, its own diseases and climate, and therefore each needs its own wheat varieties.” 

Wheat is usually hexaploid, having six copies of each gene, where most creatures only have two. Its DNA contains an astounding 17 billion base pairs. Rice has only around 400 million base pairs; humans comprise just 3 billion base pairs.
Images courtesy of Flickr

Hunting for the right stuff

To streamline the gene selection process, Leroy and his colleagues, Matthieu Reichstadt and Franck Giacomoni, are developing a system that automates the hunt for new genes in the wheat genome.

Called the TriAnnotPipeline, the project is part of the International Wheat Genome Sequencing Consortium, which aims to accelerate the creation of new wheat varieties.

These new varieties can be engineered to be more resilient to environmental change or better suited to other uses, such as bio-fuel, Leroy says.

After sequencing, the TriAnnotPipeline automatically searches databases for genes common to other crops, and also notes sequences that look like new genes. Researchers can then isolate these areas of interest for further study.

A lengthy process, Leroy admits, but worth it to help ensure our grandchildren can enjoy their bread and pasta as much as we do.

The TriAnnotPipeline project began in 2002 and is available on several computing platforms, including the AuverGrid, in Clermont-Ferrand, France. Since 2006 the TriAnnotPipeline has been supported by a European grant called LifeGrid, coordinated by the Conseil Regional d’Auvergne in France.

TriAnnotPipeline recently presented at the EGEE User Forum in France.

- Danielle Venton, EGEE

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