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New Software Speeds Plant Breeding Efficiency

Two Agriculture and Agri-Food Canada (AAFC) scientists have developed software that allows researchers to make genetic comparisons on varieties with the click of a mouse.

Software developments and a gene-mapping database funded by the Western Grains Research Foundation Endowment Fund are expected to vastly decrease the amount of time spent sorting through data to make genetic selections.

Daryl Somers, director of applied genomics at the Vineland Research and Innovation Centre in Vineland Station, Ontario, was working at Agriculture and Agri-Food Canada’s Cereal Research Centre in Winnipeg when he led the project. Somers collaborated on the project with a bioinformaticist, Travis Banks from the Agriculture and Agri-Food Canada Cereal Research Centre in Winnipeg.

“We were generating quite a lot of data related to DNA fingerprinting or plant genotyping. We were using that data to develop genetic maps of wheat and it occurred to me at the time that we didn’t have any great software tools to manage that data, or to give easier access to the data,” says Somers.

“We had a lot of hard copies of this information in many binders of paper in the lab. It was well organized, but when you needed a piece of information you had to get a binder down and have a look.”

Winnipeg-based Ag Canada bioinformatics specialist, Travis Banks would develop software to help address concepts or ideas Somers presented.

“In the human genetics field, there was a lot of research coming out on a topic called association mapping. It became clear in the plant world that we may be able to use association mapping to map traits to the genome. So part of the project included taking the wheat genome and attempting to create a genotyping allele database that would permit association mapping,” says Somers.

The project focused on Hard Red Spring wheat and durum wheat, producing a reference database for wheat breeders.

“It gives a whole genome fingerprint of wheat. You can tell one variety from the next very easily and you can tell what parts of the genome are different between the varieties. That’s how you start to create the associations,” he says.

“If one variety is tall versus short or early versus late, you may be able to distinguish why that is, based on these differences you find in the database. That’s the concept of association analysis.”

Some software used in the project – TASSEL, developed at Cornell University and Structure – was free software for work in corn. Somers and Banks developed additional software, Map Archive Viewer or MAV.

“Now, sitting in front of the computer, technicians and scientists looking for a piece of data that would have taken 25 minutes looking through binders can click within seconds and find what they’re looking for. It created a lot more efficiency in map construction and map archiving,” Somers said.

Plant breeders across Canada are now using the software to do association mapping.

The project produced a tool that other breeders now use in their breeding programs, that significantly changed the way they go about their daily work. They are now able to take graphical information out of the software in digital form and e-mail it to other breeders. It’s much different than how they used to do it.

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