Canada
August 5, 2009
Wheat breeders that used to search
through binders of data can now make genetic comparisons with
the click of a mouse, thanks to software developments and a gene
mapping database funded by the
Western Grains Research Foundation (WGRF) Endowment Fund.
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. Dr. 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."
Ag Canada had a bioinformatics specialist, Travis Banks, working
in Winnipeg. Somers would present a concept or idea to Banks
about a specific issue and Banks would develop software to fix
it.
"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 vs short or early vs 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 of 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.
"It's software that is graphical, that allows us to compare
genetic maps, side by side. That's an important feature. You
have to be able to compare one map to the next," he says.
"MAV has been used to archive maps, archive information behind
the maps and do comparative mapping. It took well over two years
to fine tune it, but it's also useful for any crop species.
We've given it to groups using it in rye, corn, barley, canola
and I've even used it for grapes."
"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."
Plant breeders across Canada are now using the software to do
association mapping. Somers says the durum breeder in Saskatoon
has used the MAV to map out certain genes that affect semolina
color, but also found other genomic regions based on association
mapping, that controlled that trait.
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 email it to
other breeders. It's much different than how they used to do it.
"We have had good success on both objectives. The MAV and
related free software are used routinely and have been widely
praised by both the domestic and international wheat
communities. We continue to populate the MAV software with maps
and microsatellite information. It's the primary location to
store all this critical information," says Somers.
"The allele database is now complete and it will take a few
years of analysis and expansion of both genotype and phenotype
datasets to fully realize the potential of this resource. Early
indications, using semolina colour, plant height and leaf rust
resistance show association mapping is possible, which will
enable researchers to discover genes controlling traits in an
more efficient manner."
The Endowment Fund, the original core fund of WGRF, has
supported more than 200 research projects since 1983. |
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