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Understanding gene function

Researchers are opening new paths for crop breeders.


November 15, 2007
By Helen McMenamin

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60aCanadian scientists have succeeded in uncovering many of the genes encoded
in the genetic material of wheat and canola. It is a huge task: wheat has a
vast amount of genetic material, with three sets of seven pairs of chromosomes
for a total of 42 chromosomes in each cell and each of the three sets of chromosomes
has 55,000 to 60,000 genes.

The scientists have made great progress as 11 different groups across the country
worked together to identify a significant number of the genes encoded in all
that genetic material in less than three years. New robotic techniques developed
for the human genome project have helped.

To a molecular geneticist, the gene sequence is like finally having a full
set of tools. "We can use the new information to identify the genes involved
in particular plant functions," says André Laroche, leader of the
gene identification team at Agriculture and Agri-Food Canada in Lethbridge.
"That will help us transfer specific characteristics into new varieties."

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Laroche's group is interested in enhancing crop responses to cold stress. They
have looked at genes that are active under stressful conditions and cold-hardening
in winter wheat.

Scientists can 'read' the DNA code from gene sequencing machines that identify
the units which make up the genetic code of thousands of fragments of DNA. Computer
programs overlay the small fragments to identify genes from segments of genetic
material. The chemical characterization of the DNA segments are grouped in electronic
databases.

Sequencing genes is only the first step. The next step is to tie genes to specific
activities in the plant, to find the specific function of each gene in a cell
and in a plant. This is complicated because not every gene is expressed, at
least not all the time. Many genes work together with some regulating or limiting
others. For example, winter wheat seedlings produce particular proteins when
exposed to low temperatures. By comparing proteins produced in treated and control
seedlings, researchers gain an understanding of the processes involved in hardening
of plants in fall.

"Even more important, we can see how gene activity is co-ordinated,"
says Laroche. "In complex plant functions like the development of winter-hardiness,
activation of a single gene may have a domino effect that sets off a whole cascade
of interactions."

To study the many genes that work in parallel, scientists have a new tool called
a gene chip or gene micro-array. It is a plastic wafer about half the size of
a credit card impregnated with up to 20,000 gene samples. Active genes bind
to the matching samples and can be identified and measured with a specialized
computer system.

By applying preparations from wheat seedlings exposed to different periods
of winter hardening conditions, scientists can track which genes are involved
and in what order. "Instead of looking at only one gene, we can see a large
proportion of the expressed genes," says Laroche. "We can work with
thousands of genes at the same time and see how their expression is co-ordinated.
This enables us to choose the most interesting genes to study."

So far, about 25 percent of the genes in wheat have been linked to specific
proteins. By continually comparing information sets, or libraries, developed
from different varieties and differently treated plants, scientists are gaining
a better understanding of plant processes.

When the geneticists believe a gene is particularly important, they study it
in a whole plant by inserting it into a plant embryo and regenerate the plant
in a controlled environment. These plants express the gene all the time rather
than only under specific conditions, so the trait can be studied.

The study of genes and their role in controlling the organism's function, known
as functional genomics, may dramatically change plant breeding. "Until
now, we've been working to improve crops seeing only the tip of the iceberg,"
says Laroche. "I won't say we see the whole picture yet. But, we can see
more of the iceberg than ever before.

"Until the last few years, molecular geneticists worked on one or two
genes for their whole careers. Now, we can look at virtually all the genes of
wheat at the same time. We have a much better chance of incorporating all the
genes we need in a new breeding line." -30-