El Batán, Mexico
September 3, 2007
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CIMMYT's
biotechnology team with one of the new
genotyping machines. |
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Source: CIMMYT E-News, vol
4 no.
8, August 2007
A quiet revolution is taking place
in CIMMYT’s biotechnology
labs. The team has just received a new generation of genotyping
machines. These semi-automated work-horses will make it much
easier to determine whether breeding lines contain specific
useful genes. It is hoped that this will help maize and wheat
breeders—through a process known as marker-assisted selection
(MAS)—to make breeding more effective and get crop varieties
with valuable traits to poor farmers more quickly.
Traditionally, the only way to find out whether the offspring
from a particular cross have inherited useful characteristics,
such as drought tolerance, disease resistance, or grain quality,
has been to grow them in the field and evaluate the adult
plants. MAS can speed up the breeding process, since it makes it
possible to track the presence of desired genes in every
generation. This does not bypass the need for field evaluation,
but can greatly improve the efficiency of the process. “Field
screening takes time, space, and resources, and our capacity is
limited,” explains CIMMYT maize breeder Gary Atlin, “but with
MAS we could use resources more effectively, zeroing in on the
best lines to test in the field and filtering out those that
haven’t inherited the characteristics we need.”
When researchers want to find out whether a particular line of
wheat or maize has the useful version of a gene (for example,
disease resistance rather than disease susceptibility), they use
nearby, identifiable sections of DNA known as markers, labeled
with a fluorescent dye. Different versions of markers and genes
are called alleles. DNA that is close together on the chromosome
tends to stay together over generations, so a specific allele of
a marker will be routinely inherited alongside the desired
allele of a nearby gene. Using the new capillary electrophoresis
genotyping machines, the sample is forced along a narrow
capillary tube under the influence of an electric current. A
laser at the end of the tube detects the different alleles of
the fluorescent markers, indicating to the scientist whether the
sample contains the allele they want.
The two ABI 3700 machines have been generously donated to CIMMYT
by DuPont through its
Pioneer Hi-Bred seed
business, reflecting a fruitful collaborative relationship of
more than a decade’s standing. Until now, CIMMYT has run most of
its marker-assisted selection work on manual, gel-based
electrophoresis apparatuses. In addition, analyses of genetic
relationships between different wheat or maize lines have been
run on older ABI genotyping machines, including two based on the
previous, much slower generation of gel-based machines. The new
machines can handle many more samples—96 each at a time—but it’s
the savings in hands-on time that makes the real difference.
“There’s no comparison,” says
Marilyn Warburton,
Head of CIMMYT’s Applied Biotechnology Center. “It will take us
ten minutes to load one of these new machines, whereas it takes
about four hours to make and load a manual electrophoresis gel.”
As well as being much quicker and less labor-intensive,
capillary electrophoresis makes it possible to test for more
than one marker and run more than one sample at once in each
tube. By using different colors of fluorescent dye for each
sample, markers for each can be distinguished, like teams of
runners wearing different-colored jerseys. For maximum
efficiency, scientists can also set up groups of samples to run
at slightly different times, like runners set off in a staggered
start. CIMMYT will even be able to develop a new type of marker,
known as SNPs, which allow numerous traits to be tested
simultaneously, providing more information per sample.
All of this means that the new machines have a much higher
throughput capacity, and can process many more samples for the
same labor input, drastically reducing the per-sample
cost—currently the major constraint on use of MAS. “If MAS were
significantly cheaper, I would certainly use it in maize
breeding,” says Atlin. “Effectively, it lets you quickly
transfer the genes you want into improved varieties. If you’re
doing a backcross between a donor with a desired trait and an
improved parent with good agronomic performance, you’re trying
to select for one characteristic from the donor, but against all
its other genes. With a number of markers, MAS makes it possible
to determine exactly which progeny combine the desired gene from
the donor with the good genes from the other parent. You can get
results in two generations, compared to four or five normally.”
The challenge for MAS is finding genes with substantial effects,
especially for complex traits such as drought tolerance in
maize. Atlin believes such genes are still to be found. “In the
past, donors with a single useful gene or trait but otherwise
poor agronomic qualities were very difficult to use in breeding,
as they introduced so much bad material. We can get rid of that
useless material through MAS. That opens up the field to look
for useful genes in a wider range of parents. And genotyping
technology is getting cheaper and better at finding genes all
the time.”
In wheat, the hunt for useful markers at CIMMYT is more
advanced. “We’re working with new markers to select for nematode
resistance, leaf and stem rust resistance, boron tolerance,
Fusarium resistance, and grain quality,” says Susanne
Dreisigacker, CIMMYT wheat molecular biologist. “Our current
work is all gel-based, which means running tests sample by
sample and marker by marker. Being able to run many samples at
the same time will make a huge difference.”
Other news
from DuPont |
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