Urbana, Illinois, USA
August 5, 2009
In a little over seven hours,
University of Illinois weed scientist Patrick Tranel got more
genetic information about waterhemp than in two years time in a
lab. The genetic information was obtained using pyrosequencing
technology in the Keck Center at the
University of Illinois. The
genetic sequence will allow scientists to study herbicide
resistance in waterhemp.
Ten years ago genomics was reserved for what Tranel refers to as
"important species" such as humans, cows, fruit flies, and mice.
"That's changed now that those species have been sequenced. Now
we can start doing genomics on weeds to start understanding
weeds better.
"With this type of technology, you can generate all of this
genomic data relatively cheaply and quickly, so it's worthwhile
doing in some of these non-model species like weeds. We're able
to start generating data now that five years ago would have been
cost-prohibitive." Tranel believes waterhemp is the first weed
to be partially sequenced using this technology.
The pyrosequencing machine emits a light signal that's captured
every time a nucleotide is incorporated into a growing DNA
strand. "The reason it's so fast is that it's done in parallel,"
said Tranel. "The plate has thousands of tiny wells, and a
sequencing reaction going on in every one of them
simultaneously. There's a camera that monitors the light for
each of these wells simultaneously and so in one seven and a
half hour run you generate a million reads."
Tranel explained that although more traditional herbicide
resistance research takes years, it's more gene-specific. "We
sampled plants, brought them back to the green house, grew them
up, confirmed that they were resistant and then we started
crossing a resistant plant with a sensitive plant. We look at
its progeny to see if the resistance is inherited to understand
the genetics — if it's a dominant trait or a recessive
trait.
"Pyrosequencing is more like just throwing out a fishing net --
we know we're going to get continued resistance to other
herbicides which can affect other genes. And we don't want to
spend two years culling to find that gene every time. This is a
way that we can get all of the genes at once."
All of the data is publically available. "There's a website
where you can go and get the 43 million base pairs of sequence.
So anyone can get it and use that information."
Tranel said that identifying weed resistance is an immediate
outcome of having the genetic data. "Once we obtain the sequence
of a resistance gene, we can develop molecular tests that are
specific for the resistance mutation. "We can take a sample of
waterhemp from a field that was sprayed and the waterhemp hasn't
died and we can confirm whether it is resistant or not because
we know the gene sequence and we know the mutation and the
mechanism."
Having the complete genomic data on waterhemp will help
scientists not only to identify but also to understand
resistance and how resistance evolves. "If you understand how it
evolves, that can help you devise strategies that cannot prevent
it from evolving, but at least slow the rate at which it
happens," Tranel said.
"If you use the same herbicide year after year, you're exerting
selection pressure -- you're selecting for that rare plant or
mutation that will survive. When you do that, and you kill all
of the siblings that are weaker, the mutant survives and all of
its progenies will survive and that's how resistance evolves.
It's evolution in action," Tranel said.
This genomic data will also help in answering broader questions
about weeds such as: Why are some plants weeds? What makes a
plant a weed? Is it certain genes? Is it the way the genes are
expressed?
"These are questions that 10 years ago we couldn't address
because we didn't know the genes. Now we're at the point where
we can start doing that and on a broad scale. We can do this
with waterhemp and we can do this with another weed and we can
compare the two — are there things that these two weeds
have in common that make it different from a corn plant or a
soybean plant which explains why it's weedy? This is sort of a
first step in that direction — starting to generate the
type of information that will allow us to ask these sorts of
questions."
Waterhemp is a Midwestern problem, Tranel said, but it's a
member of the genus Amaranthus which includes weeds that are a
problem worldwide such as pigweeds. "Because they all belong to
the same genus, their genomes are very conserved. So if we have
the sequence for the PPO gene in waterhemp you can use that
information to get the PPO gene in redroot pigweed. It would be
a similar sequence."
Having this information is like building a tool kit, said
Tranel. "We're developing all of these resources and putting
these resources in our freezer. When we have an interest in
resistance to herbicide A which targets enzyme B, we can go to
the freezer, or to the computer and get the sequence of the gene
for that enzyme."
Tranel said that because waterhemp is in the group of amaranthus
weeds, it's a good model for weed genomics. "A weed scientist in
Georgia, where there's a lot of Palmer amaranth — another
pigweed evolving resistance, can go straight to that data base
and get gene sequence data."
Another outcome of having this genomic data is to be able to
design markers — so you can fingerprint individual
waterhemp plants and use that information to do population
genetic studies.
"If you see herbicide resistance in northern Illinois and a year
later you see the same resistance in a population in southern
Illinois, one of the things you want to know in managing
resistance is, did resistance evolve or occur here once and then
a farmer moved a combine and that's how resistance got down
here? Or did resistance occur here and independently down in
southern Illinois?"
Understanding how the resistance occurred has implications for
weed management. "If it's evolving multiple times, you need to
pay attention to what you're doing in your field whereas if it
evolved once and is moving around then you've got to pay
attention to what your neighbors are doing. It's important to
know how it's evolving, how it's spreading.
"If you have these genetic fingerprinting tools, which we're
able to do because of this research, you can go look at these
populations and see, are these genetically similar, which would
suggest that it was a movement event. If they're completely
different, then that would suggest that it's evolving
independently."
Funding for this research was supported by the Illinois Soybean
Association. Sampling the Waterhemp (Amaranthus tuberculatus)
Genome Using Pyrosequencing Technology will be published in a
2009 issue of Weed Science.
Author: Debra Levey Larson |
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