Understanding how weeds are resistant to herbicides
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 U of I. 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.
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.
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."
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," said Tranel.
Original publication: "Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology"; Weed Science 2009.
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