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Agronomy Day 2009

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Tour A

The Naked Truth: Waterhemp’s DNA Revealed

Patrick Tranel
Patrick Tranel
Professor of Molecular Weed Science
Department of Crop Sciences

Waterhemp (Amaranthus tuberculatus) is a weed that needs no introduction to Illinois farmers. Its biological characteristics combined with its propensity to evolve resistance to herbicides have caused more than one farmer to awake in the middle of the night in a cold sweat. Not surprisingly, it continues to receive significant attention by weed scientists at the University of Illinois.

A revolution that has taken place in biological research over the past few years is what is called next-generation sequencing technology. This technology has made DNA sequencing dramatically faster and more affordable. A small genome sequencing project that might have cost $1 million and taken years to complete just a couple of years ago can now be done for about $10,000 in a matter of weeks. What this means is that sophisticated genomics research that previously was cost prohibitive for researchers studying anything but the most “important” organisms (e.g., humans, E. coli, fruit flies, and Arabidopsis) is now accessible even to the lowly weed scientist.

Through funding provided in large part by the Illinois Soybean Association, next-generation sequencing technology has been applied to waterhemp. We obtained over 150 million nucleotides of waterhemp DNA sequence. Although this represents only about one-fifth of the total waterhemp genome, actual genes (rather than intervening “junk” DNA, which makes up a large portion of the genome) were selectively targeted for much of the sequencing. Thus, we now have DNA sequence for most of waterhemp’s genes.

Such a wealth of data is wonderful and exciting to a scientist, but how does this information help us to manage waterhemp? One example, which will be discussed in detail, is in diagnosing herbicide-resistant populations. Now that we have DNA sequence information for essentially every currently known herbicide target site gene, it is relatively easy to identify specific mutations that confer target-site resistance. In fact, we are now positioned to do this even for herbicides to which we currently do not yet have resistance. For example, waterhemp with resistance to the bleaching herbicides such as Balance, Callisto, Impact, and Laudis has not yet been reported. The growing popularity of this class of herbicides foreshadows the evolution of waterhemp populations with resistance to them. Since we now have DNA sequence for the gene encoding the target site (HPPD), we will be ready to investigate this resistance when it occurs. Similarly, we have sequence of the glutamine synthetase gene, which encodes the target site of glufosinate (Liberty and Ignite) and thus we will be better prepared to address resistance issues in waterhemp should glufosinateresistant soybean become more common across the Illinois landscape.

From a practical point of view, DNA sequence information of herbicide target-site genes and identification of specific mutations or changes within these genes that confer herbicide resistance enable the development of rapid tests for resistance confirmation. For example, we developed a lab-based assay to identify resistance to protox-inhibiting herbicides (e.g., Cobra, Flexstar, Blazer) in waterhemp, and have used this to test numerous samples sent to us by farmers, technical reps, etc. Currently, we are in the process of developing a lab-based assay to identify glyphosateresistant waterhemp plants.

Herbicide resistance is but one realm in which waterhemp DNA sequence information will contribute to management of this species. One thing we can be sure of: waterhemp will continue to evolve and confront farmers with management challenges. Sophisticated science is needed for this sophisticated weed.

change and challenge