Weed genomics

A group of scientists have been working on gene mapping projects to help answer many of the common questions in weed science: What makes a weed “weedy? What is the genetic basis for herbicide resistance? Can we develop better-targeted weed treatments or alter weeds to make them easier to control?

According to the Weed Science Society of America (WSSA), to date, scientists have mapped the genomes of six weeds known to cause significant crop losses, including horseweed (Erigeron canadensis aka Conyza canadensis), Palmer amaranth (Amaranthus palmeri), waterhemp (Amaranthus tuberculatus), smooth pigweed (Amaranthus hybridus), red rice/feral rice (Oryza sativa), and kochia (Kochia scoparia aka Bassia scoparia). Partial draft genomes are available for at least 35 additional weed species.

Scientists say mapping weed genomes is especially complex due to the high level of repetition typically found in a weed’s DNA.

“It’s like trying to work on a puzzle made up largely of pieces that are precisely the same, but each occupying a unique place in the total picture,” says Eric Patterson, a weed geneticist at Michigan State University. “How do you determine which piece goes where?”

Sorting out the repetitive content can be time consuming and expensive, and it requires the right expertise and tools. However, new technologies are reducing the cost of genome assembly and are helping weed scientists produce more complete and accurate maps of gene sequences.

In addition, efforts are underway to advance weed genomics through collaboration. One example is the International Weed Genomics Consortium, an organization spearheaded by Todd Gaines of Colorado State University with support from weed science colleagues around the globe. Consortium members are working together to set priorities, share tools and resources, and build reference genomes for the world’s most troublesome weed species.

“By deepening our understanding of weeds, we hope to find ways to delay the evolution of resistance and to open the door to new, more sustainable approaches to integrated weed management,” Gaines says.

To date, scientists from the University of Illinois have used their understanding of Palmer amaranth genetics to develop a test that can rapidly screen seed mixtures to detect whether they contain seeds from this troublesome weed. And a team at Scientists at Rothamsted Research conducted a successful lab experiment using what they know about the blackgrass genome. They were able to silence specific genes and make herbicide-resistant blackgrass weeds susceptible to treatment.

The WSSA reports the gene mapping project could determine new and more targeted weed management strategies; how we might alter weed populations to reduce their competitiveness and make them easier to control; understand how to improve a crop’s ability to compete more effectively against weeds; and uncover patterns related to when and where invasive weeds have been introduced and use the information to develop strategies that can limit new introductions.

The science behind the research

The goal of genome mapping is to understand how the various components of the genome (nucleotides) are arranged. With a draft genome, there might be thousands of small, assembled fragments, but how they fit together remains unknown. This fragmentation limits the mapping’s usefulness. In reference genomes, the sequence has been determined. There are uninterrupted segments of DNA with few gaps or errors. Draft genomes with partial assemblies may be sufficient to understand population biology or the evolutionary relationships among weed species. They may also be sufficient to develop molecular level tools for identifying specific weed species. Reference genomes, though, are needed to tackle more complex questions, such as the biology underlying weedy traits and how complex factors interact to produce herbicide resistance.

Scientists have uncovered a wide range of new insights from genome sequencing projects. For example, when Midwest farmers discovered that seed mixes used on Conservation Reserve Program (CRP) acreage contained Palmer amaranth, alarm bells went off. The weed is extremely aggressive and hard to treat. Seed growers needed a way to ensure their mixtures were Palmer amaranth-free. Researchers at the University of Illinois were able to use their understanding of genetics to develop a rapid screening test that can detect the presence of Palmer amaranth DNA in seed mixtures — helping to prevent the introduction of this problematic weed into CRP acreage across the country. In another example, glyphosate-resistant horseweed has caused yield losses of up to 83% in soybean and up to 46% in cotton. Researchers have used genomics to understand how some populations of horseweed in Canada evolved very high levels of glyphosate resistance. They used the information to document the first populations of horseweed in the U.S. that exhibit the same high levels of resistance. It is hoped this early detection can lead to integrated controls that prevent the spread of herbicide-resistant horseweed.

Before gene sequencing, it was hard for scientists to understand the mechanisms involved in the evolution of herbicide resistance. Now they have learned there is no single genetic “cause.” Instead, there are multiple pathways for the evolution of resistant traits, making genetic analysis of troublesome weeds especially important. Researchers have identified five “superfamilies” of genes that are likely involved. They are large, diverse and part of the underlying pathways weeds use to survive the stresses they encounter in their environment.

Photo by Tau’olunga

Genetic differences between male and female weeds can influence the spread of herbicide resistance. Researchers at the University of Illinois have successfully sequenced the DNA for male and female Palmer amaranth and waterhemp plants to identify the genetic basis of sex determination. This reproductive difference promotes outcrossing and genetic diversity, which can promote the evolution and spread of herbicide-resistant populations. Using data sets compiled from sex-specific and sex-biased genome sequences, researchers were able to distinguish between male and female plants from multiple, geographically-distinct Palmer amaranth and waterhemp populations with a 95% or greater accuracy. What does this mean for the future of weed control? Both Palmer amaranth and waterhemp are resistant to multiple herbicides. It is possible to imagine how genes might be modified to ensure all offspring from Palmer amaranth and waterhemp plants growing in a given location would be of the same sex — causing the population to collapse.

Researchers working on the horseweed genome have determined that repeated use of glyphosate has led to multiple mutations that have caused an increased expression of transporter genes and of glutathione S-tranferase and glycosyltransferases enzymes. Understanding the genetic basis of resistance may pave the way for using CRISPR/Cas technology to insert a new gene sequence that would replace those herbicide-resistant traits.

Goosegrass (Eleusine indica) is one of the most common and destructive agricultural weeds in the world. It is incredibly resilient, with the ability to survive extreme drought, heat and low mowing. It also has evolved resistance to at least seven classes of herbicides. An international team of researchers mapped the weed’s genome — an important first step in understanding why goosegrass is so successful and can adapt so quickly. They were able to identify multiple goosegrass genes associated with herbicide resistance. The same team uncovered genetic markers related to disease resistance, drought resistance and other goosegrass traits. Understanding these important pathways may suggest new molecular targets for herbicide development and for other novel weed management strategies.

For more: www.wssa.net

Source: Weed Science Society of America