Deciphering the Mechanism of Glyphosate Resistance in Amaranthus palmeri by Cytogenomics

In agriculture, various chemicals are used to control the weeds. Out of which, glyphosate is an important herbicide invariably used in the cultivation of glyphosate-resistant crops to control weeds. Overuse of glyphosate results in the evolution of glyphosate-resistant weeds. Evolution of glyphosate resistance (GR) in <i>Amaranthus palmeri</i> (AP) is a serious concern in the USA. Investigation of the mechanism of GR in AP identified different resistance mechanisms of which <i>5-enolpyruvylshikimate-3-phosphate synthase</i> (<i>EPSPS</i>) gene amplification is predominant. Molecular analysis of GR AP identified the presence of a 5- to &#x3e;160-fold increase in copies of the <i>EPSPS</i> gene than in a glyphosate-susceptible (GS) population. This increased copy number of the <i>EPSPS</i> gene increased the genome size ranging from 3.5 to 11.8%, depending on the copy number compared to the genome size of GS AP. FISH analysis using a 399-kb <i>EPSPS</i> cassette derived from bacterial artificial chromosomes (BACs) as probes identified that amplified <i>EPSPS</i> copies in GR AP exist in extrachromosomal circular DNA (eccDNA) in addition to the native copy in the chromosome. The <i>EPSPS</i> gene-containing eccDNA having a size of ∼400 kb is termed <i>EPSPS</i>-eccDNA and showed somatic mosacism in size and copy number. <i>EPSPS</i>-eccDNA has a genetic mechanism to tether randomly to mitotic or meiotic chromosomes during cell division or gamete formation and is inherited to daughter cells or progeny generating copy number variation. These eccDNAs are stable genetic elements that can replicate and exist independently. The genomic characterization of the <i>EPSPS</i> locus, along with the flanking regions, identified the presence of a complex array of repeats and mobile genetic elements. The cytogenomics approach in understanding the biology of <i>EPSPS</i>-eccDNA sheds light on various characteristics of <i>EPSPS</i>-eccDNA that favor GR in AP.

Biochemical and Rapid Molecular Analyses to Identify Glyphosate Resistance in Lolium spp.

Lolium spp. are troublesome weeds mainly found in winter cereal crops worldwide, including Europe. In recent years resistant mechanisms have been evolved to several important herbicides. In this study we investigated the mechanisms responsible for conferring glyphosate resistance in some Lolium spp. populations. A holistic approach was used, based on dose-response experiments, determination of shikimic acid concentration in plant leaf tissue, as well as molecular analyses. More specifically, in three Lolium spp. populations the existence of a mutation in the Pro-106 codon of the 5-enolpyruvylshikimate-3 phosphate synthase (EPSPS) gene was investigated as well as the relative transcript levels of four ABC-transporter genes were monitored at three time points after glyphosate application. The results demonstrated that glyphosate resistance is a multifactor phenomenon. Relative transcript levels of the ABC-transporter genes were abundant at very early time points after glyphosate treatments. Dose-response experiments and shikimate analyses were in accordance with the findings of the quantitative PCR (qPCR) analyses. We suggest that relative expression ratio of ABC-transporter genes can be a useful tool to rapidly identify Lolium spp. populations resistant to glyphosate.

UAV-Assisted Thermal Infrared and Multispectral Imaging of Weed Canopies for Glyphosate Resistance Detection

The foundation of contemporary weed management practices in many parts of the world is glyphosate. However, dependency on the effectiveness of herbicide practices has led to overuse through continuous growth of crops resistant to a single mode of action. In order to provide a cost-effective weed management strategy that does not promote glyphosate-resistant weed biotypes, differences between resistant and susceptible biotypes have to be identified accurately in the field conditions. Unmanned Aerial Vehicle (UAV)-assisted thermal and multispectral remote sensing has potential for detecting biophysical characteristics of weed biotypes during the growing season, which includes distinguishing glyphosate-susceptible and glyphosate-resistant weed populations based on canopy temperature and deep learning driven weed identification algorithms. The objective of this study was to identify herbicide resistance after glyphosate application in true field conditions by analyzing the UAV-acquired thermal and multispectral response of kochia, waterhemp, redroot pigweed, and common ragweed. The data were processed in ArcGIS for raster classification as well as spectral comparison of glyphosate-resistant and glyphosate-susceptible weeds. The classification accuracy between the sensors and classification methods of maximum likelihood, random trees, and Support Vector Machine (SVM) were compared. The random trees classifier performed the best at 4 days after application (DAA) for kochia with 62.9% accuracy. The maximum likelihood classifier provided the highest performing result out of all classification methods with an accuracy of 75.2%. A commendable classification was made at 8 DAA where the random trees classifier attained an accuracy of 87.2%. However, thermal reflectance measurements as a predictor for glyphosate resistance within weed populations in field condition was unreliable due to its susceptibility to environmental conditions. Normalized Difference Vegetation Index (NDVI) and a composite reflectance of 842 nm, 705 nm, and 740 nm wavelength managed to provide better classification results than thermal in most cases.

How Many Ways Can Nature Kill the Goose That Laid the Golden Egg? – The Many Mechanisms of Evolved Glyphosate Resistance

Weeding has been the bane of humanity since the dawn of agriculture. For about 70 years, synthetic herbicides have removed much of the drudgery of this onerous task. Glyphosate was introduced as a non-selective herbicide in 1974. Its ideal properties made it a very popular herbicide, and the introduction of glyphosate-resistant (GR) crops allowed its use as a selective herbicide, greatly expanding its use to become the most used herbicide on earth. For farmers who used glyphosate in GR crops, it was the golden age of weed management, as this technology significantly improved the efficacy and reduced the cost of weed management. Weed management was also simplified, an asset that was particularly valuable to part-time farmers. Furthermore, this technology provided the environmental benefits (reduced soil loss and fossil fuel use) of significantly reducing tillage. Farmers saved billions of US$, and weed management became more effective and simple. Indeed, to many farmers, glyphosate with GR crops became the goose that laid the golden egg. After more than 20 years of use, the first cases of GR weeds were reported in the latter 1990s. After a lag period of less than 10 years after the first GR weed was reported, the number of species reported to have evolved glyphosate resistance began to increase in a linear fashion, reaching 53 species in 2021, third only to atrazine (66 species), a much older herbicide and to ALS inhibitors (168 species), which include several different herbicides used in numerous crops since the 1980s. The long lag phase before any resistance was detected led some to believe by the mid-1990s that evolution of resistance was improbable. By this time, glyphosate use was greatly increasing, especially in GR crops, an ideal situation for the evolution of resistance. After this, the number of glyphosate-resistance cases exploded, and the mechanisms of resistance to many of these cases of resistance were determined. A recent, short commentary detailed these mechanisms after a new mechanism of resistance was reported. The number of mechanisms for resistance to no other herbicide comes close to those of glyphosate. In the present paper, we briefly describe the many evolved mechanisms by which weeds have evolved resistance to glyphosate.

Rapid increase in glyphosate resistance and confirmation of dicamba-resistant kochia (Bassia scoparia) in Manitoba

Increased adoption of crops with stacked traits conferring glyphosate and dicamba resistance, and recent confirmation of kochia [<i>Bassia scoparia</i> (L.) A.J. Scott] biotypes resistant to these herbicides in Alberta and Saskatchewan, warrant surveillance of herbicide-resistant kochia in Manitoba. A randomized-stratified survey of 315 sites in Manitoba was conducted in the fall of 2018. Overall, 58% of the kochia populations tested were glyphosate-resistant, while 1% were dicamba-resistant. This survey documents rapid increase in glyphosate-resistant kochia over a five-year time frame, and also confirms the first cases of kochia in Manitoba with dicamba resistance alone and in combination with glyphosate resistance.