Fitness Cost Associated With Enhanced EPSPS Gene Copy Number and Glyphosate Resistance in an Amaranthus tuberculatus Population

Inferring herbicide non-target-site cross-resistance from dose response and mixture treatments

BACKGROUND

Herbicide cross-resistance is of increasing concern because it compromises the effectiveness of both existing and new chemical options. However, a common misconception is that if a weed population shows dose-response shifts to two herbicides, it is cross-resistant to both. The possibility that individual plants may possess different resistance mechanisms is often overlooked.

RESULTS

To better characterise non-target-site cross-resistance, we propose that the accession be treated with mixtures of the two herbicides of interest. A population model could be used to simulate the expected dose responses to the mixtures, assuming different cross-resistance levels in the population, as well as synergistic or antagonistic effects between the two herbicides. The simulated responses can then be compared with the actual responses, and the cross-resistance level approximated. We demonstrated this approach from a mathematical standpoint and validated it with experimental data from glasshouse tests on four well-characterised biotypes of Lolium multiflorum and two commercial herbicides, clodinafop and iodosulfuron. Results also showed that understanding chemical interactions such as synergy and antagonism is crucial to a better estimate of cross-resistance levels.

CONCLUSION

Because this method utilises standard dose-response tests, it is potentially easier and less time-consuming than those involving plant cloning or divergent recurrent selection. Quick characterisation of the degree of cross-resistance provides important insights as to whether chemical rotations or mixtures can still effectively control the weed population displaying resistances to multiple herbicides. This approach could be applied more broadly in cross-resistance studies with other xenobiotics. © 2025 Society of Chemical Industry.

Increase in IAA levels by EPSPS copy number variation relates to fitness advantage in Eleusine indica

BACKGROUND

Long-term use of chemical weed control has led to some weedy species evolving herbicide resistance traits with fitness advantage. Our previous studies revealed glyphosate resistance in an Eleusine indica population due to copy number variation of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) comes with fitness advantage under non-competitive conditions. Here, transcriptomics and targeted metabolomics were used to investigate physiological basis associated with the fitness advantage.

RESULTS

Relative copy number of EPSPS gene and plant dry weight of the glyphosate-resistant (R) population was 88.3- and 1.2- times, respectively, higher than that in the wild type (WT) plants that were isolated from within the R population. Seven genes were screened to be relevant to fitness growth trait by RNA-seq. The level of aromatic amino acids Tryptophan (Trp), Phenylalanine (Phe) and Tyrosine (Tyr), products in the shikimate pathway catalyzed by EPSPS, was 1.2-times higher in R compared to the WT plants. The metabolites associated with Trp metabolism indole-3-acetic acid (IAA), 3-indolepropionic acid (IPA), indole-3-acetamide (IAM) in the R plants were 2.0-, 1.8- and 1.4- times higher than that in the WT plants, respectively.

CONCLUSION

All the results indicate that fitness advantage in the studied R E. indica population may be caused by higher IAA production due to over-expression of the EPSPS gene and pleiotropically by elevated carbon metabolism. The findings in this research can provide reference information for control strategies to the glyphosate-resistant E. indica. © 2025 Society of Chemical Industry.

EPSPS gene amplification in a glyphosate-resistant population of Italian ryegrass (Lolium multiflorum) from Oregon

BACKGROUND

Lolium multiflorum Lam. (Italian ryegrass, annual ryegrass) is both a weed and a crop in Oregon. Because it is commonly managed using chemical controls, herbicide-resistant populations have evolved within the seed production region. A glyphosate-resistant population was identified in Yamhill County, Oregon, in a fallow field previously cropped with perennial ryegrass.

RESULTS

Dose-response studies showed that the glyphosate-resistant population, OR12, was nine-fold more resistant to glyphosate than the susceptible population. No EPSPS amino acid substitutions known to confer glyphosate resistance were observed via gene sequencing. Quantitative polymerase chain reaction (qPCR) of genomic DNA revealed a mean 30-fold increase in EPSPS gene copies in the OR12 population. Biomass after glyphosate treatment was correlated with EPSPS gene copy number of individual plants.

CONCLUSION

This is the first known report of glyphosate resistance associated with EPSPS gene amplification to arise in L. multiflorum populations in Oregon. © 2024 Society of Chemical Industry. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Functional characterization of novel mutations in the conserved region of EPSPS for herbicide resistance in pigeonpea: structure-based coherent design

Prospectively, agroecosystems for the growth of crops provide the potential fertile, productive, and tropical environment which attracts infestation by weedy plant species that compete with the primary crop plants. Infestation by weed is a major biotic stress factor faced by pigeonpea that hampers the productivity of the crop. In the modern era with the development of chemicals the problem of weed infestation is dealt with armours called herbicides. The most widely utilized, post-emergent, broad-spectrum herbicide has an essential active ingredient called glyphosate. Glyphosate mechanistically inhibits a chloroplastic enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) by competitively interacting with the PEP binding site which hinders the shikimate pathway and the production of essential aromatic amino acids (Phe, Tyr, Trp) and other secondary metabolites in plants. Moreover, herbicide spray for weed management is lethal to both the primary crop and the weeds. Therefore, it is critical to develop herbicide-resistant crops for field purposes to reduce the associated yield and economic losses. In this study, the in-silico analysis drove the selection and validation of the point mutations in the conserved region of the EPSPS gene, which confers efficient herbicide resistance to mutated-CcEPSPS enzyme along with the retention of the normal enzyme function. An optimized in-silico validation of the target mutation before the development of the genome-edited resistant plant lines is a prerequisite for testing their efficacy as a proof of concept. We validated the combination of GATIPS mutation for its no-cost effect at the enzyme level via molecular dynamic (MD) simulation.Communicated by Ramaswamy H. Sarma.

Phytochemical Cue for the Fitness Costs of Herbicide-Resistant Weeds

Despite increasing knowledge of the fitness costs of viability and fecundity involved in the herbicide-resistant weeds, relatively little is known about the linkage between herbicide resistance costs and phytochemical cues in weed species and biotypes. This study demonstrated relative fitness and phytochemical responses in six herbicide-resistant weeds and their susceptible counterparts. There were significant differences in the parameters of viability (growth and photosynthesis), fecundity fitness (flowering and seed biomass) and a ubiquitous phytochemical (-)-loliolide levels between herbicide-resistant weeds and their susceptible counterparts. Fitness costs occurred in herbicide-resistant Digitaria sanguinalis and Leptochloa chinensis but they were not observed in herbicide-resistant Alopecurus japonicas, Eleusine indica, Ammannia arenaria, and Echinochloa crus-galli. Correlation analysis indicated that the morphological characteristics of resistant and susceptible weeds were negatively correlated with (-)-loliolide concentration, but positively correlated with lipid peroxidation malondialdehyde and total phenol contents. Principal component analysis showed that the lower the (-)-loliolide concentration, the stronger the adaptability in E. crus-galli and E. indica. Therefore, not all herbicide-resistant weeds have fitness costs, but the findings showed several examples of resistance leading to improved fitness even in the absence of herbicides. In particular, (-)-loliolide may act as a phytochemical cue to explain the fitness cost of herbicide-resistant weeds by regulating vitality and fecundity.

Rapid weed adaptation and range expansion in response to agriculture over the past two centuries

North America has experienced a massive increase in cropland use since 1800, accompanied more recently by the intensification of agricultural practices. Through genome analysis of present-day and historical samples spanning environments over the past two centuries, we studied the effect of these changes in farming on the extent and tempo of evolution across the native range of the common waterhemp (Amaranthus tuberculatus), a now pervasive agricultural weed. Modern agriculture has imposed strengths of selection rarely observed in the wild, with notable shifts in allele frequency trajectories since agricultural intensification in the 1960s. An evolutionary response to this extreme selection was facilitated by a concurrent human-mediated range shift. By reshaping genome-wide diversity across the landscape, agriculture has driven the success of this weed in the 21st century.