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.

Weed Response to Co-Application of Herbicides and Acephate in Cotton

Determining compatibility of pesticides is important in developing effective management practices and adjusting to outbreaks of pests in cotton (Gossypium hirsutism L.). Field experiments were conducted in 2013 and 2014 to determine the effect of chloroacetamide herbicides with residual activity only and acephate with foliar activity against thrips (Frankliniella spp.) on control of emerged weeds by glyphosate, glufosinate, and a mixture of these herbicides. The residual herbicides acetochlor and S-metolachlor as well as the insecticide acephate did not affect control of emerged common ragweed (Ambrosia artemisiifolia L.) and Palmer amaranth (Amaranthus palmeri Watts.). Results from these trials indicate that weed control will not be compromised with co-application of glufosinate, glyphosate, and glufosinate plus glyphosate with acetochlor or S-metolachlor applied alone or with acephate.

Weed Management and Economics in Dicamba-Tolerant Cotton

Increasing populations of glyphosate-resistant Palmer amaranth [Amaranthus palmeri (S.) Wats.] have increased weed management costs for Texas High Plains cotton [Gossypium hirsutum (L.)] producers. The introduction of dicamba-tolerant cotton varieties and registration of dicamba formulations for postemergence use, combined with residual herbicides, can effectively control Palmer amaranth. Field studies were conducted in 2018 and 2019 near Lubbock, TX, USA to evaluate Palmer amaranth control and economics of weed management in dicamba-, glufosinate-, glyphosate-, and conventional cotton systems. The most consistent season-long Palmer amaranth control was achieved with the dicamba-tolerant system in both years. In 2018, greatest lint yields were achieved with dicamba-tolerant system when compared to the conventional and glufosinate-tolerant systems. In 2018, greatest gross margin above weed management costs were achieved with the dicamba-tolerant and glyphosate-tolerant systems. Greatest lint yield was achieved with the dicamba-tolerant and conventional systems in 2019 and greatest gross margins were achieved with the dicamba-tolerant system. Total variable costs were similar across all systems, with greater seed/technology and herbicide costs in dicamba-tolerant and glufosinate-tolerant systems, compared to higher tillage and hand hoeing costs in glyphosate-tolerant and conventional systems.

Biochemical Basis for the Time-of-Day Effect on Glufosinate Efficacy against Amaranthus palmeri

Glufosinate, a glutamine synthetase (GS) inhibitor, often provides variable weed control depending on environmental conditions such as light, temperature and humidity at the time of application. Midday applications normally provide improved efficacy compared to applications at dawn or dusk. We investigated the biochemical basis for the time-of-day effect on glufosinate efficacy in Amaranthus palmeri. GS1/GS2 gene expression and GS1/GS2 protein abundance were assessed in different parts (young leaves, old leaves, and roots) of plants incubated in the dark compared to those in the light. The turnover of GS total activity was also evaluated overtime following glufosinate treatment at midday compared to dusk application. The results suggest that GS in A. palmeri is less expressed and less abundant in the dark compared to in the light. Midday application of glufosinate under intense light conditions following application provide full control of A. palmeri plants. Consequently, these plants are unable to recover GS activity by de novo protein synthesis. Full activity of GS is required for complete inhibition by the irreversible inhibitor glufosinate. Therefore, glufosinate applications should always be performed in the middle of the day when sunlight is intense, to prevent weed escapes from the herbicide treatment.

Remote Sensing for Palmer Amaranth (Amaranthus palmeri S. Wats.) Detection in Soybean (Glycine max (L.) Merr.)

Field studies were conducted in 2016 and 2017 to determine if multispectral imagery collected from an unmanned aerial vehicle (UAV) equipped with a five-band sensor could successfully identify Palmer amaranth (Amaranthus palmeri) infestations of various densities growing among soybeans (Glycine max [L.] Merr.). The multispectral sensor captures imagery from five wavebands: 475 (blue), 560 (green), 668 (red), 840 (near infrared [NIR]), and 717 nm (red-edge). Image analysis was performed to examine the spectral properties of discrete Palmer amaranth and soybean plants at various weed densities using these wavebands. Additionally, imagery was subjected to supervised classification to evaluate the usefulness of classification as a tool to differentiate the two species in a field setting. Date was a significant factor influencing the spectral reflectance values of the Palmer amaranth densities. The effects of altitude on reflectance were less clear and were dependent on band and density being evaluated. The near infrared (NIR) waveband offered the best resolution in separating Palmer amaranth densities. Spectral separability in the other wavebands was less defined, although low weed densities were consistently able to be discriminated from high densities. Palmer amaranth and soybean were found to be spectrally distinct regardless of imaging date, weed density, or waveband. Soybean exhibited overall lower reflectance intensity than Palmer amaranth across all wavebands. The reflectance of both species within blue, green, red, and red-edge wavebands declined as the season progressed, while reflectance in NIR increased. Near infrared and red-edge wavebands were shown to be the most useful for species discrimination and maintained their utility at most weed densities. Palmer amaranth weed densities were found to be spectrally distinct from one another in all wavebands, with greatest distinction when using the red, NIR and red-edge wavebands. Supervised classification in a two-class system was consistently able to discriminate between Palmer amaranth and soybean with at least 80% overall accuracy. The incorporation of a weed density component into these classifications introduced an error of 65% or greater into these classifications. Reducing the number of classes in a supervised classification system could improve the accuracy of discriminating between Palmer amaranth and soybean.

Palmer Amaranth (Amaranthaceae) and At-Plant Insecticide Impacts on Tarnished Plant Bug (Hemiptera: Miridae) and Injury to Seedling Cotton Terminals

The direct effect of Palmer amaranth, Amaranthus palmeri Watson, on cotton growth and development is well documented, but its indirect effect through harboring feeding insects is less understood. Palmer amaranth emerged with cotton and remaining in the field for 30 days increased tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), populations compared with a weed-free system. Weedy systems noted up to 49% more damaged terminals than weed-free systems, with cotton yield decreasing as damaged terminals increased at one of two locations. Thrips (Thysanoptera: Thripidae) populations were effectively controlled with Aeris® (Bayer, St. Louis, MO) seed treatment (imidacloprid + thiodicarb at 0.375 mg active ingredient per seed), but there was no correlation between thrips infestations and increasing damaged cotton terminals. However, Aeris seed treatment significantly reduced the occurrence of damaged cotton terminals. In a second experiment, Palmer amaranth infesting an area adjacent to a weed-free cotton field had maximum damaged terminals of 51% on the cotton row proximal to the weedy area, with the distal cotton row (44 m away) having 8% terminal damage. Cotton yield significantly decreased as damaged terminals increased. A final bioassay experiment further evaluated the influence of seed treatment on tarnished plant bug feeding impacting cotton seedlings. With Aeris seed treatment, tarnished plant bug mortality was 97%, compared with 37% for nontreated seed. Results suggest tarnished plant bug infestations increased where Palmer amaranth was present in cotton fields. Additionally, greater Palmer amaranth infestations led to an increase in damaged cotton terminals and lower yields.

Influence of herbicides on germination and quality of Palmer amaranth (Amaranthus palmeri) seed

Lab and greenhouse studies were conducted to evaluate the effects of chemical treatments applied to Palmer amaranth seeds or gynoecious plants retaining seeds on seed germination and quality. Treatments applied to physiologically mature Palmer amaranth seed included acifluorfen, dicamba, ethephon, flumioxazin, fomesafen, halosulfuron, linuron, metribuzin, oryzalin, pendimethalin, pyroxasulfone, S-metolachlor, saflufenacil, trifluralin, and 2,4-D plus crop oil concentrate applied at 1 and 2× the suggested use rates from the manufacturer. Germination was reduced by 20% from 2,4-D, 15% from dicamba, and 13% from halosulfuron and pyroxasulfone. Dicamba, ethephon, halosulfuron, oryzalin, trifluralin, and 2,4-D decreased the average seedling length by at least 50%. Due to the observed effect of dicamba, ethephon, halosulfuron, oryzalin, trifluralin, and 2,4-D, these treatments were applied to gynoecious Palmer amaranth inflorescence at the 2× registered application rates to evaluate their effects on progeny seed. Dicamba decreased seed germination by 24%, whereas all other treatments were similar to the control. Crush tests showed seed viability was greater than 95%; thus, dicamba did not have a strong effect on seed viability. No treatments applied to Palmer amaranth inflorescence affected average seedling length; therefore, chemical treatments did not affect the quality of seeds that germinated.