Journal articles: 'EPSPS gene amplification'

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Chatham, Laura A., Kevin W. Bradley, Greg R. Kruger, James R. Martin, Micheal D. K. Owen, Dallas E. Peterson, Jugulam Mithila, and Patrick J. Tranel. "A Multistate Study of the Association Between Glyphosate Resistance and EPSPS Gene Amplification in Waterhemp (Amaranthus tuberculatus)." Weed Science 63, no. 3 (September 2015): 569–77. http://dx.doi.org/10.1614/ws-d-14-00149.1.

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Waterhemp is an increasingly problematic weed in the U.S. Midwest, having now evolved resistances to herbicides from six different site-of-action groups. Glyphosate-resistant waterhemp in the Midwest is especially concerning given the economic importance of glyphosate in corn and soybean production. Amplification of the target-site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) was found to be the mechanism of glyphosate resistance in Palmer amaranth, a species closely related to waterhemp. Here, the relationship between glyphosate resistance and EPSPS gene amplification in waterhemp was investigated. Glyphosate dose response studies were performed at field sites with glyphosate-resistant waterhemp in Illinois, Kansas, Kentucky, Missouri, and Nebraska, and relative EPSPS copy number of survivors was determined via quantitative real-time polymerase chain reaction (qPCR). Waterhemp control increased with increasing glyphosate rate at all locations, but no population was completely controlled even at the highest rate (3,360 g ae ha−1). EPSPS gene amplification was present in plants from four of five locations (Illinois, Kansas, Missouri, and Nebraska) and the proportion of plants with elevated copy number was generally higher in survivors from glyphosate-treated plots than in plants from the untreated control plots. Copy number magnitude varied by site, but an overall trend of increasing copy number with increasing rate was observed in populations with gene amplification, suggesting that waterhemp plants with more EPSPS copies are more resistant. Survivors from the Kentucky population did not have elevated EPSPS copy number. Instead, resistance in this population was attributed to the EPSPS Pro106Ser mutation. Results herein show a quantitative relationship between glyphosate resistance and EPSPS gene amplification in some waterhemp populations, while highlighting that other mechanisms also confer glyphosate resistance in waterhemp.

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Malone, Jenna M., Sarah Morran, Neil Shirley, Peter Boutsalis, and Christopher Preston. "EPSPS gene amplification in glyphosate-resistant Bromus diandrus." Pest Management Science 72, no. 1 (May 6, 2015): 81–88. http://dx.doi.org/10.1002/ps.4019.

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Chatham, Laura A., Chenxi Wu, Chance W. Riggins, Aaron G. Hager, Bryan G. Young, Gordon K. Roskamp, and Patrick J. Tranel. "EPSPS Gene Amplification is Present in the Majority of Glyphosate-Resistant Illinois Waterhemp (Amaranthus tuberculatus) Populations." Weed Technology 29, no. 1 (March 2015): 48–55. http://dx.doi.org/10.1614/wt-d-14-00064.1.

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With the frequency of glyphosate-resistant waterhemp increasing throughout the Midwest, the identification of resistant populations has become important for managing this species. However, high-throughput screening for glyphosate resistance in the greenhouse is tedious and inefficient. Research was conducted to document the occurrence of glyphosate-resistant waterhemp throughout the state of Illinois, and to determine whether a molecular assay for 5-enolypyruvyl-shikimate-3-phosphate synthase (EPSPS) gene amplification can be used as an alternative means to detect resistant populations. Populations throughout the state of Illinois were collected in 2010 and screened for glyphosate resistance using a whole-plant assay in a greenhouse, and survivors were examined for EPSPS gene amplification. Of 80 populations investigated, 22 were glyphosate resistant based on the greenhouse screen, and gene amplification was identified in 20 (91%) of the resistant populations. Although there are multiple mechanisms for glyphosate resistance in waterhemp, a molecular test for EPSPS gene amplification provides a rapid alternative for identification of glyphosate resistance in most populations.

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Gaines, Todd A., Alice A. Wright, William T. Molin, Lothar Lorentz, Chance W. Riggins, Patrick J. Tranel, Roland Beffa, Philip Westra, and Stephen B. Powles. "Identification of Genetic Elements Associated with EPSPS Gene Amplification." PLoS ONE 8, no. 6 (June 10, 2013): e65819. http://dx.doi.org/10.1371/journal.pone.0065819.

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Koo, Dal-Hoe, Rajendran Sathishraj, Bernd Friebe, and Bikram S. Gill. "Deciphering the Mechanism of Glyphosate Resistance in Amaranthus palmeri by Cytogenomics." Cytogenetic and Genome Research 161, no. 12 (2021): 578–84. http://dx.doi.org/10.1159/000521409.

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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 Amaranthus palmeri (AP) is a serious concern in the USA. Investigation of the mechanism of GR in AP identified different resistance mechanisms of which 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification is predominant. Molecular analysis of GR AP identified the presence of a 5- to >160-fold increase in copies of the EPSPS gene than in a glyphosate-susceptible (GS) population. This increased copy number of the EPSPS 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 EPSPS cassette derived from bacterial artificial chromosomes (BACs) as probes identified that amplified EPSPS copies in GR AP exist in extrachromosomal circular DNA (eccDNA) in addition to the native copy in the chromosome. The EPSPS gene-containing eccDNA having a size of ∼400 kb is termed EPSPS-eccDNA and showed somatic mosacism in size and copy number. EPSPS-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 EPSPS 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 EPSPS-eccDNA sheds light on various characteristics of EPSPS-eccDNA that favor GR in AP.

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Chen, Jingchao, Cuilan Jiang, Hongjuan Huang, Shouhui Wei, Zhaofeng Huang, Huimin Wang, Dandan Zhao, and Chaoxian Zhang. "Characterization of Eleusine indica with gene mutation or amplification in EPSPS to glyphosate." Pesticide Biochemistry and Physiology 143 (November 2017): 201–6. http://dx.doi.org/10.1016/j.pestbp.2017.09.012.

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Pline-Srnic, Wendy. "Physiological Mechanisms of Glyphosate Resistance." Weed Technology 20, no. 2 (June 2006): 290–300. http://dx.doi.org/10.1614/wt-04-131r.1.

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Glyphosate, a nonselective herbicide and also the world's most widely used herbicide, inhibits 5-enol-pyruvylshikimate-3-phosphate synthase (EPSPS), an enzyme in the aromatic amino acid biosynthetic pathway. Because of its broad-spectrum and potent weed control and favorable environmental characteristics, attempts to engineer glyphosate resistance have been intensive in the past few decades. The use of at least three different mechanisms has conferred glyphosate resistance in normally sensitive crop species. Early work focused on progressive adaptation of cultured plant cells to stepwise increases in glyphosate concentrations. The resulting cells were resistant to glyphosate because of EPSPS overexpression, EPSPS gene amplification, or increased enzyme stability. Further work aimed to achieve resistance by transforming plants with glyphosate metabolism genes. An enzyme from a soil microorganism, glyphosate oxidoreductase (GOX), cleaves the nitrogen– carbon bond in glyphosate yielding aminomethylphosphonic acid. Another metabolism gene, glyphosateN-acetyl transferase (gat), acetylates and deactivates glyphosate. A third mechanism, and the one found in all currently commercial glyphosate-resistant crops, is the insertion of a glyphosate-resistant form of the EPSPS enzyme. Several researchers have used site-directed mutagenesis or amino acid substitutions of EPSPS. However, the most glyphosate-resistant EPSPS enzyme to date has been isolated fromAgrobacteriumspp. strain CP4 and gives high levels of resistance in planta. Weeds resistant to glyphosate have offered further physiological mechanisms for glyphosate resistance. Resistant field bindweed had higher levels of 3-deoxy-d-arbino-heptulosonate 7-phosphate synthase, the first enzyme in the shikimate pathway, suggesting that increased carbon flow through the shikimate pathway can provide glyphosate resistance. Resistant goosegrass has reduced translocation of glyphosate out of the treated area. Although glyphosate resistance has been achieved by numerous mechanisms, currently the only independent physiological mechanism to give adequate and stable resistance to glyphosate for commercialization of glyphosate-resistant crops has been glyphosate-resistant forms of EPSPS.

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Chen, Jingchao, Hongjuan Huang, Chaoxian Zhang, Shouhui Wei, Zhaofeng Huang, Jinyi Chen, and Xu Wang. "Mutations and amplification of EPSPS gene confer resistance to glyphosate in goosegrass (Eleusine indica)." Planta 242, no. 4 (May 22, 2015): 859–68. http://dx.doi.org/10.1007/s00425-015-2324-2.

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Salas, Reiofeli A., Franck E. Dayan, Zhiqiang Pan, Susan B. Watson, James W. Dickson, Robert C. Scott, and Nilda R. Burgos. "EPSPS gene amplification in glyphosate-resistant Italian ryegrass (Lolium perenne ssp. multiflorum) from Arkansas." Pest Management Science 68, no. 9 (July 19, 2012): 1223–30. http://dx.doi.org/10.1002/ps.3342.

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Ghanizadeh, Hossein, Andrew G. Griffiths, Christopher E. Buddenhagen, Craig B. Anderson, and Kerry C. Harrington. "A PCR plus restriction enzyme-based technique for detecting target-enzyme mutations at position Pro-106 in glyphosate-resistant Lolium perenne." PLOS ONE 16, no. 2 (February 2, 2021): e0246028. http://dx.doi.org/10.1371/journal.pone.0246028.

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The first step in managing herbicide-resistant weeds is to confirm their resistance status. It is, therefore, crucial to have a rapid, reliable and cost-effective technique to assess samples for herbicide resistance. We designed and evaluated three derived cleaved amplified polymorphic sequence (dCAPS) markers for detecting glyphosate resistance in Lolium perenne. conferred by non-synonymous mutations at codon-106 in the enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. The dCAPS markers involve amplification of the target region, digestion of the amplified products with restriction enzymes and gel-based visualisation of the digested products. The results showed that all three dCAPS markers could successfully detect mutations at codon-106 in the target enzyme. The dCAPS markers can also inform us of the zygosity state of the resistance allele and was confirmed by sequencing the target region of the EPSPS gene. The markers described here are effective quick tests for the monitoring and evaluation of the target-enzyme mechanism of glyphosate resistance in Lolium perenne.

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Okumu, Martha N., Petrus J. Robbertse, Barend J. Vorster, and Carl F. Reinhardt. "The Molecular, Morphological and Genetic Characterization of Glyphosate Resistance in Conyza bonariensis from South Africa." Plants 11, no. 21 (October 24, 2022): 2830. http://dx.doi.org/10.3390/plants11212830.

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Six Conyza bonariensis (L.) Cronquist populations were screened in a pot experiment at the University of Pretoria’s Hatfield experimental farm to evaluate and confirm the degree of glyphosate response. Resistance factors ranged from 2.7- to 24.8-fold compared to the most susceptible biotype. Partial sequencing of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene found no mutation at the Thr102, Ala103 or Pro106 positions. EPSPS mRNA expression levels in glyphosate-resistant biotypes (Swellendam and Piketberg seed sampling sites) were comparable or lower than those in susceptible biotypes (George and Fauresmith sites). Additionally, the highest expression level was reported in the susceptible Fauresmith biotype. These results indicate that glyphosate resistance in the tested resistant biotypes is not caused by target-site mutations and EPSPS gene amplification. Leaf surface characteristics can influence the spread and subsequent absorption of glyphosate. The study established non-significant results in the amount of leaf wax and insufficient mean separations in cuticle thickness and trichome density data. Therefore, the observed differences in response of biotypes to glyphosate treatment could not be attributed conclusively to differences in the leaf morphological characteristics investigated. Results from the inheritance study were consistent with glyphosate resistance being inherited in an incompletely dominant manner when plants were treated with glyphosate herbicide at 900 g ae ha−1.

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Ribeiro, Daniela N., Zhiqiang Pan, Stephen O. Duke, Vijay K. Nandula, Brian S. Baldwin, David R. Shaw, and Franck E. Dayan. "Involvement of facultative apomixis in inheritance of EPSPS gene amplification in glyphosate-resistant Amaranthus palmeri." Planta 239, no. 1 (October 20, 2013): 199–212. http://dx.doi.org/10.1007/s00425-013-1972-3.

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Vila-Aiub, Martin M., Sou S. Goh, Todd A. Gaines, Heping Han, Roberto Busi, Qin Yu, and Stephen B. Powles. "No fitness cost of glyphosate resistance endowed by massive EPSPS gene amplification in Amaranthus palmeri." Planta 239, no. 4 (January 3, 2014): 793–801. http://dx.doi.org/10.1007/s00425-013-2022-x.

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Ng, C. H., R. Wickneswary, S. Salmijah, Y. T. Teng, and B. S. Ismail. "Glyphosate resistance in Eleusine indica (L.) Gaertn. from different origins and polymerase chain reaction amplification of specific alleles." Australian Journal of Agricultural Research 55, no. 4 (2004): 407. http://dx.doi.org/10.1071/ar03155.

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Glyphosate-resistant populations of Eleusine indica (L.) Gaertn. were found in 4 areas in Malaysia that had received repeated applications of glyphosate for a period ranging from 5 to 15 years. The resistance ratios calculated from dose-response experiments were 2.9 (Chaah), 2.1 (Lenggeng), 3.3 (Bidor), and 2.8 (Temerloh). Two-point mutations were detected in position 875 within the 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) gene resistant population, causing a C to T transition leading to Pro106 to Ser106 substitution in Bidor and Temerloh or C to A transversion leading to Pro106 to Thr106 substitution in Chaah. Sequence comparisons of the 3115 bp of the EPSPS gene revealed identical sequences in both the susceptible (S) and resistant (R) populations of Lenggeng. The identical sequences in both the Lenggeng populations, S and R, suggest that the resistance mechanism found in Lenggeng R may be different from Chaah R, Bidor R, and Temerloh R. The polymerase chain reaction (PCR) amplification of specific alleles (PASA) was developed to detect 2 distinct single-point mutations, probably conferring herbicide resistance in Chaah R, Bidor R, and Temerloh R. PASA profiles showed only one DNA fragment for the entire S population and 2 different additional fragments, each specific for one resistance allele, for the R population.

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Spier Camposano, Hailey, William T. Molin, and Christopher A. Saski. "Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations." PLOS ONE 17, no. 9 (September 14, 2022): e0260906. http://dx.doi.org/10.1371/journal.pone.0260906.

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The discovery of non-chromosomal circular DNA offers new directions in linking genome structure with function in plant biology. Glyphosate resistance through EPSPS gene copy amplification in Palmer amaranth was due to an autonomously replicating extra-chromosomal circular DNA mechanism (eccDNA). CIDER-Seq analysis of geographically distant glyphosate sensitive (GS) and resistant (GR) Palmer Amaranth (Amaranthus palmeri) revealed the presence of numerous small extra-chromosomal circular DNAs varying in size and with degrees of repetitive content, coding sequence, and motifs associated with autonomous replication. In GS biotypes, only a small portion of these aligned to the 399 kb eccDNA replicon, the vehicle underlying gene amplification and genetic resistance to the herbicide glyphosate. The aligned eccDNAs from GS were separated from one another by large gaps in sequence. In GR biotypes, the eccDNAs were present in both abundance and diversity to assemble into a nearly complete eccDNA replicon. Mean sizes of eccDNAs were similar in both biotypes and were around 5kb with larger eccDNAs near 25kb. Gene content for eccDNAs ranged from 0 to 3 with functions that include ribosomal proteins, transport, metabolism, and general stress response genetic elements. Repeat content among smaller eccDNAs indicate a potential for recombination into larger structures. Genomic hotspots were also identified in the Palmer amaranth genome with a disposition for gene focal amplifications as eccDNA. The presence of eccDNA may serve as a reservoir of genetic heterogeneity in this species and may be functionally important for survival.

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Koo, Dal-Hoe, William T. Molin, Christopher A. Saski, Jiming Jiang, Karthik Putta, Mithila Jugulam, Bernd Friebe, and Bikram S. Gill. "Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weedAmaranthus palmeri." Proceedings of the National Academy of Sciences 115, no. 13 (March 12, 2018): 3332–37. http://dx.doi.org/10.1073/pnas.1719354115.

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Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs).Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplifiedEPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplifiedEPSPScopies in glyphosate-resistant (GR)A. palmeriare present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock’s postulated innate systems [McClintock B (1978)Stadler Genetics Symposium] that can rapidly produce soma variation, amplifyEPSPSgenes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution.

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Chahal, Parminder S., Vijay K. Varanasi, Mithila Jugulam, and Amit J. Jhala. "Glyphosate-Resistant Palmer Amaranth (Amaranthus palmeri) in Nebraska: Confirmation, EPSPS Gene Amplification, and Response to POST Corn and Soybean Herbicides." Weed Technology 31, no. 1 (January 2017): 80–93. http://dx.doi.org/10.1614/wt-d-16-00109.1.

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Palmer amaranth is the most problematic weed in agronomic crop production fields in the United States. A Palmer amaranth biotype was not controlled with sequential applications of glyphosate in glyphosate-resistant (GR) soybean production field in south-central Nebraska. The seeds of the putative GR Palmer amaranth biotype were collected in the fall of 2015. The objectives of this study were to (1) confirm GR Palmer amaranth and determine the level of resistance in a whole-plant dose-response bioassay, (2) determine the copy number of 5-enolpyruvylshikimate-3-phosphate (EPSPS) gene, the molecular target of glyphosate, and (3) evaluate the response of GR Palmer amaranth biotype to POST corn and soybean herbicides with different modes-of-action. Based on the effective dose required to control 90% of plants (ED90), the putative GR Palmer amaranth biotype was 37- to 40-fold resistant to glyphosate depending on the glyphosate-susceptible (GS) used as a baseline population.EPSPSgene amplification was present in the GR Palmer amaranth biotype with up to 32 to 105 EPSPS copies compared to the known GS biotypes. Response of GR Palmer amaranth to POST corn and soybean herbicides suggest reduced sensitivity to atrazine, hydroxyphenylpyruvate dioxygenase (HPPD)- (mesotrione, tembotrione, and topramezone), acetolactate synthase (ALS)- (halosulfuron-methyl), and protoporphyrinogen oxidase (PPO)- (carfentrazone and lactofen) inhibitors. GR Palmer amaranth was effectively controlled (>90%) with glufosinate applied at 593 g ai ha−1with ≥95% reduction in biomass. More research is needed to determine whether this biotype exhibits multiple resistant to other group of herbicides and evaluate herbicide programs for effective management in corn and soybean.

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Adu‐Yeboah, Patricia, Jenna M. Malone, Benjamin Fleet, Gurjeet Gill, and Christopher Preston. "EPSPS gene amplification confers resistance to glyphosate resistant populations of Hordeum glaucum Stued (northern barley grass) in South Australia." Pest Management Science 76, no. 4 (December 2, 2019): 1214–21. http://dx.doi.org/10.1002/ps.5671.

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Singh, Monika, Deepa Pal, Payal Sood, and Gurinderjit Randhawa. "Construct-Specific Loop-Mediated Isothermal Amplification: Rapid Detection of Genetically Modified Crops with Insect Resistance or Herbicide Tolerance." Journal of AOAC INTERNATIONAL 103, no. 5 (March 26, 2020): 1191–200. http://dx.doi.org/10.1093/jaoacint/qsaa043.

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Abstract Background Insect resistant and herbicide tolerant genetically modified (GM) events have been approved in many countries. Screening methods could facilitate preliminary testing to check the GM status, which may target control elements, transgenes, and marker genes or construct regions. Among these, methods targeting the construct region, i.e., the junction between two genetic elements of a transgenic cassette are more specific. Objective Loop-mediated isothermal amplification (LAMP) assays targeting three construct regions were developed; between Cauliflower Mosaic Virus 35S promoter and cry1Ac gene (p35S-cry1Ac), cry2Ab2 gene and nos terminator (cry2Ab2-tnos), and cp4-epsps gene and nos terminator (cp4epsps-tnos). Method LAMP assays were performed by incubation at constant temperatures for selected targets. Positive amplification was detected as a change in color from orange to green on addition of SYBR® Green dye in visual LAMP and as real-time amplification curves in real-time LAMP. Results These assays showed acceptable specificity and sensitivity. Visual LAMP was found to be sensitive enough to detect as low as 0.005%, equivalent to two target copies. Real-time LAMP assays were able to detect as low as four copies of the target within 40 min, making them suitable for rapid on-site testing for GM organisms (GMO). Practical utility was also verified using spiked test samples. Conclusions These assays could be employed to address some of the biosafety or post-release monitoring issues, as well as to check for approved and unapproved GM events in a country. Highlights LAMP assays targeting three construct regions have been developed, enabling screening for approved or unapproved GMO.

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Singh, Shilpa, Vijay Singh, Amy Lawton-Rauh, Muthukumar V. Bagavathiannan, and Nilda Roma-Burgos. "EPSPSGene Amplification Primarily Confers Glyphosate Resistance among Arkansas Palmer amaranth (Amaranthus palmeri) Populations." Weed Science 66, no. 3 (January 26, 2018): 293–300. http://dx.doi.org/10.1017/wsc.2017.83.

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AbstractResearch was conducted to determine whether resistance to glyphosate among Palmer amaranth (Amaranthus palmeriS. Watson) populations within the U.S. state of Arkansas was due solely to increasedEPSPSgene copy number and whether gene copy number is correlated with resistance level to glyphosate. One hundred and fifteenA. palmeriaccessions were treated with 840 g ae ha−1glyphosate. Twenty of these accessions, selected to represent a broad range of responses to glyphosate, underwent further testing. Seven of the accessions were controlled with this dose; the rest were resistant. The effective dose to cause 50% injury (ED50) for susceptible accessions ranged from 28 to 207 g ha−1. The glyphosate-resistant (GR) accessions had ED50values ranging from 494 to 1,355 g ha−1, a 3- to 48-fold resistance level compared with the susceptible standard (SS). The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene relative copy number was determined for 20 accessions, 4 plants accession−1. Resistant plants from five GR accessions (38% of resistant plants tested) did not have increasedEPSPSgene copies. Resistant plants from the remaining eight GR accessions (62% of resistant plants tested) had 19 to 224 moreEPSPSgene copies than the SS. Among the accessions tested, injury declined 4% with every additionalEPSPScopy. ED50values were directly correlated withEPSPScopy number. The highly resistant accession MIS11-B had an ED50of 1,355 g ha−1and 150 gene copies. Partial sequences ofEPSPSfrom GR accessions withoutEPSPSamplification did not contain any of the known resistance-conferring mutations. Nearly 40% of GR accessions putatively harbor non–target site resistance mechanisms. Therefore, elevatedEPSPSgene copy number is associated with glyphosate resistance amongA. palmerifrom Arkansas.

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Spaunhorst, Douglas J., Haozhen Nie, James R. Todd, Julie M. Young, Bryan G. Young, and William G. Johnson. "Confirmation of herbicide resistance mutations Trp574Leu, ΔG210, and EPSPS gene amplification and control of multiple herbicide-resistant Palmer amaranth (Amaranthus palmeri) with chlorimuron-ethyl, fomesafen, and glyphosate." PLOS ONE 14, no. 3 (March 26, 2019): e0214458. http://dx.doi.org/10.1371/journal.pone.0214458.

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Giacomini, Darci, Philip Westra, and Sarah M. Ward. "Impact of Genetic Background in Fitness Cost Studies: An Example from Glyphosate-Resistant Palmer Amaranth." Weed Science 62, no. 1 (March 2014): 29–37. http://dx.doi.org/10.1614/ws-d-13-00066.1.

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Since its discovery in 2005, glyphosate-resistant Palmer amaranth has become a major problem for many farmers in the southern United States. One mechanism of resistance found in a Georgia population of glyphosate-resistant Palmer amaranth is amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene throughout the genome, with some resistant plants containing and expressing more than 100EPSPSgenes. Such high numbers ofEPSPSgenes and protein production could result in a fitness cost to resistant plants due to (1) metabolic cost of overproduction of this enzyme and (2) disruption of other genes after insertion of theEPSPSgene. A greenhouse experiment was set up to investigate differences in growth and reproduction between glyphosate-susceptible and -resistant Palmer amaranth plants. Measurements included growth rate, plant height/volume ratio, final biomass, photosynthetic rate, inflorescence length, pollen viability, and seed set. This study found no significant fitness costs for plants with the resistance trait. This study also provided a clear example of how controlling for genetic background is important in fitness cost studies and how potentially misleading results can be obtained if only a few fitness traits are measured. These results indicate that glyphosate-resistant Palmer amaranth plants with highEPSPSgene copy numbers are likely to persist in field populations, even in the absence of glyphosate, potentially leading to long-term loss of glyphosate as a control option for Palmer amaranth.

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Jabeen, Asma, Rida Batool, and Nazia Jamil. "Micrococcus yunnanensis and Psychrobacter sp. as Potential Producers of Polymers from Hot Spring." Industria: Jurnal Teknologi dan Manajemen Agroindustri 11, no. 1 (April 30, 2022): 1–9. http://dx.doi.org/10.21776/ub.industria.2022.011.01.1.

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Polyhydroxyalkanoates (PHAs) and exopolysaccharides (EPSs) are biopolymers bacteria under nutrient-limiting conditions. In this study, bacterial strains were isolated from hot springs. Soil samples were collected from Tatta Pani, Azad Kashmir, Pakistan. Bacterial strains AJ2 and AJ3 were selected due to their ability to produce PHAs and EPSs. Phylogenetic analysis showed that strain AJ2 was Micrococcus yunnanensis and AJ3 was Psychrobacter sp. Three carbon sources (glucose, glycerol, and molasses) were used for polymer production. The effect of high pH (8) and high temperature (55 °C) was checked on PHAs and EPSs production. The highest yield of PHAs was given by strain AJ3 (89.43%) with molasses. When grown at 55 °C for 24 hours, strain AJ3 showed the highest PHAs accumulation, 79% with glucose. At alkaline pH 8, strain AJ3 gave 34% PHAs with molasses. The highest EPSs production was observed for strain AJ3. AJ3 gave 70g/L of EPSs with both glucose and glycerol. The amplification of the phaC gene was done to confirm the genetic basis of PHAs production. FTIR analysis showed clear bands at 1722 cm-1 and 2925 cm-1 representing the carbonyl and alkyl groups of PHAs, respectively.

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Chen, Jingchao, Hailan Cui, Xiaoyan Ma, Yan Ma, and Xiangju Li. "Distribution Differences in the EPSPS Gene in Chromosomes Between Glyphosate-Resistant and -Susceptible Goosegrass (Eleusine indica)." Weed Science, November 25, 2019, 1–28. http://dx.doi.org/10.1017/wsc.2019.72.

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Abstract Glyphosate is a popular herbicide used to control goosegrass [Eleusine indica (L.) Gaertn.], one of the most troublesome weeds in cotton fields. However, high selection pressure has led to some populations being difficult to control in cotton fields in China. In this study, levels of glyphosate resistance were quantified and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) amplification was confirmed. In addition, distribution of the EPSPS gene among the chromosomes was also investigated using fluorescence in situ hybridization (FISH) methodology. One population (AHCZ) was confirmed to be glyphosate resistant with a resistance index of 3.4 and significantly reduced shikimate accumulation compared to susceptible population. All examined individuals exhibited no mutations in the EPSPS gene in AHCZ. Expression and copy numbers of EPSPS in the AHCZ population were 5.7 and 15.4 times higher, respectively, than in the susceptible population. A positive correlation was identified between signal intensities of primary anti-EPSPS antibody and copy numbers of the EPSPS protein, as indicated by immunoblot analysis. FISH results revealed that, in mitotic metaphase chromosomes, signals were observed dispersed across two sets of homologous chromosomes in a resistant individual (copy number = 31), while in susceptible individuals, signals were only partially detected in one set of homologous chromosomes. In interphase nuclei, EPSPS signals were brightest in resistant individual compared to those that were susceptible. In conclusion, one E. indica population from a cotton field in the Anhui Province has evolved resistance to glyphosate, and EPSPS gene amplification was confirmed as the resistant mechanism.

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Cahoon, Charles W., David L. Jordan, Patrick J. Tranel, Alan C. York, Chance Riggins, Richard Seagroves, Matthew Inman, Wesley Everman, and Ramon Leon. "In-field assessment of EPSPS amplification on fitness cost in mixed glyphosate-resistant and -sensitive populations of Palmer amaranth (Amaranthus palmeri)." Weed Science, October 24, 2022, 1–20. http://dx.doi.org/10.1017/wsc.2022.60.

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ABSTRACT Comparing fitness of herbicide-resistant and –susceptible weed biotypes is important to managing herbicide resistance. Previous research suggests there is little to no fitness penalty from amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene (a mechanism of glyphosate resistance) in Palmer amaranth (Amaranthus palmeri S. Watson) in controlled studies in the greenhouse or growth chamber. A field study was conducted in North Carolina at three locations naturally infested with A. palmeri to determine vegetative, reproductive, and germination fitness of plants with and without EPSPS amplification grown season-long with cotton (Gossypium hirsutum L.). Seed number was not correlated with EPSPS copy number. However, when plants were binned into two groups, those having an EPSPS copy number equal to or greater than 2 (relative to reference genes) and those having an EPSPS copy number less than 2, plant fresh weight and seed number was 1.4 and 1.6 times greater, respectively, for plants with less than 2 EPSPS copies. Amaranthus palmeri height and seed germination, and yield of cotton, did not differ when comparing the two binned groups. These data suggest that A. palmeri plants with EPSPS amplification are relatively less fit in the absence of glyphosate, but this reduced fitness does not translate into differences in interference with cotton.

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Oliveira, Maxwel C., Darci A. Giacomini, Nikola Arsenijevic, Gustavo Vieira, Patrick J. Tranel, and Rodrigo Werle. "Distribution and validation of genotypic and phenotypic glyphosate and PPO-nhibitor resistance in Palmer amaranth (Amaranthus palmeri) from southwestern Nebraska." Weed Technology, July 9, 2020, 1–12. http://dx.doi.org/10.1017/wet.2020.74.

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Abstract Failure to control Palmer amaranth with glyphosate and protoporphyrinogen IX oxidase (PPO)-inhibitor herbicides was reported across southwestern Nebraska in 2017. The objectives of this study were to 1) confirm and 2) validate glyphosate and PPO-inhibitor (fomesafen and lactofen) resistance in 51 Palmer amaranth accessions from southwestern Nebraska using genotypic and whole-plant phenotypic assay correlations and cluster analysis, and 3) determine which agronomic practices might be influencing glyphosate resistance in Palmer amaranth accessions in that location. Based on genotypic assay, 88% of 51 accessions contained at least one individual with amplification (>2 copies) of the 5-enolypyruvyl-shikimate-3-phosphate synthase (EPSPS) gene, which confers glyphosate resistance; and/or a mutation in the PPX2 gene, either ΔG210 or R128G, which endows PPO-inhibitor resistance in Palmer amaranth. Cluster analysis and high correlation (0.83) between genotypic and phenotypic assays demonstrated that EPSPS gene amplification is the main glyphosate resistance mechanism in Palmer amaranth accessions from southwestern Nebraska. In contrast, there was poor association between genotypic and phenotypic responses for PPO-inhibitor resistance, which was attributed to segregation for PPO-inhibitor resistance within these accessions and/or the methodology that was adopted herein. Genotypic assays can expedite the process of confirming known glyphosate and PPO-inhibitor resistance mechanisms in Palmer amaranth from southwestern Nebraska and other locations. Phenotypic assays are also a robust method for confirming glyphosate resistance but not necessarily PPO-inhibitor resistance in Palmer amaranth. Moreover, random forest analysis of glyphosate resistance in Palmer amaranth indicated that EPSPS gene amplification, county, and current and previous crops are the main factors influencing glyphosate resistance within that geographic area. Most glyphosate-susceptible Palmer amaranth accessions were found in a few counties in areas with high crop diversity. Results presented here confirm the spread of glyphosate resistance and PPO-inhibitor resistance in Palmer amaranth accessions from southwestern Nebraska and demonstrate that less diverse cropping systems are an important driver of herbicide resistance evolution in Palmer amaranth.

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Cockerton, Helen M., Shiv S. Kaundun, Lieselot Nguyen, Sarah Jane Hutchings, Richard P. Dale, Anushka Howell, and Paul Neve. "Fitness Cost Associated With Enhanced EPSPS Gene Copy Number and Glyphosate Resistance in an Amaranthus tuberculatus Population." Frontiers in Plant Science 12 (June 29, 2021). http://dx.doi.org/10.3389/fpls.2021.651381.

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The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. The growth and fitness of seed families with contrasting levels of glyphosate resistance was assessed in the absence of glyphosate to determine their ability to compete for resources under intra- and interspecific competition. We identified a positive correlation between the level of glyphosate resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus identifying gene amplification as the mechanism of resistance within the population. Resistant A. tuberculatus plants were found to have a lower competitive response when compared to the susceptible phenotypes with 2.76 glyphosate resistant plants being required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.

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Shyam, Chandrima, Ednaldo A. Borgato, Dallas E. Peterson, Johanna Anita Dille, and Mithila Jugulam. "Predominance of Metabolic Resistance in a Six-Way-Resistant Palmer Amaranth (Amaranthus palmeri) Population." Frontiers in Plant Science 11 (January 14, 2021). http://dx.doi.org/10.3389/fpls.2020.614618.

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Evolution of multiple herbicide resistance in Palmer amaranth across the United States is a serious challenge for its management. Recently, a Palmer amaranth population (KCTR; Kansas Conservation Tillage Resistant) from a long-term conservation tillage research project in Kansas, United States, was found uncontrolled by several commonly used herbicides. Importantly, this field did not have a history of repeated use of some of the herbicides for which the KCTR Palmer amaranth population showed lack of control. The objectives of this study were to confirm the evolution of multiple resistances and determine possible mechanism(s) of resistance in KCTR Palmer amaranth plants. In response to post-emergence application, 28–100% of KCTR Palmer amaranth survived field recommended rates of 2,4-D, ALS-, PS II-, EPSPS-, PPO-, HPPD-inhibitor herbicides, or tank- or pre-mixture of PS II- and HPPD-inhibitor herbicides, confirming evolution of six-way resistance in this Palmer amaranth population. However, this population was found susceptible to the PS I- and glutamine synthetase inhibitor herbicides. Chlorsulfuron-, imazethapyr-, and atrazine-resistant plants did not show any previously reported mutation in ALS and psbA genes, the target sites of these herbicides, respectively. However, the survivors of glyphosate treatment showed amplification of EPSPS gene (up to 88 copies). The KCTR plants pretreated with cytochrome P450 or GST inhibitors along with atrazine, 2,4-D, lactofen, or mesotrione had significantly less biomass accumulation than those treated with herbicides alone. Plants treated with P450 inhibitor followed by imazethapyr showed moderate reduction of biomass in KCTR which was statistically similar to a susceptible Palmer amaranth population treated with imazethapyr. These results suggest predominance of metabolic resistance possibly mediated by cytochrome P450 and GST enzyme activity that may have predisposed the KCTR Palmer amaranth population to evolve resistance to multiple herbicides. This is the first report of evolution of six-way resistance in a single Palmer amaranth population. Appropriate management strategies, including integration of cultural, and mechanical, and herbicide mixtures, are warranted to control such Palmer amaranth populations.

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Journal articles on the topic 'EPSPS gene amplification'

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