The Experts below are selected from a list of 384 Experts worldwide ranked by ideXlab platform
Patrick J Tranel - One of the best experts on this subject based on the ideXlab platform.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
Pest Management Science, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:Background Amaranthus tuberculatus is a problematic weed species in Midwest USA agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). Results Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. Conclusions Resistance to HPPD inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.
-
hybridization potential between Amaranthus tuberculatus and Amaranthus albus
bioRxiv, 2021Co-Authors: Brent P. Murphy, Laura A Chatham, D M Mccormick, Patrick J TranelAbstract:The genus Amaranthus is composed of numerous annual herbs, several of which are primary driver weeds within annual production agricultural systems. In particular, Amaranthus tuberculatus, a dioecious species, is noteworthy for rapid growth rates, high fecundity, and an expanding geographic distribution. Interspecific hybridization within and between the subgenera Amaranthus and Acnidia is reported both in controlled environment and field studies, however a gap in knowledge exists with the subgenus Albersia. Interspecific hybridization may contribute to genetic diversity, and may contribute to the current range expansion of A. tuberculatus. Recently, a herbicide resistance survey of A. tuberculatus across five Midwestern states reported alleles of PPX2 similar to sequences of Amaranthus albus, a monoecious species. Here, we seek to generate empirical data for the hybridization potential of A. albus and A. tuberculatus through replicated, controlled crosses in a greenhouse. Of 65,000 progeny screened from A. albus grown with A. tuberculatus males, three were confirmed as hybrids. Hybrids were dioecious, possessed phenotypic traits of both species, and had limited to no fertility. DNA content analysis of backcross progeny suggested a polyploid state may be required for hybrid formation. Screening of 120 progeny of A. tuberculatus females grown with A. albus identified no hybrids, though a skew to female progeny was observed. The female skew may be due to apomixis or auto-pollination, the spontaneous generation of male flowers on otherwise female plants. Our results indicate that introgression between A. albus and A. tuberculatus will occur less frequently than what has often been reported from hybridization studies with different pairs of Amaranthus species.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
bioRxiv, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:BACKGROUND: Amaranthus tuberculatus is a primary driver weed species throughout the American Midwest. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS: Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance/sensitive ratio of 15.0-21.1. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556), and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS: Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
Pest Management Science, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:BACKGROUND Amaranthus tuberculatus is a problematic weed species in Midwest U.S.A. agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species. This article is protected by copyright. All rights reserved.
-
the genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus
Molecular Ecology, 2021Co-Authors: Julia M Kreiner, Patrick J Tranel, Detlef Weigel, John R Stinchcombe, Stephen I WrightAbstract:Much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, despite the increasingly recognized importance of polygenic resistance. Little work has been done to characterize the broader genomic basis of herbicide resistance, including the number and distribution of genes involved, their effect sizes, allele frequencies and signatures of selection. In this work, we implemented genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate (Round-up) resistance in the problematic agricultural weed Amaranthus tuberculatus. A GWA was able to correctly identify the known target-gene but statistically controlling for two causal target-site mechanisms revealed an additional 250 genes across all 16 chromosomes associated with non-target-site resistance (NTSR). The encoded proteins had functions that have been linked to NTSR, the most significant of which is response to chemicals, but also showed pleiotropic roles in reproduction and growth. Compared to an empirical null that accounts for complex population structure, the architecture of NTSR was enriched for large effect sizes and low allele frequencies, suggesting the role of pleiotropic constraints on its evolution. The enrichment of rare alleles also suggested that the genetic architecture of NTSR may be population-specific and heterogeneous across the range. Despite their rarity, we found signals of recent positive selection on NTSR-alleles by both window- and haplotype-based statistics, and an enrichment of amino acid changing variants. In our samples, genome-wide single nucleotide polymorphisms explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, even in a collection of individuals where 80% of resistant individuals have large-effect TSR mutations, indicating an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.
Dean E Riechers - One of the best experts on this subject based on the ideXlab platform.
-
resistance to a non selective hppd inhibiting herbicide via novel reduction dehydration glutathione conjugation in Amaranthus tuberculatus
New Phytologist, 2021Co-Authors: Jeanaflor Crystal T Concepcion, Seth A. Strom, Shiv S Kaundun, Sarahjane Hutchings, James Alan Morris, Anatoli V Lygin, Dean E RiechersAbstract:Metabolic resistance to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides is a threat for controlling waterhemp (Amaranthus tuberculatus) in the United States. We investigated resistance mechanisms to syncarpic acid-3 (SA3), a non-selective, non-commercial HPPD-inhibiting herbicide metabolically robust to Phase I oxidation, in multiple-herbicide-resistant (MHR) waterhemp populations (SIR and NEB) and HPPD inhibitor-sensitive populations (ACR and SEN). Dose-response experiments with SA3 provided ED50 -based resistant-to-sensitive ratios of at least 18-fold. Metabolism experiments quantifying parent SA3 remaining in excised leaves during a time course indicated MHR populations displayed faster rates of SA3 metabolism compared to HPPD inhibitor-sensitive populations. SA3 metabolites were identified via LC-MS-based untargeted metabolomics in whole plants. A Phase I metabolite, likely generated by cytochrome P450-mediated alkyl hydroxylation, was detected but was not associated with resistance. A Phase I metabolite consistent with ketone reduction followed by water elimination was detected, creating a putative α,β-unsaturated carbonyl resembling a Michael acceptor site. A Phase II glutathione-SA3 conjugate was associated with resistance. Our results revealed a novel reduction-dehydration-GSH conjugation detoxification mechanism. SA3 metabolism in MHR waterhemp is thus atypical compared to commercial HPPD-inhibiting herbicides. This previously-uncharacterized detoxification mechanism presents a unique opportunity for future biorational design by blocking known sites of herbicide metabolism in weeds.
-
association between metabolic resistances to atrazine and mesotrione in a multiple resistant waterhemp Amaranthus tuberculatus population
Weed Science, 2020Co-Authors: Kip E Jacobs, Carrie J Buttswilmsmeyer, Sarah R Obrien, Dean E RiechersAbstract:Metabolic resistances to atrazine (atz-R) and mesotrione (meso-R) occur in several waterhemp [Amaranthus tuberculatus (Moq.) Sauer] populations in the United States. Interestingly, although metabolic atz-R but mesotrione-sensitive A. tuberculatus populations have been reported, an Amaranthus population has not been confirmed as meso-R but atrazine-sensitive, implying an association between these traits. Experiments were designed to investigate whether the single gene conferring metabolic atz-R plays a role in meso-R. An F2 population was generated from a multiple herbicide–resistant A. tuberculatus population from McLean County, IL (MCR). A cross was made between a known meso-R male clone (MCR-6) and a herbicide-sensitive female clone from Wayne County, IL (WCS-2) to develop an F1 population. Survival of MCR-6 plants following atrazine POST treatment (14.4 kg ha−1) indicated the male parent was homozygous atz-R. F1 plants were intermated to obtain a segregating pseudo-F2 population. Dose–response and metabolic studies conducted with mesotrione using F1 plants indicated intermediate biomass reductions and metabolic rates compared with MCR-6 and WCS. F2 plants were initially treated with either mesotrione (260 g ha−1) or atrazine (2 kg ha−1) POST, and after 21 d of recovery, vegetative clones from surviving resistant plants were subsequently treated with the other herbicide. When mesotrione was applied first, the meso-R frequency was 8.2%, and when atrazine was applied first, the atz-R frequency was 75%. However, the meso-R frequency increased to 16.5% following preselection for atz-R, and 100% of surviving meso-R plants were atz-R. Our findings indicate that the gene conferring metabolic atz-R is also involved with the meso-R trait within the population tested.
-
metabolic resistance to s metolachlor in two waterhemp Amaranthus tuberculatus populations from illinois usa
Pest Management Science, 2020Co-Authors: Seth A. Strom, Aaron G. Hager, Adam S Davis, Nicholas J Seiter, Dean E RiechersAbstract:Background Two waterhemp (Amaranthus tuberculatus) populations from Illinois demonstrating multiple-resistance to acetolactate synthase (ALS)-, 4-hydroxyphenylpyruvate dioxygenase, and photosystem II (PSII)-inhibiting herbicides (designated CHR and SIR) also displayed reduced sensitivity to very-long-chain fatty acid-inhibiting herbicides, including S-metolachlor. We hypothesized that a physiological mechanism, such as enhanced metabolism, could be responsible for the reduced efficacy of S-metolachlor. Results Metabolism experiments indicated that resistant populations degraded S-metolachlor more rapidly than sensitive populations and equally as rapidly as corn 2-24 h after treatment (HAT). Resistant waterhemp and corn metabolized 90% (DT90 ) of absorbed S-metolachlor in less than 3.2 h whereas DT90 values for sensitive waterhemp exceeded 6 h. The glutathione S-transferase inhibitor 4-chloro-7-nitrobenzofurazon and cytochrome P450-inhibitor malathion decreased the amount of S-metolachlor metabolized in resistant waterhemp at 4 HAT but not in sensitive waterhemp or corn, and altered the abundance of certain metabolites in resistant waterhemp. Conclusion Results from this research demonstrate that resistance to S-metolachlor in these waterhemp populations is due to enhanced herbicide metabolism relative to sensitive populations. In addition, our results indicate that resistant waterhemp might utilize metabolic pathway(s) more intricate than either sensitive waterhemp or corn based on their metabolite profiles. © 2020 Society of Chemical Industry.
-
characterization of multiple herbicide resistant waterhemp Amaranthus tuberculatus populations from illinois to vlcfa inhibiting herbicides
Weed Science, 2019Co-Authors: Seth A. Strom, Dean E Riechers, Adam S Davis, Lisa C Gonzini, Charlie Mitsdarfer, Aaron G. HagerAbstract:Field experiments were conducted in 2016 and 2017 in Champaign County, IL, to study a waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] population (CHR) resistant to 2,4-D and 4-hydroxyphenylpyruvate dioxygenase (HPPD)-, photosystem II–, acetolactate synthase (ALS)-, and protoporphyrinogen oxidase–inhibiting herbicides. Two field experiments were designed to investigate the efficacy of very-long-chain fatty-acid (VLCFA)-inhibiting herbicides, including a comparison of active ingredients at labeled use rates and a rate titration experiment. Amaranthus tuberculatus density and control were evaluated at 28 and 42 d after treatment (DAT). Nonencapsulated acetochlor, alachlor, and pyroxasulfone provided the greatest PRE control of CHR (56% to 75%) at 28 DAT, while metolachlor, S-metolachlor, dimethenamid-P, and encapsulated acetochlor provided less than 27% control. In the rate titration study, nonencapsulated acetochlor controlled CHR more than equivalent field use rates of S-metolachlor. Subsequent dose–response experiments with acetochlor, S-metolachlor, dimethenamid-P, and pyroxasulfone in the greenhouse included three multiple herbicide–resistant (MHR) A. tuberculatus populations: CHR-M6 (progeny generated from CHR), MCR-NH40 (progeny generated from Mclean County, IL), and ACR (Adams County, IL), in comparison with a sensitive population (WUS). Both CHR-M6 and MCR-NH40 are MHR to atrazine and HPPD, and ALS inhibitors and demonstrated higher survival rates (LD50) to S-metolachlor, acetochlor, dimethenamid-P, or pyroxasulfone than ACR (atrazine resistant but HPPD-inhibitor sensitive) and WUS. Based on biomass reduction (GR50), resistant to sensitive (R:S) ratios between CHR-M6 and WUS were 7.5, 6.1, 5.5, and 2.9 for S-metolachlor, acetochlor, dimethenamid-P, and pyroxasulfone, respectively. Values were greater for MCR-NH40 than CHR-M6, and ACR was the most sensitive to all VLCFA inhibitors tested. Complete control of all populations was achieved at or below a field use rate of acetochlor. In summary, field studies demonstrated CHR is not controlled by several VLCFA-inhibiting herbicides. Greenhouse dose–response experiments corroborated field results and generated R:S ratios (LD50) ranging from 4.5 to 64 for CHR-M6 and MCR-NH40 among the four VLCFA-inhibiting herbicides evaluated.
-
Characterization of a waterhemp (Amaranthus tuberculatus) population from Illinois resistant to herbicides from five site-of-action groups
Weed Technology, 2019Co-Authors: Cody M. Evans, Dean E Riechers, Seth A. Strom, Patrick J Tranel, Adam S Davis, Aaron G. HagerAbstract:Experiments were initiated to characterize a waterhemp population (CHR) discovered in a central Illinois corn field after it was not controlled by the 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor topramezone. Field experiments conducted during 2014–2015 indicated that acetolactate synthase (ALS)-, protoporphyrinogen oxidase (PPO)-, photosystem II (PSII)-, and HPPD-inhibiting herbicides and the synthetic auxin 2,4-D did not control the CHR population. Laboratory experiments confirmed target site-based resistance mechanisms to ALS- and PPO-inhibiting herbicides. Herbicide doses required to reduce dry biomass 50% (GR50) were determined in greenhouse dose-response experiments, and indicated 16-fold resistance to the HPPD inhibitor mesotrione, 9.5-fold resistance to the synthetic auxin 2,4-D, and 252-fold resistance to the PSII inhibitor atrazine. Complementary results from field, laboratory, and greenhouse investigations indicate that the CHR population has evolved resistance to herbicides from five sites of action (SOAs): ALS-, PPO-, PSII-, and HPPD-inhibiting herbicides and 2,4-D. Herbicide use history for the field in which CHR was discovered indicates no previous use of 2,4-D.Nomenclature: Atrazine; mesotrione; topramezone; 2,4-D; waterhemp, Amaranthus tuberculatus (Moq.) Sauer; corn, Zea mays L.
Roland Beffa - One of the best experts on this subject based on the ideXlab platform.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
Pest Management Science, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:Background Amaranthus tuberculatus is a problematic weed species in Midwest USA agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). Results Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. Conclusions Resistance to HPPD inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
bioRxiv, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:BACKGROUND: Amaranthus tuberculatus is a primary driver weed species throughout the American Midwest. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS: Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance/sensitive ratio of 15.0-21.1. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556), and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS: Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
Pest Management Science, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:BACKGROUND Amaranthus tuberculatus is a problematic weed species in Midwest U.S.A. agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species. This article is protected by copyright. All rights reserved.
-
characterization of glyphosate resistance in Amaranthus tuberculatus populations
Journal of Agricultural and Food Chemistry, 2014Co-Authors: Lothar Lorentz, Todd A. Gaines, Philip Westra, Scott J Nissen, Harry Strek, Heinz W Dehne, J P Ruizsantaella, Roland BeffaAbstract:The evolution of glyphosate-resistant weeds has recently increased dramatically. Six suspected glyphosate-resistant Amaranthus tuberculatus populations were studied to confirm resistance and determine the resistance mechanism. Resistance was confirmed in greenhouse for all six populations with glyphosate resistance factors (R/S) between 5.2 and 7.5. No difference in glyphosate absorption or translocation was observed between resistant and susceptible individuals. No mutation at amino acid positions G101, T102, or P106 was detected in the EPSPS gene coding sequence, the target enzyme of glyphosate. Analysis of EPSPS gene copy number revealed that all glyphosate-resistant populations possessed increased EPSPS gene copy number, and this correlated with increased expression at both RNA and protein levels. EPSPS Vmax and Kcat values were more than doubled in resistant plants, indicating higher levels of catalytically active expressed EPSPS protein. EPSPS gene amplification is the main mechanism contributing to glyphosate resistance in the A. tuberculatus populations analyzed.
-
characterization of glyphosate resistance in Amaranthus tuberculatus populations
Journal of Agricultural and Food Chemistry, 2014Co-Authors: Lothar Lorentz, Todd A. Gaines, Philip Westra, Scott J Nissen, Harry Strek, Heinz W Dehne, J P Ruizsantaella, Roland BeffaAbstract:The evolution of glyphosate-resistant weeds has recently increased dramatically. Six suspected glyphosate-resistant Amaranthus tuberculatus populations were studied to confirm resistance and determine the resistance mechanism. Resistance was confirmed in greenhouse for all six populations with glyphosate resistance factors (R/S) between 5.2 and 7.5. No difference in glyphosate absorption or translocation was observed between resistant and susceptible individuals. No mutation at amino acid positions G101, T102, or P106 was detected in the EPSPS gene coding sequence, the target enzyme of glyphosate. Analysis of EPSPS gene copy number revealed that all glyphosate-resistant populations possessed increased EPSPS gene copy number, and this correlated with increased expression at both RNA and protein levels. EPSPS Vmax and Kcat values were more than doubled in resistant plants, indicating higher levels of catalytically active expressed EPSPS protein. EPSPS gene amplification is the main mechanism contributing to...
Todd A. Gaines - One of the best experts on this subject based on the ideXlab platform.
-
protoporphyrinogen oxidase ppo inhibitor resistant waterhemp Amaranthus tuberculatus from nebraska is multiple herbicide resistant confirmation mechanism of resistance and management
Weed Science, 2019Co-Authors: Debalin Sarangi, Todd A. Gaines, Eric L. Patterson, Trey Stephens, Abigail L Barker, Amit J. JhalaAbstract:A waterhemp [ Amaranthus tuberculatus (Moq.) J. D. Sauer] biotype (designated as “NER”) collected from a soybean [ Glycine max (L.) Merr.] production field in eastern Nebraska survived the POST application of fomesafen at the labeled rate. The objectives of this study were to (1) quantify the level of resistance to protoporphyrinogen oxidase (PPO) inhibitors (acifluorfen, fomesafen, and lactofen) applied POST, (2) determine the mechanism of PPO-inhibitor resistance in the NER biotype, (3) determine whether NER possessed multiple resistance to acetolactate synthase (ALS)-, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS)-, and photosystem II (PSII)-inhibiting herbicides, and (4) control NER with POST soybean herbicides. A whole-plant dose–response bioassay revealed that the NER biotype was 4- to 6-fold resistant to PPO-inhibiting herbicides depending on the known susceptible biotype (S1 or S2) used for comparison. A Kompetitive Allele Specific PCR (KASP™) assay was developed and performed for rapid and robust detection of the ΔG210 mutation (deletion of a codon) in the PPX2L gene. All samples of the NER biotype tested positive for the ΔG210 mutation. Dose–response bioassays confirmed that the NER biotype was resistant to three additional herbicide sites of action. Chlorimuron and imazethapyr, both ALS inhibitors, applied at 32X the labeled rate resulted in Amaranthus tuberculatus is the first confirmed weed species in Nebraska to evolve resistance to four distinct herbicide sites of action, leaving no POST herbicide choice for effective control in glyphosate-resistant and conventional (non-transgenic) soybean.
-
protoporphyrinogen oxidase ppo inhibitor resistant waterhemp Amaranthus tuberculatus from nebraska is multiple herbicide resistant confirmation mechanism of resistance and management
Weed Science, 2019Co-Authors: Debalin Sarangi, Todd A. Gaines, Eric L. Patterson, Trey Stephens, Abigail L Barker, Amit J. JhalaAbstract:A waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] biotype (designated as “NER”) collected from a soybean [Glycine max (L.) Merr.] production field in eastern Nebraska survived the POST application of fomesafen at the labeled rate. The objectives of this study were to (1) quantify the level of resistance to protoporphyrinogen oxidase (PPO) inhibitors (acifluorfen, fomesafen, and lactofen) applied POST, (2) determine the mechanism of PPO-inhibitor resistance in the NER biotype, (3) determine whether NER possessed multiple resistance to acetolactate synthase (ALS)-, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS)-, and photosystem II (PSII)-inhibiting herbicides, and (4) control NER with POST soybean herbicides. A whole-plant dose–response bioassay revealed that the NER biotype was 4- to 6-fold resistant to PPO-inhibiting herbicides depending on the known susceptible biotype (S1 or S2) used for comparison. A Kompetitive Allele Specific PCR (KASP™) assay was developed and performed for rapid and robust detection of the ΔG210 mutation (deletion of a codon) in the PPX2L gene. All samples of the NER biotype tested positive for the ΔG210 mutation. Dose–response bioassays confirmed that the NER biotype was resistant to three additional herbicide sites of action. Chlorimuron and imazethapyr, both ALS inhibitors, applied at 32X the labeled rate resulted in <80% reduction in the aboveground biomass of the NER biotype. The same biotype was 3- and 7-fold resistant to glyphosate (EPSPS inhibitor) and atrazine (PSII inhibitor), respectively. Glufosinate, 2,4-D choline plus glyphosate, and dicamba were the only soybean POST herbicides that controlled NER effectively (≥92% aboveground biomass reduction). Amaranthus tuberculatus is the first confirmed weed species in Nebraska to evolve resistance to four distinct herbicide sites of action, leaving no POST herbicide choice for effective control in glyphosate-resistant and conventional (non-transgenic) soybean.
-
metabolism of 2 4 dichlorophenoxyacetic acid contributes to resistance in a common waterhemp Amaranthus tuberculatus population
Pest Management Science, 2018Co-Authors: Marcelo Rodrigues Alves De Figueiredo, Patrick J Tranel, Todd A. Gaines, Philip Westra, Lacy J Leibhart, Zachary J Reicher, Scott J Nissen, Mark L Bernards, Greg R Kruger, Mithila JugulamAbstract:BACKGROUND Synthetic auxins such as 2,4-dichlorophenoxyacetic acid (2,4-D) have been widely used for selective control of broadleaf weeds since the mid-1940s. In 2009, an Amaranthus tuberculatus (common waterhemp) population with 10-fold resistance to 2,4-D was found in Nebraska, USA. The 2,4-D resistance mechanism was examined by conducting [14 C] 2,4-D absorption, translocation and metabolism experiments. RESULTS No differences were found in 2,4-D absorption or translocation between resistant and susceptible A. tuberculatus plants. Resistant plants metabolized [14 C] 2,4-D more rapidly than did susceptible plants. The half-life of [14 C] 2,4-D in susceptible plants was 105 h, compared with 22 h in resistant plants. Pretreatment with the cytochrome P450 inhibitor malathion inhibited [14 C] 2,4-D metabolism in resistant plants and reduced the 2,4-D dose required for 50% growth inhibition (GR50 ) of resistant plants by 7-fold to 27 g ha-1 , similar to the GR50 for susceptible plants in the absence of malathion. CONCLUSION Our results demonstrate that rapid 2,4-D metabolism is a contributing factor to resistance in A. tuberculatus, potentially mediated by cytochrome P450. Metabolism-based resistance to 2,4-D could pose a serious challenge for A. tuberculatus control because of the potential for cross-resistance to other herbicides. © 2017 Society of Chemical Industry.
-
Inheritance of Mesotrione Resistance in an Amaranthus tuberculatus (var. rudis) Population from Nebraska, USA
Frontiers Media S.A., 2018Co-Authors: Maxwel C. Oliveira, Todd A. Gaines, Amit J. Jhala, Stevan Z. KnezevicAbstract:A population of Amaranthus tuberculatus (var. rudis) evolved resistance to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicides (mesotrione, tembotrione, and topramezone) in Nebraska. The level of resistance was the highest to mesotrione, and the mechanism of resistance in this population is metabolism-based likely via cytochrome P450 enzymes. The increasing number of weeds resistant to herbicides warrants studies on the ecology and evolutionary factors contributing for resistance evolution, including inheritance of resistance traits. In this study, we investigated the genetic control of mesotrione resistance in an A. tuberculatus population from Nebraska, USA. Results showed that reciprocal crosses in the F1 families exhibited nuclear inheritance, which allows pollen movement carrying herbicide resistance alleles. The mode of inheritance varied from incomplete recessive to incomplete dominance depending upon the F1 family. Observed segregation patterns for the majority of the F2 and back-cross susceptible (BC/S) families did not fit to a single major gene model. Therefore, multiple genes are likely to confer metabolism-based mesotrione resistance in this A. tuberculatus population from Nebraska. The results of this study aid to understand the genetics and inheritance of a non-target-site based mesotrione resistant A. tuberculatus population from Nebraska, USA
-
Reversing resistance to tembotrione in an Amaranthus tuberculatus (var. rudis) population from Nebraska, USA with cytochrome P450 inhibitors.
Pest management science, 2017Co-Authors: Maxwel C. Oliveira, Todd A. Gaines, Amit J. Jhala, Franck E. Dayan, Eric L. Patterson, Stevan Z. KnezevicAbstract:BACKGROUND A population of Amaranthus tuberculatus (var. rudis) was confirmed resistant to 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibitor herbicides (mesotrione, tembotrione, and topramezone) in a seed corn/soybean rotation in Nebraska. Further investigation confirmed a non-target-site resistance mechanism in this population. The main objective of this study was to explore the role of cytochrome P450 inhibitors for restoring the efficacy of HPPD-inhibitor herbicides on the HPPD-inhibitor resistant A. tuberculatus population from Nebraska, USA (HPPD-R). RESULTS Enhanced metabolism via cytochrome P450 enzymes is the mechanism of resistance in HPPD-R. Amitrole partially restored the activity of mesotrione, whereas malathion, amitrole, and piperonyl butoxide restored the activity of tembotrione and topramezone in HPPD-R. While corn was injured through malathion followed by mesotrione application a week after treatment, the injury was transient, and the crop recovered. CONCLUSION The use of cytochrome P450 inhibitors with tembotrione may provide a new way for controlling HPPD-inhibitor resistant A. tuberculatus, but further research is needed to identify the cytochrome P450 candidate gene(s) conferring metabolism-based resistance. The results presented here aid to gain an insight into non-target-site resistance weed management strategies.
Brent P. Murphy - One of the best experts on this subject based on the ideXlab platform.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
Pest Management Science, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:Background Amaranthus tuberculatus is a problematic weed species in Midwest USA agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). Results Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. Conclusions Resistance to HPPD inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.
-
hybridization potential between Amaranthus tuberculatus and Amaranthus albus
bioRxiv, 2021Co-Authors: Brent P. Murphy, Laura A Chatham, D M Mccormick, Patrick J TranelAbstract:The genus Amaranthus is composed of numerous annual herbs, several of which are primary driver weeds within annual production agricultural systems. In particular, Amaranthus tuberculatus, a dioecious species, is noteworthy for rapid growth rates, high fecundity, and an expanding geographic distribution. Interspecific hybridization within and between the subgenera Amaranthus and Acnidia is reported both in controlled environment and field studies, however a gap in knowledge exists with the subgenus Albersia. Interspecific hybridization may contribute to genetic diversity, and may contribute to the current range expansion of A. tuberculatus. Recently, a herbicide resistance survey of A. tuberculatus across five Midwestern states reported alleles of PPX2 similar to sequences of Amaranthus albus, a monoecious species. Here, we seek to generate empirical data for the hybridization potential of A. albus and A. tuberculatus through replicated, controlled crosses in a greenhouse. Of 65,000 progeny screened from A. albus grown with A. tuberculatus males, three were confirmed as hybrids. Hybrids were dioecious, possessed phenotypic traits of both species, and had limited to no fertility. DNA content analysis of backcross progeny suggested a polyploid state may be required for hybrid formation. Screening of 120 progeny of A. tuberculatus females grown with A. albus identified no hybrids, though a skew to female progeny was observed. The female skew may be due to apomixis or auto-pollination, the spontaneous generation of male flowers on otherwise female plants. Our results indicate that introgression between A. albus and A. tuberculatus will occur less frequently than what has often been reported from hybridization studies with different pairs of Amaranthus species.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
bioRxiv, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:BACKGROUND: Amaranthus tuberculatus is a primary driver weed species throughout the American Midwest. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS: Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance/sensitive ratio of 15.0-21.1. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556), and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS: Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species.
-
genetic architecture underlying hppd inhibitor resistance in a nebraska Amaranthus tuberculatus population
Pest Management Science, 2021Co-Authors: Brent P. Murphy, Roland Beffa, Patrick J TranelAbstract:BACKGROUND Amaranthus tuberculatus is a problematic weed species in Midwest U.S.A. agricultural systems. Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) are an important chemistry for weed management in numerous cropping systems. Here, we characterize the genetic architecture underlying the HPPD-inhibitor resistance trait in an A. tuberculatus population (NEB). RESULTS Dose-response studies of an F1 generation identified HPPD-inhibitor resistance as a dominant trait with a resistance factor of 15.0-21.1 based on dose required for 50% growth reduction. Segregation analysis in a pseudo-F2 generation determined the trait is moderately heritable (H2 = 0.556) and complex. Bulk segregant analysis and validation with molecular markers identified two quantitative trait loci (QTL), one on each of Scaffold 4 and 12. CONCLUSIONS Resistance to HPPD-inhibitors is a complex, largely dominant trait within the NEB population. Two large-effect QTL were identified controlling HPPD-inhibitor resistance in A. tuberculatus. This is the first QTL mapping study to characterize herbicide resistance in a weedy species. This article is protected by copyright. All rights reserved.
-
Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri.
Genome biology and evolution, 2020Co-Authors: Jacob S. Montgomery, Brent P. Murphy, Darci A. Giacomini, Bridgit Waithaka, Christa Lanz, Ruth Campe, Jens Lerchl, Andreas Landes, Fanny Gatzmann, Antoine JanssenAbstract:Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri are agronomically important weed species. Here, we present the most contiguous draft assemblies of these three species to date. We utilized a combination of Pacific Biosciences long-read sequencing and chromatin contact mapping information to assemble and order sequences of A. palmeri to near-chromosome-level resolution, with scaffold N50 of 20.1 Mb. To resolve the issues of heterozygosity and coassembly of alleles in diploid species, we adapted the trio binning approach to produce haplotype assemblies of A. tuberculatus and A. hybridus. This approach resulted in an improved assembly of A. tuberculatus, and the first genome assembly for A. hybridus, with contig N50s of 2.58 and 2.26 Mb, respectively. Species-specific transcriptomes and information from related species were used to predict transcripts within each assembly. Syntenic comparisons of these species and Amaranthus hypochondriacus identified sites of genomic rearrangement, including duplication and translocation, whereas genetic map construction within A. tuberculatus highlighted the need for further ordering of the A. hybridus and A. tuberculatus contigs. These multiple reference genomes will accelerate genomic studies in these species to further our understanding of weedy evolution within Amaranthus.