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Patrick J. Tranel – One of the best experts on this subject based on the ideXlab platform.

  • Male-specific Y-chromosomal regions in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri).
    The New phytologist, 2020
    Co-Authors: Jacob S. Montgomery, Darci A. Giacomini, Detlef Weigel, Patrick J. Tranel
    Abstract:

    Amaranthus tuberculatus and Amaranthus palmeri are agronomically important weed species, both with stable dioecious reproductive systems. An understanding of the genetic basis of sex determination may lead to new methods of managing these troublesome weeds. Previous research identified genomic sequences associated with maleness in each species. Male-specific sequences were used to identify genomic regions in both species that are believed to contain sex-determining genes, i.e. the male-specific Y (MSY) region. These regions were compared to understand if sex determination is controlled via the same physiological pathway and if dioecy evolved independently. A contiguously assembled candidate MSY region identified in Amaranthus palmeri is approximately 1.3 Mb with 121 predicted gene models. In Amaranthus tuberculatus, several contigs, with combined length of 4.6 Mb and with 147 gene models, were identified as belonging to the MSY region. Synteny was not detected between the two species’ candidate MSY regions but they shared two predicted genes. With lists of candidate genes for sex determination containing fewer than 200 in each species, future research can address whether sex determination is controlled via similar physiological pathways and whether dioecy has indeed evolved independently in these species.

  • Coevolution of Resistance to PPO Inhibitors in Waterhemp (Amaranthus tuberculatus) and Palmer Amaranth (Amaranthus palmeri)
    Weed Science, 2019
    Co-Authors: Kathryn J. Lillie, Darci A. Giacomini, Jonathan D. Green, Patrick J. Tranel
    Abstract:

    The first case of evolved protoporphyrinogen oxidase (PPO)-inhibitor resistance was observed in 2001 in common waterhemp [Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif]. This resistance in A. tuberculatus is most commonly conferred by deletion of the amino acid glycine at the 210th position (ΔGly-210) of the PPO enzyme (PPO2) encoded by PPX2. In a field in Kentucky in 2015, inadequate control of Amaranthus plants was observed following application of a PPO inhibitor. Morphological observations indicated that survivors included both A. tuberculatus and Palmer amaranth (Amaranthus palmeri S. Watson). Research was conducted to confirm species identities and resistance and then to determine whether resistance evolved independently in the two species or via hybridization. Results from a quantitative PCR assay based on the ribosomal internal transcribed spacer confirmed that both A. tuberculatus and A. palmeri coexisted in the field. The mutation conferring ΔGly-210 in PPO2 was identified in both species; phylogenetic analysis of a region of PPX2, however, indicated that the mutation evolved independently in the two species. Genotyping of greenhouse-grown plants that survived lactofen indicated that all A. tuberculatus survivors, but only a third of A. palmeri survivors, contained the ΔGly-210 mutation. Consequently, A. palmeri plants were evaluated for the presence of an arginine to glycine or methionine substitution at position 128 of PPO2 (Arg-128-Gly and Arg-128-Met). The Arg-128-Gly substitution was found to account for resistance that was not accounted for by the ΔGly-210 mutation in plants from the A. palmeri population. Results from this study provide a modern-day example of both parallel and convergent evolution occurring within a single field.

  • Sex-Specific Markers for Waterhemp (Amaranthus tuberculatus) and Palmer Amaranth (Amaranthus palmeri)
    Weed Science, 2019
    Co-Authors: Jacob S. Montgomery, Darci A. Giacomini, Ahmed Sadeque, Patrick J. Brown, Patrick J. Tranel
    Abstract:

    Waterhemp [ Amaranthus tuberculatus (Moq.) J. D. Sauer] and Palmer amaranth ( Amaranthus palmeri S. Watson) are troublesome weeds of row-crop production in the United States. Their dioecious reproductive systems ensure outcrossing, facilitating rapid evolution and distribution of resistances to multiple herbicides. Little is known, however, about the genetic basis of dioecy in Amaranthus species. In this work, we use restriction site–associated DNA sequencing (RAD-Seq) to investigate the genetic basis of sex determination in A. tuberculatus and A. palmeri . For each species, approximately 200 plants of each sex were sampled and used to create RAD-Seq libraries. The resulting libraries were separately bar-coded and then pooled for sequencing with the Illumina platform, yielding millions of 64-bp reads. These reads were analyzed to identify sex-specific and sex-biased sequences. We identified 345 male-specific sequences from the A. palmeri data set and 2,754 male-specific sequences in A. tuberculatus . An unexpected 723 female-specific sequences were identified in a subset of the A. tuberculatus females; subsequent research, however, indicated female specificity of these markers was limited to the population from which they were identified. Primer sets designed to specifically amplify male-specific sequences were tested for accuracy on multiple, geographically distinct populations of A. tuberculatus and A. palmeri , as well as other Amaranthus species. Two primer sets for A. palmeri and four primer sets for A. tuberculatus were each able to distinguish between male and female plants with at least 95% accuracy. In the near term, sex-specific markers will be useful to the A. tuberculatus and A. palmeri research communities (e.g., to predict sex for crossing experiments). In the long-term, this research will provide the foundational tools for detailed investigations into the molecular biology and evolution of dioecy in weedy Amaranthus species.

Darci A. Giacomini – One of the best experts on this subject based on the ideXlab platform.

  • Male-specific Y-chromosomal regions in waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri).
    The New phytologist, 2020
    Co-Authors: Jacob S. Montgomery, Darci A. Giacomini, Detlef Weigel, Patrick J. Tranel
    Abstract:

    Amaranthus tuberculatus and Amaranthus palmeri are agronomically important weed species, both with stable dioecious reproductive systems. An understanding of the genetic basis of sex determination may lead to new methods of managing these troublesome weeds. Previous research identified genomic sequences associated with maleness in each species. Male-specific sequences were used to identify genomic regions in both species that are believed to contain sex-determining genes, i.e. the male-specific Y (MSY) region. These regions were compared to understand if sex determination is controlled via the same physiological pathway and if dioecy evolved independently. A contiguously assembled candidate MSY region identified in Amaranthus palmeri is approximately 1.3 Mb with 121 predicted gene models. In Amaranthus tuberculatus, several contigs, with combined length of 4.6 Mb and with 147 gene models, were identified as belonging to the MSY region. Synteny was not detected between the two species’ candidate MSY regions but they shared two predicted genes. With lists of candidate genes for sex determination containing fewer than 200 in each species, future research can address whether sex determination is controlled via similar physiological pathways and whether dioecy has indeed evolved independently in these species.

  • Draft Genomes of Amaranthus tuberculatus, Amaranthus hybridus, and Amaranthus palmeri.
    Genome biology and evolution, 2020
    Co-Authors: Jacob S. Montgomery, Brent P. Murphy, Darci A. Giacomini, Bridgit Waithaka, Christa Lanz, Ruth Campe, Jens Lerchl, Andreas Landes, Fanny Gatzmann, Antoine Janssen
    Abstract:

    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.

  • Target Site-Based Resistance to ALS Inhibitors, Glyphosate, and PPO Inhibitors in an Amaranthus palmeri Accession from Mississippi
    American Journal of Plant Sciences, 2020
    Co-Authors: Vijay K Nandula, Darci A. Giacomini, William T. Molin
    Abstract:

    Extensive acceptance of glyphosate-resistant (GR) row crops coupled with the simultaneous increase in glyphosate usage has sped the evolution of glyphosate resistance in economically important weeds. GR Amaranthus palmeri populations are widespread across the state with some exhibiting multiple resistance to acetolactate synthase (ALS) inhibiting herbicides such as pyrithiobac. A GR and ALS inhibitor-resistant accession was also resistant to the protoporphyrinogen oxidase (PPO) inhibiting herbicide fomesafen. The PPO inhibitor resistance profile and multiple herbicide resistance mechanisms in this accession were investigated. In addition to fomesafen, resistance to postemergence applications of acifluorfen, lactofen, carfentrazone, and sulfentrazone was confirmed. There was no resistance to preemergence application of fomesafen, flumioxazin, or oxyfluorfen. Molecular analysis of the ALS gene indicated the presence of point mutations leading to single nucleotide substitutions at codons 197, 377, 574, and 653, resulting in proline-to-serine, arginine-to-glutamine, tryptophan-to-leucine, and serine-to-asparagine replacements, respectively. The resistant accession contained up to 87-fold more copies of the EPSPS gene compared to a susceptible accession. A mutation leading to a deletion of glycine at codon 210 (ΔG210) of PPO2 gene was also detected. These results indicate that the mechanism of resistance in the Palmer amaranth accession is target-site based, i.e., altered target site for ALS and PPO inhibitor resistance and gene amplification for glyphosate resistance.

Hugo R. Permingeat – One of the best experts on this subject based on the ideXlab platform.

  • Target-site resistance to ALS-inhibiting herbicides in Amaranthus palmeri from Argentina
    Pest management science, 2017
    Co-Authors: Alvaro S. Larran, Valeria E Palmieri, Valeria E. Perotti, Lucas Lieber, Daniel Tuesca, Hugo R. Permingeat
    Abstract:

    BACKGROUND Herbicide resistant weeds are a serious problem worldwide. Recently, two populations of Amaranthus palmeri with suspected cross-resistance to ALS-inhibiting herbicides (R1 and R2) were found by farmers in two locations from Argentina (Vicuna Mackenna and Totoras, respectively). We conducted studies to confirm and elucidate the mechanism of resistance. RESULTS We performed in vivo dose-response assays, and confirmed both populations had a strong resistance to chlorimuron-ethyl, diclosulam and imazethapyr when compared to a susceptible population (S). In vitro ALS activity inhibition tests only indicated a considerable resistance to imazethapyr and chlorimuron-ethyl, indicating that other non-target mechanisms could be involved in diclosulam resistance. Subsequently, molecular analysis of als nucleotide sequences revealed three single base-pair mutations conferring substitutions in amino acids previously associated with resistance to ALS inhibitors, A122, W574, and S653 CONCLUSION This is the first report of als resistant alleles in Amaranthus palmeri from Argentina. The data support the involvement of a target-site mechanism of resistance to ALS inhibiting herbicides.

  • target site resistance to acetolactate synthase als inhibiting herbicides in Amaranthus palmeri from argentina
    Pest Management Science, 2017
    Co-Authors: Alvaro S. Larran, Valeria E Palmieri, Valeria E. Perotti, Lucas Lieber, Daniel Tuesca, Hugo R. Permingeat
    Abstract:

    BACKGROUND Herbicide-resistant weeds are a serious problem worldwide. Recently, two populations of Amaranthus palmeri with suspected cross-resistance to acetolactate synthase (ALS)-inhibiting herbicides (R1 and R2) were found by farmers in two locations in Argentina (Vicuna Mackenna and Totoras, respectively). We conducted studies to confirm and elucidate the mechanism of resistance. RESULTS We performed in vivo dose–response assays, and confirmed that both populations had strong resistance to chlorimuron-ethyl, diclosulam and imazethapyr when compared with a susceptible population (S). In vitro ALS activity inhibition tests only indicated considerable resistance to imazethapyr and chlorimuron-ethyl, indicating that other non-target mechanisms could be involved in diclosulam resistance. Subsequently, molecular analysis of als nucleotide sequences revealed three single base-pair mutations producing substitutions in amino acids previously associated with resistance to ALS inhibitors, A122, W574, and S653. CONCLUSION This is the first report of als resistance alleles in A. palmeri in Argentina. The data support the involvement of a target-site mechanism of resistance to ALS-inhibiting herbicides. © 2017 Society of Chemical Industry

Muthukumar V. Bagavathiannan – One of the best experts on this subject based on the ideXlab platform.

  • Late-season surveys to document seed rain potential of Palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus) in Texas cotton.
    PloS one, 2020
    Co-Authors: Kaisa Werner, Peter A. Dotray, Debalin Sarangi, Scott A. Nolte, Muthukumar V. Bagavathiannan
    Abstract:

    Weed escapes are often present in large production fields prior to harvest, contributing to seed rain and species persistence. Late-season surveys were conducted in cotton (Gossypium hirsutum L.) fields in Texas in 2016 and 2017 to identify common weed species present as escapes and estimate seed rain potential of Palmer amaranth (Amaranthus palmeri S. Watson) and waterhemp [A. tuberculatus (Moq.) J.D. Sauer], two troublesome species with high fecundity. A total of 400 cotton fields across four major cotton-producing regions in Texas [High Plains (HP), Gulf Coast (GC), Central Texas, and Blacklands] were surveyed. Amaranthus palmeri, Texas millet [Urochloa texana (Buckley) R. Webster], A. tuberculatus, ragweed parthenium (Parthenium hysterophorus L.), and barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] were reported as the top five weed escapes in cotton fields. Amaranthus palmeri was the most prevalent weed in the HP and Lower GC regions, whereas A. tuberculatus escapes were predominantly observed in the Upper GC and Blacklands regions. On average, 9.4% of an individual field was infested with A. palmeri escapes in the Lower GC region; however, 5.1 to 8.1% of a field was infested in the HP region. Average A. palmeri density ranged from 405 (Central Texas) to 3,543 plants ha–1 (Lower GC). The greatest seed rain potential by A. palmeri escapes was observed in the upper HP region (13.9 million seeds ha–1), whereas the seed rain potential of A. tuberculatus escapes was the greatest in the Blacklands (12.9 million seeds ha–1) and the upper GC regions (9.8 million seeds ha–1). Seed rain from late-season A. palmeri and A. tuberculatus escapes is significant in Texas cotton, and effective management of these escapes is imperative for minimizing seedbank inputs and impacting weed species persistence.

  • Late-season surveys to document seed rain potential of Palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus) in Texas cotton
    , 2019
    Co-Authors: Kaisa Werner, Peter A. Dotray, Debalin Sarangi, Scott A. Nolte, Muthukumar V. Bagavathiannan
    Abstract:

    Despite the best weed control efforts, weed escapes are often present in large production fields prior to harvest, contributing to seed rain and species persistence. Late-season surveys were conducted in cotton (Gossypium hirsutum L.) fields in Texas in 2016 and 2017 to identify common weed species present as escapes and estimate seed rain potential of Palmer amaranth (Amaranthus palmeri S. Watson) and waterhemp [A. tuberculatus (Moq.) J.D. Sauer], two troublesome weed species with high fecundity. A total of 400 cotton fields across four major cotton-producing regions in Texas [High Plains (HP), Gulf Coast (GC), Central Texas, and Blacklands] were surveyed. Results have revealed that A. palmeri, Texas millet [Urochloa texana (Buckley) R. Webster], A. tuberculatus, ragweed parthenium (Parthenium hysterophorus L.), and barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] were the top five weed escapes present in cotton fields. Amaranthus palmeri was the most prevalent weed in the HP and Lower GC regions, whereas A. tuberculatus escapes were predominantly observed in the Upper GC and Blacklands regions. On average, 9.4% of an individual field was infested with A. palmeri escapes in the Lower GC region; however, it ranged between 5.1 and 8.1% in the HP region. Average A. palmeri density ranged from 405 (Central Texas) to 3,543 plants ha–1 (Lower GC). The greatest seed rain potential by A. palmeri escapes was observed in the upper HP region (13.9 million seeds ha–1), whereas the seed rain potential of A. tuberculatus escapes was the greatest in the Blacklands (12.9 million seeds ha–1) and the upper GC regions (9.8 million seeds ha–1). Results indicated that seed rain from late-season A. palmeri and A. tuberculatus escapes are significant in Texas cotton, and effective management of these escapes is imperative for minimizing seedbank inputs and impacting species persistence.

  • EPSPS Gene Amplification Primarily Confers Glyphosate Resistance among Arkansas Palmer amaranth (Amaranthus palmeri) Populations
    Weed Science, 2018
    Co-Authors: Shilpa Singh, Muthukumar V. Bagavathiannan, Vijay Singh, Amy Lawton-rauh, Nilda Roma-burgos
    Abstract:

    Research was conducted to determine whether resistance to glyphosate among Palmer amaranth (Amaranthus palmeri S. Watson) populations within the U.S. state of Arkansas was due solely to increased EPSPS gene copy number and whether gene copy number is correlated with resistance level to glyphosate. One hundred and fifteen A. palmeri accessions were treated with 840 g ae ha-1 glyphosate. 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 ED50 values ranging from 494 to 1,355g 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 increased EPSPS gene copies. Resistant plants from the remaining eight GR accessions (62% of resistant plants tested) had 19 to 224 more EPSPS gene copies than the SS. Among the accessions tested, injury declined 4% with every additional EPSPS copy. ED50 values were directly correlated with EPSPS copy number. The highly resistant accession MIS11-B had an ED50 of 1,355 g ha-1 and 150 gene copies. Partial sequences of EPSPS from GR accessions without EPSPS amplification did not contain any of the known resistance-conferring mutations. Nearly 40% of GR accessions putatively harbor non-target site resistance mechanisms. Therefore, elevated EPSPS gene copy number is associated with glyphosate resistance among A. palmeri from Arkansas.

William T. Molin – One of the best experts on this subject based on the ideXlab platform.

  • homogeneity among glyphosate resistant Amaranthus palmeri in geographically distant locations
    PLOS ONE, 2020
    Co-Authors: William T. Molin, Eric L Patterson, Christopher A. Saski
    Abstract:

    Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri S. Watson in 2006, resistant populations have been reported in 28 states. The mechanism of resistance is amplification of a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, and is unique to glyphosate-resistant plants. The replicon contains a single copy of the 10-kb 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene which causes the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. It is not known whether the resistance by this amplification mechanism evolved once and then spread across the country or evolved independently in several locations. To compare genomic representation and variation across the EPSPS replicon, whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. The high sequence conservation among GR biotypes with very few polymorphisms which were widely distributed across the USA further supports the hypothesis that glyphosate resistance most likely originated from a single population. We show that the replicon from different populations was unique to GR plants and had similar levels of amplification.

  • Autonomous replication sequences from the Amaranthus palmeri eccDNA replicon enable replication in yeast
    , 2020
    Co-Authors: William T. Molin, Allison Yaguchi, Mark Blenner, Christopher Saski
    Abstract:

    Abstract Objective: The objective of the research presented here was to determine whether autonomous replication sequences (ARS) discovered in the eccDNA replicon of glyphosate resistant Amaranthus palmeri enable self-replication in a yeast system. Results: Sequence analysis of the eccDNA replicon revealed a region of sharp changes in A+T/G+C content with characteristic bending indicative of an autonomous replication sequence. Further sequence analysis revealed an extended autonomous replication sequence (EACS) in close proximity to multiple DNA unwinding element (DUE) sequences. This region of the eccDNA replicon enabled autonomous replication of an ARS-less yeast plasmid.

  • homogeneity among glyphosate resistant Amaranthus palmeri in geographically distant locations
    bioRxiv, 2020
    Co-Authors: William T. Molin, Eric L Patterson, Christopher A. Saski
    Abstract:

    Since the initial report of glyphosate-resistant (GR) Amaranthus palmeri (S) Wats. in 2006, resistant populations have been reported in more than 28 states. It is not known whether the resistance evolved once and spread across the country or evolved independently in several locations. Glyphosate resistance in A. palmeri is due to amplification of the 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS ) gene and the concomitant increased expression of EPSP synthase, the target enzyme of glyphosate. The amplified unit, a 399-kb extrachromosomal circular DNA, called the EPSPS replicon, is unique to glyphosate-resistant plants and contains one copy of the 10-kb EPSPS gene. To compare genomic representation and variation across the EPSPS replicon , whole genome shotgun sequencing (WGS) and mapping of sequences from both GR and susceptible (GS) biotypes to the replicon consensus sequence was performed. A single leaf from each of two plants from each population were combined as a sample. Sampling of GR biotypes from AZ, KS, GA, MD and DE and GS biotypes from AZ, KS and GA revealed complete contiguity and deep representation with sequences from GR plants, but lack of homogeneity and contiguity with breaks in coverage were observed with sequences from GS biotypes. Very few polymorphisms were identified among GR individuals indicating high sequence conservation among the EPSPS replicons from GR populations widely separated across the USA. These results support the hypothesis that glyphosate resistance most likely originated from a single location or population and rapidly spread across the USA. We show that the replicon has spread across the country to different populations with similar levels of amplification with little to no sequence variation.