First Report of Kochia (Bassia scoparia) with Cross-Resistance to Dicamba and Fluroxypyr in Western Kansas

2019 ◽  
Vol 33 (2) ◽  
pp. 335-341 ◽  
Author(s):  
Vipan Kumar ◽  
Randall S. Currie ◽  
Prashant Jha ◽  
Phillip W. Stahlman
Keyword(s):  
Great Plains ◽  
Dose Response ◽  
Cover Crops ◽  
Gene Copy Number ◽  
Dry Weight ◽  
Gene Copy ◽  
Cross Resistance ◽  
Control Programs ◽  
Gene Copies ◽  
Whole Plant

AbstractEvolution and rapid spread of herbicide-resistant (HR) kochia has become a significant challenge for growers in the U.S. Great Plains. The main objectives of this research were to confirm and characterize the response of putative auxinic HR (Aux-HR) kochia accessions (designated as KS-4A, KS-4D, KS-4H, KS-10A, KS-10-G, and KS-10H) collected from two different corn fields near Garden City, KS, to dicamba and fluroxypyr and to determine the EPSPS gene copy number to detect whether those accessions were also resistant to glyphosate. Single-dose experiments indicated that putative Aux-HR kochia accessions had 78% to 100% and 85% to 100% survivors when treated with dicamba (560 g ae ha−1) and fluroxypyr (235 g ae ha−1), respectively. Whole-plant dicamba dose–response studies revealed that the selected Aux-HR accessions had 2.9- to 15.1- and 3.1- to 9.4-fold resistance to dicamba relative to two susceptible accessions (MT-SUS and KS-SUS). In a separate fluroxypyr dose–response experiment, the selected Aux-HR accessions also exhibited 3.8- to 7.3- and 3.0- to 8.6-fold resistance to fluroxypyr on the basis of shoot fresh and dry weight responses, respectively. The confirmed Aux-HR kochia accessions also had 3 to 13 EPSPS gene copies relative to MT-SUS and KS-SUS accessions (each with 1 EPSPS gene copy). These results suggest that the putative Aux-HR kochia accessions from Kansas had developed moderate to high levels of cross-resistance to dicamba and fluroxypyr and low to high levels of resistance to glyphosate. This is the first confirmation of kochia accessions with cross-resistance to dicamba and fluroxypyr in Kansas. Growers should use diverse kochia control programs, including the proper use of dicamba and fluroxypyr stewardship, use of cover crops, occasional tillage, diversified crop rotations, and alternative effective herbicides to prevent further evolution and spread of Aux-HR kochia on their fields.

scholarly journals Effect of EPSPS Gene Copy Number and Glyphosate Selection on Fitness of Glyphosate-Resistant Bassia Scoparia in The Field

2021 ◽  
Author(s):  
Charlemagne Ajoc Lim ◽  
Prashant Jha ◽  
Vipan Kumar ◽  
Alan T. Dyer
Keyword(s):  
Sugar Beet ◽  
Seed Production ◽  
Great Plains ◽  
Copy Number ◽  
Gene Copy Number ◽  
Reproductive Traits ◽  
Gene Copy ◽  
Epsps Gene ◽  
Gene Copies

Abstract The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. We tested the hypothesis of reduced GR B. scoparia fitness (reproductive traits) to increasing glyphosate rates (applied as single or sequential applications) potentially experienced within a GR sugar beet field. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2,214 g ae ha− 1 or higher prevented seed production in B. scoparia plants with 2–4 (low levels of resistance) and 5–6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2–6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.

Confirmation of Glyphosate-Resistant Horseweed (Conyza canadensis) in Montana Cereal Production and Response to POST Herbicides

2017 ◽  
Vol 31 (6) ◽  
pp. 799-810 ◽  
Author(s):  
Vipan Kumar ◽  
Prashant Jha ◽  
Amit J. Jhala
Keyword(s):  
Great Plains ◽  
Dose Response ◽  
Best Management Practices ◽  
Management Practices ◽  
Dry Weight ◽  
Shoot Dry Weight ◽  
Greenhouse Study ◽  
Whole Plant ◽  
Cereal Production ◽  
Sites Of Action

In recent years, horseweed has become an increasing problem in Montana. To confirm and characterize the level of glyphosate resistance, seeds were collected from putative glyphosate-resistant (GR) horseweed (GR-MT) plants in a wheat–fallow field in McCone County, MT. Known GR (GR-NE) and glyphosate-susceptible (GS-NE) horseweed accessions from Lincoln, NE, were included for comparison in dose–response and shikimate accumulation studies. Whole-plant glyphosate dose–response experiments conducted at the early- (5- to 8-cm diameter) and late- (12- to 15-cm diameter) rosette stages of horseweed indicated that GR-MT accessions had a 2.5- to 4.0-fold level of resistance to glyphosate relative to the GS-NE accession, on the basis of shoot dry weight (GR50values). The level of resistance was 3.1- to 7.9-fold on the basis of visually assessed injury estimates (I50values). At the whole-plant level, about 2.1- to 4.5-fold higher shikimate accumulation was observed in the GS-NE accession compared with the GR-MT and GR-NE accessions over a 10-d period after glyphosate was applied at 1,260 g ae ha−1. In a separate greenhouse study, all three horseweed accessions were also screened with alternate POST herbicides registered for use in wheat–fallow rotations. The majority of the tested herbicides provided ≥90% injury at the field-use rates for all three horseweed accessions 3 wk after treatment. This is the first published report on the occurrence of GR horseweed in Montana cereal production. Increased awareness and adoption of best management practices, including the use of diversified (based on multiple sites of action) herbicide programs highlighted in this study, would aid in mitigating the further spread of GR horseweed in the cereal production fields of the U.S. Great Plains.

Confirmation of Glyphosate-Resistant Kochia (Kochia scoparia) from Sugar Beet Fields in Idaho and Oregon

2017 ◽  
Vol 32 (1) ◽  
pp. 27-33 ◽  
Author(s):  
Vipan Kumar ◽  
Joel Felix ◽  
Don Morishita ◽  
Prashant Jha
Keyword(s):  
Sugar Beet ◽  
Copy Number ◽  
Cropping Systems ◽  
Gene Copy Number ◽  
Glyphosate Resistance ◽  
Gene Copy ◽  
Resistance Level ◽  
Control Programs ◽  
Gene Copies

AbstractGlyphosate-resistant (GR) kochia is an increasing management concern in major cropping systems of the northwestern US. In 2014, we investigated four putative GR kochia accessions (designated as ALA, VAL, WIL, DB) collected from sugar beet fields in eastern Oregon and southwestern Idaho to characterize the level of evolved glyphosate resistance and determine the relationship between the 5-enol-pyruvylshikimate-3-phospate synthase (EPSPS) gene copy number and level of glyphosate resistance. TheEPSPSgene copy number was used as a molecular marker to detect GR kochia in subsequent surveys in 2015 and 2016. Based on LD50values from a whole-plant dose-response study, the four putative GR kochia populations were 2.0- to 9.6-fold more resistant to glyphosate than the glyphosate-susceptible (GS) accession. In anin vivoleaf-disk shikimate assay, leaf disks of GS kochia plants treated with 100-μM glyphosate accumulated 2.4- to 4.0-fold higher amounts of shikimate than the GR plants. The four GR accessions had 2.7 to 9.1 relativeEPSPSgene copies compared with the GS accession (<1EPSPSgene copies), and there was a linear relationship betweenEPSPSgene copy number and glyphosate resistance level (LD50values). The 2015 and 2016 GR kochia survey results indicated that about half of the collected populations from sugar beet fields in eastern Oregon had developed resistance to glyphosate whereas only one population from the Idaho collection was confirmed glyphosate resistant. This is the first confirmation of GR kochia in sugar beet fields in eastern Oregon and southwestern Idaho. Diversified weed control programs will be required to prevent further development and spread of GR kochia in sugar beet-based rotations in this region.

scholarly journals Effect of EPSPS gene copy number and glyphosate selection on fitness of glyphosate-resistant Bassia scoparia in the field

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Charlemagne Ajoc Lim ◽  
Prashant Jha ◽  
Vipan Kumar ◽  
Alan T. Dyer
Keyword(s):  
Sugar Beet ◽  
Seed Production ◽  
Great Plains ◽  
Copy Number ◽  
Gene Copy Number ◽  
Reproductive Traits ◽  
Gene Copy ◽  
Epsps Gene ◽  
Gene Copies

AbstractThe widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. With the continued use of glyphosate in GR sugar beet, the effect of increasing glyphosate rates (applied as single or sequential applications) on the fitness of GR B. scoparia individuals with variable EPSPS gene copies was tested under field conditions. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2214 g ae ha−1 or higher prevented seed production in B. scoparia plants with 2–4 (low levels of resistance) and 5–6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2–6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.

scholarly journals Nosocomial Outbreak of Carbapenemase-Producing Proteus mirabilis With Two Novel Salmonella Genomic Island 1 Variants Carrying Different blaNDM–1 Gene Copies in China

2022 ◽  
Vol 12 ◽  
Author(s):  
Lang Yang ◽  
Hong He ◽  
Qichao Chen ◽  
Kaiying Wang ◽  
Yanfeng Lin ◽  
...  
Keyword(s):  
Proteus Mirabilis ◽  
Copy Number ◽  
Genomic Island ◽  
Gene Copy Number ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Gene Copy ◽  
Nosocomial Outbreak ◽  
Gene Copy Number Variation ◽  
Gene Copies

NDM-1-producing multidrug-resistant Proteus mirabilis brings formidable clinical challenges. We report a nosocomial outbreak of carbapenem-resistant P. mirabilis in China. Six P. mirabilis strains collected in the same ward showed close phylogenetic relatedness, indicating clonal expansion. Illumina and MinION sequencing revealed that three isolates harbored a novel Salmonella genomic island 1 carrying a blaNDM–1 gene (SGI1-1NDM), while three other isolates showed elevated carbapenem resistance and carried a similar SGI1 but with two blaNDM–1 gene copies (SGI1-2NDM). Four new single nucleotide mutations were present in the genomes of the two-blaNDM–1-harboring isolates, indicating later emergence of the SGI1-2NDM structure. Passage experiments indicated that both SGI variants were stably persistent in this clone without blaNDM–1 copy number changes. This study characterizes two novel blaNDM–1-harboring SGI1 variants in P. mirabilis and provides a new insight into resistance gene copy number variation in bacteria.

Structure and transcription of the actin gene of Trypanosoma brucei

1988 ◽  
Vol 8 (5) ◽  
pp. 2166-2176 ◽  
Author(s):  
M F Ben Amar ◽  
A Pays ◽  
P Tebabi ◽  
B Dero ◽  
T Seebeck ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Splice Site ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Actin Gene ◽  
S1 Nuclease ◽  
Actin Genes ◽  
Gene Copies ◽  
Actin Mrna

In Trypanosoma brucei, the actin gene is present in a cluster of two, three, or four tandemly linked copies, depending on the strain. Each cluster seems to exist in two allelic versions, as suggested by the polymorphism of both gene number and restriction fragment length in the DNA from cloned trypanosomes. The amplification of the gene copy number probably occurs through unequal sister chromatid exchange. The chromosomes harboring the actin genes belong to the large size class. The coding sequence was 1,128 nucleotides long and showed 60 to 70% homology to other eucaryotic actin genes. Surprisingly, this homology seemed weaker with Trypanosoma congolense, Trypanosoma cruzi, Trypanosoma vivax, Trypanosoma mega, or Leishmania actin-specific sequences. The mRNA was around 1.6 kilobases long and was synthesized at the same level in bloodstream and procyclic forms of the parasite. Large RNA precursors, up to 7.7 kilobases, were found in a pattern identical in strains containing either two or three gene copies. Probing of the flanking regions of the gene with either steady-state or in vitro transcripts, as well as S1 nuclease protection and primer extension experiments, allowed mapping of the 3' splice site of the actin mRNA, 38 nucleotides upstream from the translation initiation codon. A variably sized poly(dT) tract was found about 30 base pairs ahead of the splice site. The largest detected actin mRNA precursor seemed to give rise to at least two additional stable mRNAs. The RNA polymerase transcribing the actin gene exhibited the same sensitivity to inhibition by alpha-amanitin as that transcribing both the spliced leader and the bulk of polyadenylated mRNAs.

Variable Inheritance of AmplifiedEPSPSGene Copies in Glyphosate-Resistant Palmer Amaranth (Amaranthus palmeri)

Weed Science ◽  
2018 ◽  
Vol 67 (2) ◽  
pp. 176-182 ◽  
Author(s):  
Darci A. Giacomini ◽  
Philip Westra ◽  
Sarah M. Ward
Keyword(s):  
Copy Number ◽  
Single Gene ◽  
Gene Copy Number ◽  
Transgressive Segregation ◽  
Palmer Amaranth ◽  
Gene Copy ◽  
Amaranthus Palmeri ◽  
Gene Copies ◽  
Central United States ◽  
Free Environment

AbstractGlyphosate-resistant (GR) Palmer amaranth (Amaranthus palmeriS. Watson) is considered one of the most troublesome weeds in the southern and central United States, but results of previous research to determine the mode of inheritance of this trait have been conflicting and inconclusive. In this study, we examined segregation patterns ofEPSPSgene-copy numbers in F1and F2generations ofA. palmeriand found no evidence of a Mendelian single-gene pattern of inheritance. Transgressive segregation for copy number was exhibited by several F1and all of the F2families, most likely the product ofEPSPScopy-number variation within each plant. This variation was confirmed by assaying gene-copy number across clonal generations and among individual shoots on the same plant, demonstrating thatEPSPSamplification levels vary significantly within a single plant. Increases and decreases in copy number occurred in a controlled, stress-free environment in the absence of glyphosate, indicating thatEPSPSgene amplification is a random and variable process within the plant. The ability ofA. palmerito gain or loseEPSPSgene copies is a valuable adaptive trait, allowing this species to respond rapidly to selection pressures and changing environments.

scholarly journals High variability in SSU rDNA gene copy number among planktonic foraminifera revealed by single-cell qPCR

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Tamara Milivojević ◽  
Shirin Nurshan Rahman ◽  
Débora Raposo ◽  
Michael Siccha ◽  
Michal Kucera ◽  
...  
Keyword(s):  
Single Cell ◽  
Community Composition ◽  
Copy Number ◽  
Planktonic Foraminifera ◽  
Gene Copy Number ◽  
Ssu Rdna ◽  
Gene Copy ◽  
Rdna Gene ◽  
Gene Copies ◽  
Average Gene

AbstractMetabarcoding has become the workhorse of community ecology. Sequencing a taxonomically informative DNA fragment from environmental samples gives fast access to community composition across taxonomic groups, but it relies on the assumption that the number of sequences for each taxon correlates with its abundance in the sampled community. However, gene copy number varies among and within taxa, and the extent of this variability must therefore be considered when interpreting community composition data derived from environmental sequencing. Here we measured with single-cell qPCR the SSU rDNA gene copy number of 139 specimens of five species of planktonic foraminifera. We found that the average gene copy number varied between of ~4000 to ~50,000 gene copies between species, and individuals of the same species can carry between ~300 to more than 350,000 gene copies. This variability cannot be explained by differences in cell size and considering all plausible sources of bias, we conclude that this variability likely reflects dynamic genomic processes acting during the life cycle. We used the observed variability to model its impact on metabarcoding and found that the application of a correcting factor at species level may correct the derived relative abundances, provided sufficiently large populations have been sampled.

scholarly journals Analysis of amplicons containing the esterase genes responsible for insecticide resistance in the peach-potato aphid Myzus persicae (Sulzer)

1996 ◽  
Vol 313 (2) ◽  
pp. 543-547 ◽  
Author(s):  
Linda M. FIELD ◽  
Alan L. DEVONSHIRE ◽  
Chris TYLER-SMITH
Keyword(s):  
Gene Amplification ◽  
Myzus Persicae ◽  
Gene Copy Number ◽  
Fold Increase ◽  
Gene Copy ◽  
Potato Aphid ◽  
Gene Copies ◽  
Genes Encoding ◽  
Aphid Clone ◽  
Peach Potato Aphid

The amplification of genes encoding an insecticide-detoxifying esterase (E4) in the peach-potato aphid Myzus persicae is one of the few examples where this genetic phenomenon has been shown to be involved in the response of an intact higher organism to artificial selection. Here we report quantitative and qualitative studies of the repeat units (amplicons) containing the E4 genes in a highly resistant aphid clone. Initial studies to quantify esterase sequences showed a 5-11-fold increase in resistant aphids compared with susceptible aphids, suggesting the presence of 10-22 gene copies per diploid genome. A more incisive analysis by pulsed-field gel electrophoresis confirmed the presence of about 12 copies of the E4 gene and showed them to be on about 24 kb amplicons, arranged as a tandem array of direct repeats. This, together with previous results from crossing experiments and with recent in situ hybridization studies, confirms that the E4 gene amplification in this aphid clone is heterozygous at a single locus. However, these data show that the gene amplification alone cannot account for the approx. 60 times higher levels of E4 protein and its mRNA present in this aphid clone, and therefore resistance must involve changes in both esterase gene copy number and gene expression.

Herbicide diagnostics reveal multiple patterns of synthetic auxin resistance in kochia (Bassia scoparia)

2021 ◽  
pp. 1-28
Author(s):  
Charles M. Geddes ◽  
Mallory L. Owen ◽  
Teandra E. Ostendorf ◽  
Julia Y. Leeson ◽  
Shaun M. Sharpe ◽  
...  
Keyword(s):  
Great Plains ◽  
Dose Response ◽  
Weed Management ◽  
Acetolactate Synthase ◽  
The United States ◽  
Cross Resistance ◽  
Visible Injury ◽  
Synthetic Auxin ◽  
Auxin Resistance ◽  
Sites Of Action

Abstract Herbicide-resistant (HR) kochia is a growing problem in the Great Plains region of Canada and the United States (U.S.). Resistance to up to four herbicide sites of action, including photosystem II inhibitors, acetolactate synthase inhibitors, synthetic auxins, and the 5-enolpyruvylshikimate-3-phosphate synthase inhibitor glyphosate have been reported in many areas of this region. Despite being present in the U.S. since 1993/1994, auxinic-HR kochia is a recent and growing phenomenon in Canada. This study was designed to characterize (a) the level of resistance and (b) patterns of cross-resistance to dicamba and fluroxypyr in 12 putative auxinic-HR kochia populations from western Canada. The incidence of dicamba-resistant individuals ranged among populations from 0% to 85%, while fluroxypyr-resistant individuals ranged from 0% to 45%. In whole-plant dose-response bioassays, the populations exhibited up to 6.5-fold resistance to dicamba and up to 51.5-fold resistance to fluroxypyr based on visible injury 28 days after application. Based on plant survival estimates, the populations exhibited up to 3.7-fold resistance to dicamba and up to 72.5-fold resistance to fluroxypyr. Multiple patterns of synthetic auxin resistance were observed, where one population from Cypress County, Alberta was resistant to dicamba but not fluroxypyr, while another from Rocky View County, Alberta was resistant to fluroxypyr but not dicamba based on single-dose population screening and dose-response bioassays. These results suggest that multiple mechanisms may confer resistance to dicamba and/or fluroxypyr in Canadian kochia populations. Further research is warranted to determine these mechanisms. Farmers are urged to adopt proactive non-chemical weed management tools in an effort to preserve efficacy of the remaining herbicide options available for control of HR kochia.

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