Explore the vast range of titles available.

Background Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase ( AHAS ) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

Genotoxic, biochemical, and individual organizational effects on Leptodactylus latinasus tadpoles were evaluated after exposure to an imazethapyr (IMZT)-based commercial herbicide formulation, Pivot® H (10.59% IMZT). A determination of the value of the lethal concentration (LC50) was determined as a toxicological endpoint. Alterations in animal behavior and morphological abnormalities as well as cholinesterase (ChE), catalase (CAT), and glutathione S -transferase (GST) activities were employed as individual sublethal endpoints. Micronuclei frequencies (MNs), binucleated cells (BNs), blebbed nuclei (BLs), lobed nuclei (LBs), notched nuclei (NTs), erythroplastids (EPs), and evaluation of DNA strand breaks were employed as genotoxic endpoints. All biomarkers were evaluated after 48 and 96 h of exposure to concentrations of IMZT within 0.07–4.89 mg/L. LC50 96h values of 1.01 and 0.29 mg/L IMZT were obtained for Gosner stages 25 and 36, respectively. Irregular swimming, diamond body shape, and decreased frequency of keratodonts were detected at both sampling times. Results showed that IMZT increased GST activity and MN frequency at 48 and 96 h of exposure. Other nuclear abnormalities were also observed in the circulating erythrocytes of tadpoles, i.e., NT and BL values after 48 h, and LN, BL, and EP values after 96 h. Finally, results showed that IMZT within 0.07–0.22 mg/L increased the genetic damage index in tadpoles exposed for both exposure times (48 and 96 h). This study is the first to report the sublethal biochemical effects of IMZT in anurans and is also the first report using L. latinasus tadpoles as a bioindicator for ecotoxicological studies.

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

Background and aimsImazethapyr (IM) is a chiral herbicide with two enantiomers, with a much stronger herbicidal effect of R-IM than S-IM. Pesticide residues are a common problem, and multi-generation cultivation method can reveal the consequences of long-term pesticide residues.MethodsThis study verified the effects of R-IM on the growth of Arabidopsis thaliana and rhizosphere microorganisms by treating A. thaliana with different concentrations of R-IM successively passaging experimental rhizospheres for three generations, and measured the changes of A. thaliana rhizosphere microbes.ResultsThe growth of A. thaliana treated with R-IM (0.5 g/ha and 1.5 g/ha) was significantly inhibited especially after successive generations of culture. At the same time, R-IM treatment decreased chlorophyll and chlorophyll parameters to inhibit the photosynthetic efficiency, and it also reshaped the rhizosphere bacterial community structure of A. thaliana. This bio-effect was transmitted to the next generation of plants along with the soil microbiota.ConclusionsThe treatment of A. thaliana by R-IM in multi-generation culture resulted in an increasingly obvious growth inhibitory effect, the higher concentration of R-IM inhibited A. thaliana more strongly, and changed the abundance of rhizosphere microbes. With the cultivation of generations, the influence of pesticide residues on plants also became significant.

In order to improve both resistance to lepidopteran pests and resistance to the herbicide imazethapyr in mainstay japonica varieties of the Huang-Huai rice region, Sanming dominant genic male sterile (S-DGMS) rice was used as a platform to facilitate the pyramiding of functional genes and the replacement of the genomic background. Twelve novel lines were developed, each carrying a crystal toxin gene conferring resistance to lepidopteran pests and the ALS 627N allele conferring resistance to herbicide imazethapyr in the background of a mainstay japonica variety. The genomic background of the 12 novel lines was examined using 48 specified molecular markers, and each line carried less than two polymorphic markers relative to the corresponding mainstay variety. All 12 lines displayed high resistance to lepidopteran pests and the herbicide imazethapyr. The major agronomic traits of the 12 lines showed no difference relative to the responding mainstay variety when sprayed with pesticide. The popularization of the 12 japonica lines could reduce the use of pesticides and provide highly efficient control of weeds and weedy rice in the future, thus promoting the development of japonica rice production. Therefore, S-DGMS rice could be a powerful tool for the genetic improvement of target traits in rice.

Weed control is the most important constraint of autumn-sown chickpea production. Field experiments were conducted at three sites to evaluate the yield response of autumn-sown rainfed chickpea and weed control with PRE pendimethalin, POST pyridate, PRE isoxaflutole, preemergence (PRE) and postemergence (POST) of imazethapyr through hand-weeded, untreated and weed free checks. The results showed that pyridate was the safest option for weed control in chickpea. The highest grain yield of chickpea was obtained with application of pyridate followed by isoxaflutolein three sites. Imazethapyr and metribuzin caused higher visual injuries than the other treatments. Furthermore, the applications of pyridate, isoxaflutole, metribuzin, and pendimethalin, as well as PRE and POST imazethapyr were found to reduce the total weed densities (averaged for three locations) by as much as 76, 75, 75.4, 43, 64, and 64.5% within 30 days after treatments, respectively.

Herbicide resistance is broadly recognized as the adaptive evolution of weed populations to the intense selection pressure imposed by the herbicide applications. Here, we tested whether tran- scriptional gene silencing (TGS) and RNA-directed DNA Methylation (RdDM) pathways modulate resistance to commonly applied herbicides. Using Arabidopsis thaliana wild-type plants exposed to sublethal doses of glyphosate, imazethapyr, and 2,4-D, we found a partial loss of TGS and increased susceptibility to herbicides in six out of 11 tested TGS/RdDM mutants. Mutation in REPRESSOR OF SILENCING 1 (ROS1), that plays an important role in DNA demethylation, leading to strongly in- creased susceptibility to all applied herbicides, and imazethapyr in particular. Transcriptomic analysis of the imazethapyr-treated wild type and ros1 plants revealed a relation of the herbicide upregu- lated genes to chemical stimulus, secondary metabolism, stress condition, flavonoid biosynthesis, and epigenetic processes. Hypersensitivity to imazethapyr of the flavonoid biosynthesis component TRANSPARENT TESTA 4 (TT4) mutant plants strongly suggests that ROS1-dependent accumulation of flavonoids is an important mechanism for herbicide stress response in A. thaliana. In summary, our study shows that herbicide treatment affects transcriptional gene silencing pathways and that misregulation of these pathways makes Arabidopsis plants more sensitive to herbicide treatment.

Recently, farmers in Brazil have observed a decline in efficacy of glyphosate, chlorimuron, and imazethapyr control of smooth pigweed (Amaranthus hybridus L.). The objectives of this study were to quantify the resistance of Amaranthus in Brazil to glyphosate and acetolactate synthase (ALS)-inhibiting herbicides, elucidate the mechanism of resistance, and assess the frequency of shifts in sensitivity to glyphosate and chlorimuron in Brazil. Dose–response assays were conducted in a greenhouse with glyphosate, chlorimuron, and imazethapyr. This was followed by sequencing of the EPSPS and ALS genes. Additionally, 740 Amaranthus populations across several Brazilian states were monitored over 4 yr, subjected to a single discriminatory dose of glyphosate and chlorimuron. The populations BR18Asp051 and BR21Asp205 were resistant to glyphosate, chlorimuron, and imazethapyr. The elevated resistance level to glyphosate in these populations is attributed to multiple amino acid substitutions (TAP-IVS) in the EPSPS gene; and cross-resistance to sulfonylureas and imidazolinones is conferred by the Trp-574-Leu substitution in the ALS gene in both populations. Overall, resistance distribution indicated that 88% of the sampled populations were considered sensitive to glyphosate, while 66% were sensitive to chlorimuron. Furthermore, 10% of the samples demonstrated multiple resistance to both active ingredients. A shift in glyphosate sensitivity was observed in four states in Brazil; however, sensitivity shifts to chlorimuron were more widely dispersed in Brazilian agricultural regions.

A comprehensive, Wisconsin state-wide assessment of waterhemp response to a diverse group of herbicide sites of action has not been conducted. Our objective was to characterize the response of a state-wide collection of waterhemp accessions to postemergence (POST) and preemergence (PRE) herbicides commonly used in corn and soybean in Wisconsin. Greenhouse experiments were conducted with more than 80 accessions from 27 counties. POST treatments included 2,4-D, atrazine, dicamba, fomesafen, glufosinate, glyphosate, imazethapyr, and mesotrione at 1× and 3× label rates. PRE treatments included atrazine, fomesafen, mesotrione, metribuzin, and S-metolachlor at 0.5×, 1×, and 3× label rates. Ninety-eight percent and 88% of the accessions exhibited ≥50% plant survival after exposure to imazethapyr and glyphosate POST 3× rate, respectively. Seventeen percent, 16%, and 3% of the accessions exhibited ≥50% plant survival after exposure to 2,4-D, atrazine, and dicamba, respectively, applied POST at the 1× rate. Survival of all accessions was ≤25% after exposure to 2,4-D or dicamba applied POST at the 3× rate, or glufosinate, fomesafen, and mesotrione applied POST at either rate evaluated. No plant of any accession survived exposure to glufosinate at either rate. Forty-five percent and 3% of the accessions exhibited <90% plant density reduction after exposure to atrazine applied PRE at the 3× rate and fomesafen PRE at the 1× rate, respectively. Plant density reduction of all accessions was ≥96% after exposure to fomesafen applied PRE at the 3× rate, or metribuzin, S-metolachlor, and mesotrione applied PRE at the 1× rate. Our results suggest that waterhemp resistance to imazethapyr and glyphosate applied POST is widespread in Wisconsin, whereas resistance to 2,4-D, atrazine, and dicamba applied POST is present to a lower extent. One accession (A75, Fond du Lac County) exhibited multiple resistance to imazethapyr, atrazine, glyphosate, and 2,4-D when applied POST. Overall, atrazine applied PRE was ineffective for waterhemp control in Wisconsin. Proactive resistance management and the use of effective PRE and POST herbicides are fundamental for waterhemp management in Wisconsin. Nomenclature: atrazine; dicamba; fomesafen; glufosinate; glyphosate; imazethapyr; mesotrione; metribuzin; S-metolachlor; 2,4-D; waterhemp, Amaranthus tuberculatus (Moq.) Sauer; corn, Zea mays (L.); soybean, Glycine max (L.) Merr.

Glufosinate resistance was previously confirmed in three Palmer amaranth accessions from Arkansas (MSR1, MSR2, and CCR). Greenhouse screening results suggested the presence of multiple herbicide resistance. Therefore, this study aimed to determine the postemergence resistance profile of these three glufosinate-resistant Palmer amaranth accessions. Field experiments were also conducted to assess preemergence and postemergence herbicide options to control the accession with the highest glufosinate resistance level (MSR2). A dose-response assay with the three resistant accessions and two susceptible standards was conducted with the herbicides 2,4-D, atrazine, dicamba, diuron, fomesafen, glyphosate, imazethapyr, and mesotrione. The preemergence and postemergence field experiments with MSR2 evaluated 15 and 16 single active ingredients, respectively. The Palmer amaranth accessions that carried glufosinate resistance were also confirmed to be resistant to six other postemergence herbicides: 2,4-D, diuron, fomesafen, glyphosate, imazethapyr, and mesotrione. CCR is also resistant to dicamba. Therefore, accessions MSR1, MSR2, and CCR have evolved resistance to postemergence herbicides pertaining to seven sites of action. A shift toward increased tolerance to atrazine has also been observed among all resistant accessions. Overall, field preemergence treatments with atrazine, pyroxasulfone, or trifludimoxazin obtained the highest MSR2 control levels at all evaluation times and the lowest number of seedlings emerging at 3 and 6 wk after treatment. In the postemergence experiment, only paraquat obtained MSR2 control levels above 90% at all ratings. The lowest number of alive MSR2 plants was observed after postemergence treatments with paraquat or trifludimoxazin. Fields near where glufosinate resistance has been confirmed in Palmer amaranth will likely demand a more diverse and proactive management strategy that relies on combinations of chemical, cultural, and mechanical control tactics. Future efforts should focus on sequential applications and mixture, the elucidation of all resistance mechanisms in the evaluated accessions, and soil-applied dose-response.