Response of conventional sunflower cultivars to drift rates of synthetic auxin herbicides

The agrochemical industry has launched several new synthetic auxin herbicides in rice to combat increasing numbers of herbicide resistant weeds to other modes of action. Excessive or inappropriate use of these herbicides has resulted in unintended consequences near the sites of application, such as herbicide drift. This study was conducted to determine the impact of drift of quinclorac and florpyrauxifen-benzyl+penoxsulam (FBP) on the yield and yield components of two sunflower cultivars. In a growth chamber experiment, quinclorac and FBP were applied to 2-4 true leaf stages at rates ranging from 2.93 to 93.75 and from 0.51 to 16.25 g ai ha-1, respectively. Nonlinear regression analyses indicated that the cultivar Bosfora was more sensitive to quinclorac and FBP than the cultivar Tunca. In field experiments, these sunflower cultivars were treated with drift rates of quinclorac (<375 g ai ha-1) and FBP (<65 g ai ha-1) when they were at the 8-10 true leaf stage. Quinclorac and FBP drift rates resulted in up to 52-61% and 85-100% injury and 82-88% and 100% yield loss, respectively. Crop injury and yield data clearly showed that cultivar Bosfora was more sensitive to FBP and quinclorac rates than cultivar Tunca, and both cultivars were more sensitive to FBP than quinclorac. In our work, we also found that plant height reduction caused by quinclorac at early growth stages may be a valuable indicator to evaluate crop injury and yield loss.

Enhanced metabolic detoxification is associated with fluroxypyr resistance in Bassia scoparia

Auxin-mimic herbicides chemically mimic the phytohormone indole-3-acetic-acid (IAA). Within the auxin-mimic herbicide class, the herbicide fluroxypyr has been extensively used to control kochia (Bassia scoparia). A 2014 field survey for herbicide resistance in kochia populations across Colorado identified a putative fluroxypyr-resistant (Flur-R) population that was assessed for response to fluroxypyr and dicamba (auxin-mimics), atrazine (photosystem II inhibitor), glyphosate (EPSPS inhibitor), and chlorsulfuron (acetolactate synthase inhibitor). This population was resistant to fluroxypyr and chlorsulfuron but sensitive to glyphosate, atrazine, and dicamba. Subsequent dose-response studies determined that Flur-R was 40 times more resistant to fluroxypyr than a susceptible population (J01-S) collected from the same field survey (LD50 720 and 20 g ae ha-1, respectively). Auxin-responsive gene expression increased following fluroxypyr treatment in Flur-R, J01-S, and in a dicamba-resistant, fluroxypyr-susceptible line 9,425 in an RNA-sequencing experiment. In Flur-R, several transcripts with molecular functions for conjugation and transport were constitutively higher expressed, such as glutathione S-transferases (GSTs), UDP-glucosyl transferase (GT), and ATP binding cassette transporters (ABC transporters). After analyzing metabolic profiles over time, both Flur-R and J01-S rapidly converted [14C]-fluroxypyr ester, the herbicide formulation applied to plants, to [14C]-fluroxypyr acid, the biologically active form of the herbicide, and three unknown metabolites. The formation and flux of these metabolites were faster in Flur-R than J01-S, reducing the concentration of phytotoxic fluroxypyr acid. One unique metabolite was present in Flur-R that was not present in the J01-S metabolic profile. Gene sequence variant analysis specifically for auxin receptor and signaling proteins revealed the absence of non-synonymous mutations affecting auxin signaling and binding in candidate auxin target site genes, further supporting our hypothesis that non-target site metabolic degradation is contributing to fluroxypyr resistance in Flur-R.

Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica

Genomic structural variation (SV) has profound effects on organismal evolution; often serving as a source of novel genetic variation. Gene copy number variation (CNV), one type of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially with environmental stress. Resistance to the widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important grass, Eleusine indica (goosegrass); however, the origin and mechanism of these CNVs remain elusive in many weed species due to limited genetic and genomic resources. To study this CNV in goosegrass, we present high-quality reference genomes for glyphosate-susceptible and -resistant goosegrass lines and fine-assembles of the duplication of glyphosate's target site gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). We reveal a unique rearrangement of EPSPS involving chromosome subtelomeres. This discovery adds to the limited knowledge of the importance of subtelomeres as genetic variation generators and provides another unique example for herbicide resistance evolution.

Homoeologous evolution of the allotetraploid genome of Poa annua L

BACKGROUND

Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua's diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua's evolutionary novelty.

RESULTS

We find that the diploids diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua's B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis.

CONCLUSIONS

The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding.

Identification of two Eleusine indica (goosegrass) biotypes of cool-season turfgrass resistant to dithiopyr

BACKGROUND

Turfgrass managers reported poor Eleusine indica control following applications of the mitosis-inhibiting herbicide dithiopyr in cool-season turfgrass. Field, glasshouse, and laboratory experiments were conducted to understand the response of these biotypes to dithiopyr and prodiamine.

RESULTS

In field experiments at two locations with putative dithiopyr-resistant E. indica, preemergence applications of dithiopyr provided no E. indica control. Single applications of the protoporphyrinogen oxidase (PPO)-inhibitor, oxadiazon, provided > 85% control at these locations. When subjected to agar-based bioassays, root growth of putative resistant biotypes planted with 0.01 mmol L^-1 dithiopyr was slightly reduced (< 25%) whereas roots were completely inhibited in the susceptible biotype. Glasshouse whole plant rate-response experiments found that the cytochrome P450 inhibitor, piperonyl butoxide (PBO), did not increase the sensitivity of these putative resistant biotypes to dithiopyr. Sequencing of α-tubulin 1 (TUA1) revealed a Leu-136-Phe substitution in both dithiopyr-resistant populations.

CONCLUSION

Eleusine indica biotypes with resistance to dithiopyr are present in cool-season turfgrass systems in the United States. Resistance is possibly related to a single nucleotide polymorphism (SNP) of an α-tubulin gene. If turfgrass managers suspect resistance to dithiopyr, oxadiazon can still be an effective alternative for preemergence control. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genomic-based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America

Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that (i) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that (ii) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS duplication genotypes, one having geographical associations with the Northern Plains and the other with the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.

Differential expression of genes associated with non-target site resistance in Poa annua with target site resistance to acetolactate synthase inhibitors

BACKGROUND

Poa annua is a pervasive grassy, self-pollinating, weed that has evolved resistance to 10 different herbicide modes-of-action, third most of all weed species. We investigated constitutive overexpression of genes associated with non-target site resistance (NTSR) in POAAN-R3 and the response of those genes when treated with trifloxysulfuron despite the biotype having a known target site mutation in acetolactate synthase (ALS).

RESULTS

Despite having an ALS target site mutation, POAAN-R3 still had a transcriptomic response to herbicide application that differed from a susceptible biotype. We observed differential expression of genes associated with transmembrane transport and oxidation-reduction activities, with differences being most pronounced prior to herbicide treatment.

CONCLUSIONS

In the P. annua biotype we studied with confirmed target site resistance to ALS inhibitors, we also observed constitutive expression of genes regulating transmembrane transport, as well as differential expression of genes associated with oxidative stress after treatment with trifloxysulfuron. This accumulation of mechanisms, in addition to the manifestation of target site resistance, could potentially increase the chance of survival when plants are challenged by different modes of action.

A needle in a seedstack: an improved method for detection of rare alleles in bulk seed testing through KASP

BACKGROUND

Amaranthus palmeri is an aggressive and prolific weed species with major impact on agricultural yield and is a prohibited noxious weed across the Midwest. Morphological identification of A. palmeri from other Amaranthus species is extremely difficult in seeds, which has led to genetic testing for seed identification in commercial seed lots.

RESULTS

We created an inexpensive and reliable genetic test based on novel, species-specific, single nucleotide polymorphisms (SNPs) from GBS (Genotyping by Sequencing) data. We report three SNP-based genetic tests for identifying A. palmeri alone or in a mixed pool of Amaranthus spp. Sensitivity ranged from 99.8 to 100%, specificity from 99.59 to 100%. Accuracy for all three tests is > 99.7%. All three are capable of reliably detecting one A. palmeri seed in a pool of 200 Amaranthus spp. seeds. The test was validated across 20 populations of A. palmeri, along with eight other Amaranthus species, the largest and most genetically diverse panel of Amaranthus samples to date.

CONCLUSION

Our work represents a marked improvement over existing commercial assays resulting in an identification assay that is (i) accurate, (ii) robust, (iii) easy to interpret and (iv) applicable to both leaf tissue and pools of up to 200 seeds. Included is a data transformation method for calling of closely grouped competitive fluorescence assays. We also present a comprehensive GBS dataset from the largest geographic panel of Amaranthus populations sequenced. Our approach serves as a model for developing markers for other difficult to identify species. © 2021 Society of Chemical Industry.

Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance

In the last decade, Amaranthus tuberculatus has evolved resistance to 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-hydroxyphenylpyruvate dioxygenase inhibitors in multiple states across the midwestern United States. Two populations resistant to both mode-of-action groups, one from Nebraska (NEB) and one from Illinois (CHR), were studied using an RNA-seq approach on F2 mapping populations to identify the genes responsible for resistance. Using both an A. tuberculatus transcriptome assembly and a high-quality grain amaranth (A. hypochondriacus) genome as references, differential transcript and gene expression analyses were conducted to identify genes that were significantly over- or underexpressed in resistant plants. When these differentially expressed genes (DEGs) were mapped on the A. hypochondriacus genome, physical clustering of the DEGs was apparent along several of the 16 A. hypochondriacus scaffolds. Furthermore, single-nucleotide polymorphism calling to look for resistant-specific (R) variants, and subsequent mapping of these variants, also found similar patterns of clustering. Specifically, regions biased toward R alleles overlapped with the DEG clusters. Within one of these clusters, allele-specific expression of cytochrome  P450  81E8 was observed for 2,4-D resistance in both the CHR and NEB populations, and phylogenetic analysis indicated a common evolutionary origin of this R allele in the two populations.

Homogeneity among glyphosate-resistant Amaranthus palmeri in geographically distant locations

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.

Annual bluegrass (Poa annua) resistance to indaziflam applied early-postemergence

BACKGROUND

Indaziflam is an alkylazine herbicide used to control annual bluegrass (Poa annua L.). Several locations in the southeastern USA reported poor annual bluegrass control following treatment with indaziflam during autumn 2015. A series of controlled environment experiments were conducted to confirm putative resistance to indaziflam in annual bluegrass collected from these field locations.

RESULTS

Indaziflam (25 g ha^-1 ) effectively controlled all putative-resistant annual bluegrass collections when applied preemergence (PRE), but was ineffective when applied early-postemergence (< 2.5 cm plant height; BBCH scale = 1; EPOST). In agarose-based plate assays, EPOST I₅₀ values for putative-resistant collections ranged from 2424 to 4305 pm compared with 633 pm for the herbicide-susceptible control; therefore, resistance indexes (R/S) ranged from 3.8 to 6.8. Resistant collections were not controlled by foramsulfuron, flumioxazin, glyphosate, glufosinate, metribuzin, pronamide, or simazine applied EPOST. Indaziflam content in herbicide-susceptible annual bluegrass was greater than a resistant collection from 0 to 10 days after treatment (DAT). Susceptibility was not restored when resistant collections were treated with indaziflam plus 1-aminobenzotriazole (10 mg L^-1 ), tebuconazole (1510 g ha^-1 ), or malathion (400 g ha^-1 ).

CONCLUSIONS

This is a first report of resistance to indaziflam in any plant. Additionally, we confirm that these annual bluegrass collections are resistant to several other herbicidal modes-of-action. It is unclear if this multi-herbicide resistance is due to a single resistance gene, multiple resistance genes, non-target site mechanisms, or a combination thereof. Additional research to better understand resistance mechanisms in these annual bluegrass collections is warranted. © 2020 Society of Chemical Industry.

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

Increased copy number of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene confers resistance to glyphosate, the world's most-used herbicide. There are typically three to eight EPSPS copies arranged in tandem in glyphosate-resistant populations of the weed kochia (Kochia scoparia). Here, we report a draft genome assembly from a glyphosate-susceptible kochia individual. Additionally, we assembled the EPSPS locus from a glyphosate-resistant kochia plant by sequencing select bacterial artificial chromosomes from a kochia bacterial artificial chromosome library. Comparing the resistant and susceptible EPSPS locus allowed us to reconstruct the history of duplication in the structurally complex EPSPS locus and uncover the genes that are coduplicated with EPSPS, several of which have a corresponding change in transcription. The comparison between the susceptible and resistant assemblies revealed two dominant repeat types. Additionally, we discovered a mobile genetic element with a FHY3/FAR1-like gene predicted in its sequence that is associated with the duplicated EPSPS gene copies in the resistant line. We present a hypothetical model based on unequal crossing over that implicates this mobile element as responsible for the origin of the EPSPS gene duplication event and the evolution of herbicide resistance in this system. These findings add to our understanding of stress resistance evolution and provide an example of rapid resistance evolution to high levels of environmental stress.

Predicting herbicide movement across semi-permeable membranes using three phase partitioning

Herbicide efficacy depends on herbicides crossing cell and organelle membranes. We evaluated an artificial membrane system to understand how herbicides cross biological membranes. This understanding aids in predicting herbicide behavior in planta and, consequently, efficacy, mode of action, and whether active transporter-based herbicide resistance mechanisms may be possible. Five herbicides with different log Kow and pKa values were assessed: glyphosate, 2,4-D, clopyralid, sulfentrazone and glufosinate. The artificial membrane apparatus included four semipermeable membranes containing buffers with pH 2.7, 5 and/or 7.4, floating in a bath of diethyl ether. These conditions were based on the pH from different cellular compartments and the pKa for these herbicides. Changes in herbicide concentration due to movement were measured using radioactivity or liquid chromatography mass spectrometry. In general, herbicide behavior followed the pattern predicted by their calculated pKa and log Kow. Herbicides added to an acidic phase (pH 2.7) were more mobile than when they were added to the more basic phase (pH 7.4), except when herbicide's pKa was lower than the pH of the starting phase. Clopyralid, 2,4-D, and sulfentrazone showed significant acid trapping behavior due to their weak acid functional groups. Sulfentrazone and 2,4-D had a high affinity for the nonpolar, diethyl ether bath, especially when they were protonated at low pH. Our findings illustrate the robustness of the system to provide predictions about herbicide behavior at the subcellular level.

Molecular mechanisms of adaptive evolution revealed by global selection for glyphosate resistance

The human-directed, global selection for glyphosate resistance in weeds has revealed a fascinating diversity of evolved resistance mechanisms, including herbicide sequestration in the vacuole, a rapid cell death response, nucleotide polymorphisms in the herbicide target (5-enolpyruvylshikimate-3-phosphate synthase, EPSPS) and increased gene copy number of EPSPS. For this latter mechanism, two distinct molecular genetic mechanisms have been observed, a tandem duplication mechanism and a large extrachromosomal circular DNA (eccDNA) that is tethered to the chromosomes and passed to gametes at meiosis. These divergent mechanisms have a range of consequences for the spread, fitness, and inheritance of resistance traits, and, particularly in the case of the eccDNA, demonstrate how evolved herbicide resistance can generate new insights into plant adaptation to contemporary environmental stress.

Interspecific and intraspecific transference of metabolism-based mesotrione resistance in dioecious weedy Amaranthus

Pollen-mediated gene flow (PMGF) might play an important role in dispersing herbicide resistance alleles in dioecious weedy Amaranthus species. Field experiments in a concentric donor-receptor design were conducted to quantify two sets of PMGF studies, an interspecific (Amaranthus tuberculatus × Amaranthus palmeri) and an intraspecific (A. tuberculatus × A. tuberculatus). In both studies, PMGF was evaluated using a resistant A. tuberculatus phenotype with enhanced mesotrione detoxification via P450 enzymes as a source of resistance alleles. For interspecific hybridization, more than 104 000 putative hybrid seedlings were screened with three markers, one phenotypic and two molecular. The two molecular markers used, including 2-bp polymorphisms in the internal transcribed spacer region, distinguished A. palmeri, A. tuberculatus and their hybrids. Results showed that 0.1% hybridization between A. tuberculatus × A. palmeri occurred under field research conditions. For intraspecific hybridization, 22 582 seedlings were screened to assess the frequency of gene flow. The frequency of gene flow (F_GF ) varied with distance, direction and year of the study. The farthest distance for 90% reduction of F_GF was at 69 m in 2015 however, after averaging across directions it was 13.1 and 26.1 m in 2014 and 2015, respectively. This study highlights the transfer of metabolism-based mesotrione resistance from A. tuberculatus to A. palmeri under field research conditions. The results presented here might aid in the rapid detection of A. palmeri among other Amaranthus species and show that PMFG could be expediting the increase of herbicide resistance in A. palmeri and A. tuberculatus across US crop production areas.

Increased chalcone synthase (CHS) expression is associated with dicamba resistance in Kochia scoparia

BACKGROUND

Resistance to the synthetic auxin herbicide dicamba is increasingly problematic in Kochia scoparia. The resistance mechanism in an inbred dicamba-resistant K. scoparia line (9425R) was investigated using physiological and transcriptomics (RNA-Seq) approaches.

RESULTS

No differences were found in dicamba absorption or metabolism between 9425R and a dicamba-susceptible line, but 9425R was found to have significantly reduced dicamba translocation. Known auxin-responsive genes ACC synthase (ACS) and indole-3-acetic acid amino synthetase (GH3) were transcriptionally induced following dicamba treatment in dicamba-susceptible K. scoparia but not in 9425R. Chalcone synthase (CHS), the gene regulating synthesis of the flavonols quertecin and kaemperfol, was found to have twofold higher transcription in 9425R both without and 12 h after dicamba treatment. Increased CHS transcription co-segregated with dicamba resistance in a forward genetics screen using an F₂ population.

CONCLUSION

Prior work has shown that the flavonols quertecin and kaemperfol compete with auxin for intercellular movement and vascular loading via ATP-binding cassette subfamily B (ABCB) membrane transporters. The results of this study support a model in which constitutively increased CHS expression in the meristem produces more flavonols that would compete with dicamba for intercellular transport by ABCB transporters, resulting in reduced dicamba translocation. © 2017 Society of Chemical Industry.

The power and potential of genomics in weed biology and management

There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the 'state of the art' in genomics and weed genomics, including technologies, applications, and on-going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research. © 2018 Society of Chemical Industry.

Reversing resistance to tembotrione in an Amaranthus tuberculatus (var. rudis) population from Nebraska, USA with cytochrome P450 inhibitors

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 in 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. Although 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 of 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. © 2017 Society of Chemical Industry.

Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay?

Seeds exist in the vulnerable state of being unable to repair the chemical degradation all organisms suffer, which slowly ages seeds and eventually results in death. Proposed seed aging mechanisms involve all classes of biological molecules, and degradation of total RNA has been detected contemporaneously with viability loss in dry-stored seeds. To identify changes specific to mRNA, we examined the soybean (Glycine max) seed transcriptome, using new, whole-molecule sequencing technology. We detected strong evidence of transcript fragmentation in 23-year-old, compared with 2-year-old, seeds. Transcripts were broken non-specifically, and greater fragmentation occurred in longer transcripts, consistent with the proposed mechanism of molecular fission by free radical attack at random bases. Seeds died despite high integrity of short transcripts, indicating that functions encoded by short transcripts are not sufficient to maintain viability. This study provides an approach to probe the asymptomatic phase of seed aging, namely by quantifying transcript degradation as a function of storage time.

Glyphosate Resistance and EPSPS Gene Duplication: Convergent Evolution in Multiple Plant Species

One of the increasingly widespread mechanisms of resistance to the herbicide glyphosate is copy number variation (CNV) of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. EPSPS gene duplication has been reported in 8 weed species, ranging from 3 to 5 extra copies to more than 150 extra copies. In the case of Palmer amaranth (Amaranthus palmeri), a section of >300 kb containing EPSPS and many other genes has been replicated and inserted at new loci throughout the genome, resulting in significant increase in total genome size. The replicated sequence contains several classes of mobile genetic elements including helitrons, raising the intriguing possibility of extra-chromosomal replication of the EPSPS-containing sequence. In kochia (Kochia scoparia), from 3 to more than 10 extra EPSPS copies are arranged as a tandem gene duplication at one locus. In the remaining 6 weed species that exhibit EPSPS gene duplication, little is known about the underlying mechanisms of gene duplication or their entire sequence. There is mounting evidence that adaptive gene amplification is an important mode of evolution in the face of intense human-mediated selection pressure. The convergent evolution of CNVs for glyphosate resistance in weeds, through at least 2 different mechanisms, may be indicative of a more general importance for this mechanism of adaptation in plants. CNVs warrant further investigation across plant functional genomics for adaptation to biotic and abiotic stresses, particularly for adaptive evolution on rapid time scales.

Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS)

Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.

Indaziflam: a new cellulose-biosynthesis-inhibiting herbicide provides long-term control of invasive winter annual grasses

BACKGROUND

Indaziflam is a cellulose-biosynthesis-inhibiting (CBI) herbicide that is a unique mode of action for resistance management and has broad spectrum activity at low application rates. This research further explores indaziflam's activity on monocotyledons and dicotyledons and evaluates indaziflam's potential for restoring non-crop sites infested with invasive winter annual grasses.

RESULTS

Treated Arabidopsis, downy brome, feral rye and kochia were all susceptible to indaziflam in a dose-dependent manner. We confirmed that indaziflam has increased activity on monocots (average GR₅₀  = 231 pm and 0.38 g AI ha^-1 ) at reduced concentrations compared with dicots (average GR₅₀  = 512 pm and 0.87 g AI ha^-1 ). Fluorescence microscopy confirmed common CBI symptomologies following indaziflam treatments, as well as aberrant root and cell morphology. Across five application timings, indaziflam treatments resulted in superior invasive winter annual grass control 2 years after treatment (from 84 ± 5.1% to 99 ± 0.5%) compared with imazapic (36% ± 1.2%). Indaziflam treatments significantly increased biomass and species richness of co-occurring species 2 years after treatment.

CONCLUSION

Indaziflam's increased activity on monocots could provide a new alternative management strategy for long-term control of multiple invasive winter annual grasses that invade >23 million ha of US rangeland. Indaziflam could potentially be used to eliminate the soil seed bank of these invasive grasses, reduce fine fuel accumulation and ultimately increase the competitiveness of perennial co-occuring species. © 2017 Society of Chemical Industry.

A KASP Genotyping Method to Identify Northern Watermilfoil, Eurasian Watermilfoil, and Their Interspecific Hybrids

The invasive aquatic plant Eurasian watermilfoil (Myriophyllum spicatum L.) can hybridize with the related North American native species northern watermilfoil (M. sibiricum Kom.). Hybrid watermilfoil (M. spicatum × M. sibiricum) populations have higher fitness and reduced sensitivity to some commonly used aquatic herbicides, making management more difficult. There is growing concern that management practices using herbicides in lakes with mixed populations of watermilfoil species may further select for hybrid individuals due to the difference in herbicide sensitivity. Accurate and cost-effective identification of rare hybrid individuals within populations is therefore critical for herbicide management decisions. Here we describe KASP assays for three SNPs in the ITS region to genotype individuals from both parental watermilfoil species and their hybrid, using synthesized plasmids containing the respective sequences as positive controls. Using KASP we genotyped 16 individuals from one lake and 23 individuals from a second lake, giving a highly accurate picture of Myriophyllum species distribution dynamics. We identified one hybrid individual among 16 samples from one lake, a discovery rate of <10%. Discriminant analysis showed that while a single SNP was generally sufficient for genotyping an individual, using multiple SNPs increased the reliability of genotyping. In the future, the ability to genotype many samples will provide the ability to identify the presence of rare individuals, such as a less common parental species or the inter-specific hybrid. Lakes with complex species distribution dynamics, such as a low proportion of hybrids, are where herbicide application must be carefully chosen so as not to select for the more vigorous and less herbicide-sensitive hybrid individuals.

Pollen-mediated gene flow from glyphosate-resistant common waterhemp (Amaranthus rudis Sauer): consequences for the dispersal of resistance genes

Gene flow is an important component in evolutionary biology; however, the role of gene flow in dispersal of herbicide-resistant alleles among weed populations is poorly understood. Field experiments were conducted at the University of Nebraska-Lincoln to quantify pollen-mediated gene flow (PMGF) from glyphosate-resistant (GR) to -susceptible (GS) common waterhemp using a concentric donor-receptor design. More than 130,000 common waterhemp plants were screened and 26,199 plants were confirmed resistant to glyphosate. Frequency of gene flow from all distances, directions, and years was estimated with a double exponential decay model using Generalized Nonlinear Model (package gnm) in R. PMGF declined by 50% at <3 m distance from the pollen source, whereas 90% reduction was found at 88 m (maximum) depending on the direction of the pollen-receptor blocks. Amplification of the target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), was identified as the mechanism of glyphosate resistance in parent biotype. The EPSPS gene amplification was heritable in common waterhemp and can be transferred via PMGF, and also correlated with glyphosate resistance in pseudo-F2 progeny. This is the first report of PMGF in GR common waterhemp and the results are critical in explaining the rapid dispersal of GR common waterhemp in Midwestern United States.

EPSPS Gene Copy Number and Whole-Plant Glyphosate Resistance Level in Kochia scoparia

Glyphosate-resistant (GR) Kochia scoparia has evolved in dryland chemical fallow systems throughout North America and the mechanism of resistance involves 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene duplication. Agricultural fields in four states were surveyed for K. scoparia in 2013 and tested for glyphosate-resistance level and EPSPS gene copy number. Glyphosate resistance was confirmed in K. scoparia populations collected from sugarbeet fields in Colorado, Wyoming, and Nebraska, and Montana. Glyphosate resistance was also confirmed in K. scoparia accessions collected from wheat-fallow fields in Montana. All GR samples had increased EPSPS gene copy number, with median population values up to 11 from sugarbeet fields and up to 13 in Montana wheat-fallow fields. The results indicate that glyphosate susceptibility can be accurately diagnosed using EPSPS gene copy number.

Confirmation and mechanism of glyphosate resistance in tall windmill grass (Chloris elata) from Brazil

BACKGROUND

Overreliance on glyphosate as a single tool for weed management in agricultural systems in Brazil has selected glyphosate-resistant populations of tall windmill grass (Chloris elata Desv.).

RESULTS

Two C. elata populations, one glyphosate resistant (GR) and one glyphosate susceptible (GS), were studied in detail for a dose-response experiment and for resistance mechanism. The dose causing 50% reduction in dry weight was 620 g a.e. ha(-1) for GR and 114 g ha(-1) for GS, resulting in an R/S ratio of 5.4. GS had significantly higher maximum (14) C-glyphosate absorption into the treated leaf (51.3%) than GR (39.5%), a difference of 11.8% in maximum absorption. GR also retained more (14) C-glyphosate in the treated leaf (74%) than GS (51%), and GR translocated less glyphosate (27%) to other plant parts (stems, roots and root exudation) than GS (36%). There were no mutations at the Pro106 codon in the gene encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). There was no difference in EPSPS genomic copy number or EPSPS transcription between GS and GR populations.

CONCLUSION

Based on these data, reduced glyphosate absorption and increased glyphosate retention in the treated leaf contribute to glyphosate resistance in this C. elata population from Brazil. © 2015 Society of Chemical Industry.

Isolation and characterization of antibiotic LL-AC541

A new basic, water-soluble antibiotic designated LL-AC541, produced by a strain of Streptomyces hygroscopicus (NRRL 3111), was isolated as a hydrochloride salt; [alpha](D) (25), - 58 degrees , melting point, 200 to 215 C (decomposition). It is structurally related to streptothricin but does not contain beta-lysine. Isolation procedures, physicochemical properties, antimicrobial spectrum, and in vivo testing results are presented. Another very closely related antibiotic obtained from the same fermentation is briefly described.

Isolation of the bromo analogue of caldariomycin from Caldariomyces fumago

When bromide ion was substituted for chloride in the growth medium of Caldariomyces fumago, a new substance was produced. It was isolated by solvent extraction and purified by alumina chromatography. Examination of the physicochemical properties of the substance led to its identification as the bromo analogue of the normal metabolite, caldariomycin. Thus, biological substitution of bromine for chlorine has been demonstrated in the metabolic formation of a purely aliphatic secondary mold metabolite.