Unravelling the genetic bases of non-target-site-based resistance (NTSR) to herbicides: a major challenge for weed science in the forthcoming decade

Cover crops, hormones and herbicides: Priming an integrated weed management strategy

Herbicide weed resistance has been a major issue of conventional global row crop agriculture for decades. Still current strategies and novel technologies available to address weed resistance are mainly herbicide-based. Thus, there is a need for innovative means of integrated weed management strategies. Our approach proposed herein integrates cover crops, plant hormones and pre-emergence (PRE) herbicides as part of weed management programs. Plant hormones such as gibberellic acid (GA₃) and abscisic acid (ABA) have the potential to induce seed germination and seed dormancy, respectively. Prior to crop emergence, plant hormones are tank mixed with PRE herbicides and sprayed to cover crop residue. Two strategies are proposed (1) PRE herbicides + GA₃ and (2) PRE herbicide + ABA. The hormones provide different results; GA₃ is likely to stimulate a more uniform weed seed germination, thus enhancing efficacy of PRE herbicides. Conversely, ABA could promote weed seed dormancy, reducing selection pressure and weed infestations until crop canopy closure. Much research is needed to understand the impact of hormones on weed and crop species, optimize products and rates, and compatibility of hormones with herbicides and cover crops. If successful, this approach could open a new opportunity for agricultural business, enhance farming sustainability by reducing dependence on herbicides and minimizing agronomic, economic and environmental issues related to weed resistance.

Pro-197-Ser Mutation in ALS and High-Level GST Activities: Multiple Resistance to ALS and ACCase Inhibitors in Beckmannia syzigachne

American sloughgrass (Beckmannia syzigachne Steud.) is one of the most troublesome weeds infesting wheat and canola fields in China. Some biotypes cannot be controlled, either by acetolactate synthase (ALS) or acetyl coenzyme A carboxylase (ACCase) inhibitors, which are the main herbicides for controlling this weed. However, very few studies have investigated multiple resistance mechanism in B. syzigachne. In this study, a B. syzigachne biotype with a high resistance to ALS inhibitors we have reported was also showed relatively lower resistance to ACCase inhibitors, with a resistance index around 7. RNA-seq analysis was used to investigate the factors responsible for multiple resistance, and 60,108 unigenes were assembled by de novo transcriptome assembly and then annotated across eight databases. A Pro-197-Ser mutation was identified in the ALS gene by SNPs analysis and validated by PCR, while no mutation was identified in the ACCase gene. Nineteen candidate metabolic genes were screened and their overexpression was confirmed by qPCR. The expression of GST-T3 and GST-U6 in resistant plants ranged from 7.5- to 109.4-folds than that in susceptible ones at different times after two kinds of herbicide treatment. In addition, GST activities in resistant plants were 3.0-5.0 times higher than that in susceptible plants. Other novel resistance factors also showed high correlation with multiple resistance which included four genes encoding disease resistance proteins, a transcription factor (MYC3), and one gene conferring blight resistance. In this research, a B. syzigachne biotype was confirmed to have evolved multiple resistance to ACCase and ALS inhibitors. The Pro-197-Ser mutation in ALS gene and high-level GST activities were confirmed responsible for the multiple resistance. Characterized disease-resistance proteins, transcription factor, and blight-resistance proteins may play an essential role in these multiple herbicide resistance.

Identification and expression of main genes involved in non-target site resistance mechanisms to fenoxaprop-p-ethyl in Beckmannia syzigachne

BACKGROUND

Non-target-site resistance (NTSR) to herbicides is a serious threat to global agriculture. Although metabolic resistance is the dominant mechanism of NTSR, the molecular mechanisms are not yet well-characterized. This study aimed to uncover the likely metabolism-related genes in Beckmannia syzigachne (American sloughgrass) resistant to fenoxaprop-p-ethyl.

RESULTS

Ultra-performance liquid chromatography - tandem mass spectrometry experiments showed that the resistant American sloughgrass biotype (R, SD-04-SS) showed enhanced degradation of this herbicide compared to the susceptible biotype (S, SD-12). R and S biotype were harvested at 24 h after fenoxaprop-p-ethyl treatment to conduct RNA sequencing (RNA-Seq) analysis to investigate the likely fenoxaprop-p-ethyl metabolic genes. The RNA-Seq libraries yield 417 969 980 clean reads. The de novo assembly generated 115 112 unigenes, of which 57 906 unigenes were annotated. Finally, we identified 273 cytochrome P450s, 178 oxidases, 47 glutathione S-transferases (GSTs), 166 glucosyltransferases (GTs) and 180 ABC transporter genes to determine the likely fenoxaprop-p-ethyl metabolism-related genes in R biotype. Twelve overlapping up-regulated genes in the R biotype (fenoxaprop-p-ethyl-treated R/non-treated R, fenoxaprop-p-ethyl-treated R/fenoxaprop-p-ethyl-treated S) were identified by RNA-Seq and the results were validated using qRT-PCR. Ten were identified as fenoxaprop-p-ethyl metabolism-related genes, including three P450s (homologous to CYP71D7, CYP99A2 and CYP71D10), one GST (homologous to GSTF1), two GTs (homologous to UGT90A1 and UGT83A1) and four oxidase genes.

CONCLUSION

This work demonstrates that the NTSR mechanism by means of enhanced detoxification of fenoxaprop-p-ethyl in American sloughgrass is very likely driven by herbicide metabolism related genes. The RNA-Seq data presented here provide a valuable resource for understanding the molecular mechanism of NTSR in American sloughgrass. © 2020 Society of Chemical Industry.

Evolution of generalist resistance to herbicide mixtures reveals a trade-off in resistance management

Intense selection by pesticides and antibiotics has resulted in a global epidemic of evolved resistance. In agriculture and medicine, using mixtures of compounds from different classes is widely accepted as optimal resistance management. However, this strategy may promote the evolution of more generalist resistance mechanisms. Here we test this hypothesis at a national scale in an economically important agricultural weed: blackgrass (Alopecurus myosuroides), for which herbicide resistance is a major economic issue. Our results reveal that greater use of herbicide mixtures is associated with lower levels of specialist resistance mechanisms, but higher levels of a generalist mechanism implicated in enhanced metabolism of herbicides with diverse modes of action. Our results indicate a potential evolutionary trade-off in resistance management, whereby attempts to reduce selection for specialist resistance traits may promote the evolution of generalist resistance. We contend that where specialist and generalist resistance mechanisms co-occur, similar trade-offs will be evident, calling into question the ubiquity of resistance management based on mixtures and combination therapies.

Mixtures of antibiotics or pesticides can help reduce the evolution of resistance to individual compounds. Here, Comont et al. show that in blackgrass, an important agricultural weed, herbicide mixtures do reduce specialized resistance but instead can select for a generalized resistance mechanism.

Cross-resistance mechanisms to ACCase-inhibiting herbicides in short-spike canarygrass (Phalaris brachystachys)

Herbicides that inhibit acetyl-coenzyme A carboxylase (ACCase) are commonly used to control weedy grasses such as short-spike canarygrass (Phalaris brachystachys). Two resistant biotypes of P. brachystachys (R1 and R2) were found in different winter wheat fields in Iran. This study was done to confirm the suspected resistance observed in the field and to elucidate the resistance mechanisms involved. The results indicated that the both resistant biotypes showed cross-resistance to diclofop-methyl (DM), pinoxaden (PN) and cycloxydim (CD) herbicides. Based on the herbicide dose that inhibited 50% of the ACCase activity (I₅₀), the ACCase activity of the resistant biotypes was less sensitive than the S biotype to DM, CD, and PN. No differences in translocation were detected between biotypes; most of the herbicide remained in the treated leaves. The ¹⁴C-DM metabolites were identified using thin-layer chromatography. Pre-treatment with the cytochrome P450 inhibitor ABT inhibited ¹⁴C-DM metabolism in the R1 biotype, indicating that metabolism is involved in the DM resistance in the R1 biotype. DNA sequencing studies found an Ile-1781-Thr change in both resistant biotypes, conferring cross-resistance to ACCase inhibitors. In general, in the R1 biotype which showed a higher level of resistance than that of the R2 biotype, cross-resistance was observed because of mutation and DM metabolism, while in the R2 biotype, the mutation confers resistance to ACCase-inhibiting herbicides. This is the first reported evidence of the mechanisms responsible for the resistance to ACCase herbicides in P. brachystachys. These results could be useful for improved management of resistant biotypes carrying similar mutations.

Cultivar variation for imazamox resistance in wheat (Triticum aestivum L.): Insights into enzymatic assays for early selection

Acetohydroxyacid synthase (AHAS, E.C. 2.2.1.6) is the target site of several herbicide classes including imidazolinones. Imidazolinone resistance in wheat is conferred by two major genes AhasL-D1 and AhasL-B1. The objective of this work was to evaluate the in vitro and in vivo AHAS activity and plant growth in response to imazamox of nine wheat cultivars. Dose-response curves for two-gene resistant cultivars were significantly different from the single-gene resistant and susceptible cultivars in the in vitro AHAS assay. Resistance levels at the in vivo AHAS and whole-plant assays for resistant cultivars were >10-fold higher than susceptible cultivars. Moreover, in vivo dose-response curves showed differences among cultivars with the same number of resistance genes. It was concluded that in the in vitro AHAS assay cultivar variability was due to differences in target-site sensitivity while the in vivo AHAS assay reflected the resistance at whole-plant level. Both in vitro and in vivo AHAS dose-response curves could be useful tools when exploring mechanisms involved in imidazolinone resistance in different wheat genetic backgrounds and for the selection of higher resistant genotypes.

Transcriptome Analysis Identifies Candidate Target Genes Involved in Glyphosate-Resistance Mechanism in Lolium multiflorum

Italian ryegrass (Lolium multiflorum; LOLMU) is one of the most troublesome weeds in temperate regions in the world. This weed species interfere with wheat, corn, rye, and oat, causing significant crop yield losses. This species has evolved glyphosate resistance, making it difficult to control. The mechanisms of glyphosate resistance are still unknown, and an understanding thereof will favor the development of new strategies of management. The present study is the first transcriptome study in LOLMU using glyphosate-resistant and -sensitive biotypes, aiming to identify and to provide a list of the candidate target genes related to glyphosate resistance mechanism. The transcriptome was assembled de novo, producing 87,433 contigs with an N50 of 740 bp and an average length of 575 bp. There were 92 and 54 up- and down-regulated genes, respectively, in the resistant biotype, while a total of 1683 were differentially expressed in the sensitive biotype in response to glyphosate treatment. We selected 14 highly induced genes and seven with repressed expression in the resistant biotype in response to glyphosate. Of these genes, a significant proportion were related to the plasma membrane, indicating that there is a barrier making it difficult for glyphosate to enter the cell.

Quinclorac resistance in Echinochloa phyllopogon is associated with reduced ethylene synthesis rather than enhanced cyanide detoxification by β-cyanoalanine synthase

BACKGROUND

Multiple herbicide resistant Echinochloa phyllopogon exhibits resistance to the auxin herbicide quinclorac. Previous research observed enhanced activity of the cyanide-detoxifying enzyme β-cyanoalanine synthase (β-CAS) and reduced ethylene production in the resistant line, suggesting β-CAS-mediated cyanide detoxification and insensitivity to quinclorac stimulation as the resistance mechanisms. To investigate the molecular mechanisms of quinclorac resistance, we characterized the β-CAS genes alongside plant transformation studies. The association of β-CAS activity and ethylene production to quinclorac resistance was assayed in the F6 progeny of susceptible and resistant lines of E. phyllopogon.

RESULTS

A single nucleotide polymorphism in a β-CAS1 intron deleted aberrantly spliced mRNAs and enhanced β-CAS activity in the resistant line. The enhanced activity, however, was not associated with quinclorac resistance in F6 lines. The results were supported by lack of quinclorac resistance in Arabidopsis thaliana expressing E. phyllopogon β-CAS1 and no difference in quinclorac sensitivity between β-CAS knockout and wild-type rice. Reduced ethylene production co-segregated with quinclorac resistance in F6 lines which were previously characterized to be resistant to other herbicides by an enhanced metabolism.

CONCLUSION

β-CAS does not participate in quinclorac sensitivity in E. phyllopogon. Our results suggest that a mechanism(s) leading to reduced ethylene production is behind the resistance. © 2019 Society of Chemical Industry.

Functional characterization of cytochrome P450 CYP81A subfamily to disclose the pattern of cross-resistance in Echinochloa phyllopogon

CYP81A P450s armor Echinochloa phyllopogon against diverse and several herbicide chemistries. CYP81A substrate preferences can be a basis for cross-resistance prediction and management in E. phyllopogon and other related species. Metabolism-based herbicide resistance is a major threat to agriculture, as it is unpredictable and could extend resistance to different chemical groups and modes of action, encompassing existing, novel and to-be-discovered herbicides. Limited information on the enzymes involved in herbicide metabolism has hindered the prediction of cross-resistance in weeds. Members of CYP81A subfamily in multiple herbicide resistant (MHR) Echinochloa phyllopogon were previously identified for conferring cross-resistance to six unrelated herbicide classes. This suggests a critical role of CYP81As in endowing unpredictable cross-resistances in E. phyllopogon, thus the functions of all its nine putative functional CYP81A genes to 33 herbicides from 24 chemical groups were characterized. Ectopic expression in Arabidopsis thaliana identified the CYP81As that can confer resistance to multiple and diverse herbicides. The CYP81As were further characterized for their enzymatic functions in Escherichia coli. CYP81A expression in E. coli was optimized via modification of the N-terminus, co-expression with HemA gene and culture at optimal temperature. CYP81As metabolized its herbicide substrates into hydroxylated, N-/O-demethylated or both products. The cross-resistance pattern conferred by CYP81As is geared towards all chemical groups of acetolactate synthase inhibitors and is expanded to herbicides inhibiting photosystem II, phytoene desaturase, protoporphyrinogen oxidase, 4-hydroxyphenylpyruvate dioxygenase, and 1-deoxy-D-xylulose 5-phosphate synthase. Cross-resistance to herbicides pyrimisulfan, propyrisulfuron, and mesotrione was predicted and confirmed in MHR E. phyllopogon. This study demonstrated that the functional characterization of the key enzymes for herbicide metabolism could disclose the cross-resistance pattern and identify appropriate chemical options to manage the existing and unexpected cross-resistances in E. phyllopogon.

Ethylene Biosynthesis Inhibition Combined with Cyanide Degradation Confer Resistance to Quinclorac in Echinochloa crus-galli var. mitis

Echinochloa crus-galli var. mitis has rarely been reported for herbicide resistance, and no case of quinclorac resistance has been reported so far. Synthetic auxin-type herbicide quinclorac is used extensively to control rice weeds worldwide. A long history of using quinclorac in Chinese rice fields escalated the resistance in E. crus-galli var. mitis against this herbicide. Bioassays in Petri plates and pots exhibited four biotypes that evolved into resistance to quinclorac ranking as JS01-R > AH01-R > JS02-R > JX01-R from three provinces of China. Ethylene production in these biotypes was negatively correlated with resistance level and positively correlated with growth inhibition. Determination of the related ethylene response pathway exhibited resistance in biotypes that recorded a decline in 1-aminocyclopropane-1-carboxylic acid (ACC) content, ACC synthase oxidase activities, and less inducible ACS and ACO genes expressions than the susceptible biotype, suggesting that there was a positive correlation between quinclorac resistance and ethylene biosynthesis inhibition. Cyanides produced during the ethylene biosynthesis pathway mainly degraded by the activity of β-cyanoalanine synthase (β-CAS). Resistant biotypes exhibited higher β-CAS activity than the susceptible ones. Nucleotide changes were found in the EcCAS gene of resistant biotypes as compared to sensitive ones that caused three amino acid substitutions (Asn-105-Lys, Gln-195-Glu, and Gly-298-Val), resulting in alteration of enzyme structure, increased binding residues in the active site with its cofactor, and decreased binding free energy; hence, its activity was higher in resistant biotypes. Moreover, these mutations increased the structural stability of the enzyme. In view of the positive correlation between ethylene biosynthesis inhibition and cyanide degradation with resistance level, it is concluded that the alteration in ethylene response pathway or at least variation in ACC synthase and ACC oxidase enzyme activities—due to less relative expression of ACS and ACO genes and enhanced β-CAS activity, as well as mutation and increased relative expression of EcCAS gene—can be considered as a probable mechanism of quinclorac resistance in E. crus-galli var. mitis.

Inheritance and Molecular Characterization of a Novel Mutated AHAS Gene Responsible for the Resistance of AHAS-Inhibiting Herbicides in Rapeseed (Brassica napus L.)

The use of herbicides is an effective and economic way to control weeds, but their availability for rapeseed is limited due to the shortage of herbicide-resistant cultivars in China. The single-point mutation in the acetohydroxyacidsynthase (AHAS) gene can lead to AHAS-inhibiting herbicide resistance. In this study, the inheritance and molecular characterization of the tribenuron-methyl (TBM)-resistant rapeseed (Brassica napus L.) mutant, K5, are performed. Results indicated that TBM-resistance of K5 was controlled by one dominant allele at a single nuclear gene locus. The novel substitution of cytosine with thymine at position 544 in BnAHAS1 was identified in K5, leading to the alteration of proline with serine at position 182 in BnAHAS1. The TBM-resistance of K5 was approximately 100 times that of its wild-type ZS9, and K5 also showed cross-resistance to bensufuron-methyl and monosulfuron-ester sodium. The BnAHAS1^544T transgenic Arabidopsis exhibited higher TBM-resistance than that of its wild-type, which confirmed that BnAHAS1^544T was responsible for the herbicide resistance of K5. Simultaneously, an allele-specific marker was developed to quickly distinguish the heterozygous and homozygous mutated alleles BnAHAS1^544T. In addition, a method for the fast screening of TBM-resistant plants at the cotyledon stage was developed. Our research identified and molecularly characterized one novel mutative AHAS allele in B. napus and laid a foundation for developing herbicide-resistant rapeseed cultivars.

Copper induces transcription of BcLCC2 laccase gene in phytopathogenic fungus, Botrytis cinerea

Laccases are one of many groups of inducible enzymes produced by the filamentous fungus, Botrytis cinerea during colonisation of host plant tissues. While the processes involved in laccase induction are not fully understood, Cupric ions (e.g. CuSO₄) and gallic acid (GA) have been reported as laccase inducers. This study investigates laccases activities and the expression of three laccase genes (BcLCC1, BcLCC2, BcLCC3) in three B. cinerea isolates grown in laccase-inducing medium (LIM) supplemented with CuSO₄ and GA. Laccase activity in culture filtrates with CuSO₄ increased after 48 h of growth in LIM at 24°C. The induction of BcLCC2 transcription was greatest at a concentration of 0.6 mM CuSO₄, concentrations greater than 0.6 mM inhibited fungal growth. In contrast, no laccase induction was observed in the presence of GA. Liquid chromatography-mass spectroscopy (NanoLC ESI MS/MS) analysis confirmed the presence of a 63.4 kDa protein, the BcLCC2 isoform in the culture filtrate with 0.6 mM CuSO₄. Analysis of mRNA transcripts further showed BcLCC3 was also inducible and the expression of BcLCC2 and BcLCC3 was isolate-dependent. In conclusion, CuSO₄ induces a 63.4 kDa laccase in B. cinerea by induced transcription of the BcLCC2 gene.

Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed

The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.

Herbicide resistant weeds: A call to integrate conventional agricultural practices, molecular biology knowledge and new technologies

Herbicide resistant (HR) weeds are of major concern in modern agriculture. This situation is exacerbated by the massive adoption of herbicide-based technologies along with the overuse of a few active ingredients to control weeds over vast areas year after year. Also, many other anthropological, biological, and environmental factors have defined a higher rate of herbicide resistance evolution in numerous weed species around the world. This review focuses on two central points: 1) how these factors have affected the resistance evolution process; and 2) which cultural practices and new approaches would help to achieve an effective integrated weed management. We claim that global climate change is an unnoticed factor that may be acting on the selection of HR weeds, especially those evolving into non-target-site resistance mechanisms. And we present several new tools -such as Gene Drive and RNAi technologies- that may be adopted to cope with herbicide resistance spread, as well as discuss their potential application at field level. This is the first review that integrates agronomic and molecular knowledge of herbicide resistance. It covers not only the genetic basis of the most relevant resistance mechanisms but also the strengths and weaknesses of traditional and forthcoming agricultural practices.

Omics Potential in Herbicide-Resistant Weed Management

The rapid development of omics technologies has drastically altered the way biologists conduct research. Basic plant biology and genomics have incorporated these technologies, while some challenges remain for use in applied biology. Weed science, on the whole, is still learning how to integrate omics technologies into the discipline; however, omics techniques are more frequently being implemented in new and creative ways to address basic questions in weed biology as well as the more practical questions of improving weed management. This has been especially true in the subdiscipline of herbicide resistance where important questions are the evolution and genetic basis of herbicide resistance. This review examines the advantages, challenges, potential solutions, and outlook for omics technologies in the discipline of weed science, with examples of how omics technologies will impact herbicide resistance studies and ultimately improve management of herbicide-resistant populations.

Target site as the main mechanism of resistance to imazamox in a Euphorbia heterophylla biotype

Euphorbia heterophylla is a weed species that invades extensive crop areas in subtropical regions of Brazil. This species was previously controlled by imazamox, but the continuous use of this herbicide has selected for resistant biotypes. Two biotypes of E. heterophylla from southern Brazil, one resistant (R) and one susceptible (S) to imazamox, were compared. The resistance of the R biotype was confirmed by dose-response assays since it required 1250.2 g ai ha^-1 to reduce the fresh weight by 50% versus 7.4 g ai ha^-1 for the S biotype. The acetolactate synthase (ALS) enzyme activity was studied using ALS-inhibiting herbicides from five different chemical families. The R biotype required the highest concentrations to reduce this enzyme activity by 50%. A Ser653Asn mutation was found in the ALS gene of the R biotype. The experiments carried out showed that imazamox absorption and metabolism were not involved in resistance. However, greater ¹⁴C-imazamox root exudation was found in the R biotype (~70% of the total absorbed imazamox). Target site mutation in the ALS gene is the principal mechanism that explains the imazamox resistance of the R biotype, but root exudation seems to also contribute to the resistance of this biotype.

Target-Site Mutations Conferring Herbicide Resistance

Mutations conferring evolved herbicide resistance in weeds are known in nine different herbicide sites of action. This review summarizes recently reported resistance-conferring mutations for each of these nine target sites. One emerging trend is an increase in reports of multiple mutations, including multiple amino acid changes at the glyphosate target site, as well as mutations involving two nucleotide changes at a single amino acid codon. Standard reference sequences are suggested for target sites for which standards do not already exist. We also discuss experimental approaches for investigating cross-resistance patterns and for investigating fitness costs of specific target-site mutations.

Population Genomic Approaches for Weed Science

Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.

Allelopathic Potential of Phenolic Compounds in Secale Cereale Cultivars and Its Relationship with Seeding Density

In this study, we investigated the allelopathic effect of Secale cereale cultivars on different weeds that grow in the cultivated fields of Perilla frutescens. Two S. cereale cultivars, Paldong and Singhi, were used to test the allelopathic effect on in vitro grown Digitaria ciliaris, Chenopodium album, Amaranthus lividus, Portulaca oleracea, Pinellia ternata and Commelina communis. The results indicated that S. cereale extracts affect callus growth of weeds in terms of fresh weight and percentage of growth inhibition. The inhibitory effects of both S. cereale cultivars combined with grass cover extracts were higher than using grass weeds alone. Concentrations of all identified phenolic compounds were significantly higher in the leaves extracts of Paldong compared to Singhi. Particularly, syringic acid in leaves extract of the Paldong cultivar were 12.87-fold higher than in the Singhi cultivar. The other predominant phenolic compounds such as salicylic acid, p-coumaric acid, vanillic acid, and p-hydroxybenzoic acids were 3.30, 4.63, 3.11, and 1.28 times higher, respectively, in the leaves extracts of Paldong compared to Singhi. Principal component analysis (PCA) results indicated that the composition of phenolic compounds was significantly related to cultivar types and plant parts used. In addition, biomass increase caused increased weed inhibitory capacity of S. cereale both in tillage and no-tillage regimes. These results suggest that the biomass of cover crops negatively influenced weed density.

Target-Site and Metabolic Resistance Mechanisms to Penoxsulam in Barnyardgrass (Echinochloa crus-galli (L.) P. Beauv)

Herbicide resistance identification is essential for effective chemical weed control. In this study, we quantified the differences in growth response between penoxsulam resistant (R) and sensitive (S) Echinochloa crus-galli populations, explored the changes in ALS, and performed genetic analyses to identify metabolic genes that are up-regulated by the application of penoxsulam and other common herbicides. The R population showed a 26.0-fold higher resistance to penoxsulam and varied resistance to most tested herbicides with indices ranging from 4.9 to 145.9. A Trp-574-Arg amino acid mutation in ALS and low penoxsulam ALS sensitivity were the main mechanisms underlying herbicide resistance. The penoxsulam resistance can be significantly reversed by two P450s inhibitors and one GST inhibitor. By RNA-Seq, thirty-six highly expressed contigs were selected, and 30 of them were up-regulated in the R population treated by penoxsulam. Many of these genes were significantly expressed when treated with pyroxsulam, metamifop, and quinclorac. These upregulated genes appear to be complementary for plant resistance to penoxsulam and other common herbicides.

Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover?

The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide-resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide-resistant weeds in three broad areas - the genetic basis of adaptation, evolutionary constraints, experimental evolution - and similarly discuss questions left to be answered. I then develop how one would use herbicide-resistance evolution as a model for studying eco-evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide-resistant plants as models for addressing key questions within ecology and evolution.

Transcriptome profiling to identify cytochrome P450 genes involved in penoxsulam resistance in Echinochloa glabrescens

Cytochrome P450s (P450s) confer resistance against herbicides, and this is increasingly becoming a concern for weed control. As a widespread Gramineae weed in paddy fields, Echinocloa glabrescens has become resistant to the acetolactate synthase (ALS)-inhibiting triazolopyrimidine herbicide penoxsulam. In this study, we found that the GR₅₀ of the resistant population (SHQP-R) decreased substantially from 25.6 to 5.0 and 6.2 g a.i. ha^-1 after treatment with the P450 inhibitors piperonyl butoxide (PBO) and malathion, respectively. However, P450 inhibitors almost had no effects on the susceptibility of the sensitive population (JYJD-S) to penoxsulam. To investigate the mechanisms of metabolic resistance, transcriptome sequencing analysis was performed to find candidate genes that may confer resistance to penoxsulam in E. glabrescens. A total of 233 P450 differentially expressed genes (DEGs) were identified by transcriptome sequencing. We found that the metabolic process and metabolic pathways were the most highly enriched in DEGs. Further, twenty-seven candidate P450 DEGs were selected for qPCR validation analyses. After penoxsulam treatment, the relative expression levels were significantly higher in SHQP-R than in JYJD-S. Among these, the relative expression of twenty-three P450 DEGs (eighteen from the CYP72A-71C-74A-96A-734A subfamily; five from CYP81E1-94C1-94B3-714C1-714C2) were upregulated and four P450 DEGs (from CYP724B1-711A1-707A7-97B2) were downregulated. Changes in the expression of these candidate P450 genes in E. glabrescens were in response to penoxsulam, which provides preliminary evidence for the role of P450s in herbicide metabolism in E. glabrescens. However, further functional studies on metabolic resistance to penoxsulam in a resistant E. glabrescens population are required.

Unravelling mesosulfuron-methyl phytotoxicity and metabolism-based herbicide resistance in Alopecurus aequalis: Insight into regulatory mechanisms using proteomics

Non-target-site based resistance (NTSR), a poorly understood multigenic trait, has evolved as the greatest threat to crop production worldwide, by endowing weed plants an unpredictable pattern of resistance to herbicides. Our recent work with multiple-herbicide-resistant shortawn foxtail (Alopecurus aequalis Sobol.) biotype has preliminary indicated that cytochrome P450s-involved enhanced rate of mesosulfuron-methyl metabolism may involve in the NTSR. Here by further determining the differences in glutathione S-transferase (GST) activity and uptake and metabolic rates of mesosulfuron between resistant (R) and susceptible (S) A. aequalis plants, and associating them with endogenous differently regulated proteins (DEPs) identified from combinational proteomics analyses, we provided direct evidences on the enhanced herbicide degradation in resistant plants. Subsequently, the physiological phenotypes of photosynthesis, chlorophyll fluorescence, and antioxidation were compared between R and S plants and linked with correlative DEPs, indicating a series of key pathways including solar energy capture, photosynthetic electron transport, redox homeostasis, carbon fixation, photorespiration, and reactive oxygen species scavenging in susceptible plants were broken or severely damaged by mesosulfuron stress. In comparison, resistant plants have evolved enhanced herbicide degradation to minimize the accumulation of mesosulfuron and protect the photosynthesis and ascorbate-glutathione cycle against the adverse effects of chemical injury, giving A. aequalis plants a NTSR phenotype. Additionally, three key proteins respectively annotated as esterase, GST, and glucosyltransferase were identified and enabled as potential transcriptional markers for quick diagnosing the metabolic mesosulfuron resistance in A. aequalis species.

Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might 'rescue' resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

instaGraminoid, a Novel Colorimetric Method to Assess Herbicide Resistance, Identifies Patterns of Cross-Resistance in Annual Ryegrass

Herbicide resistance in agricultural weeds is a global problem with an increasing understanding that it is caused by multiple genes leading to quantitative resistance. These quantitative patterns of resistance are not easy to decipher with mortality assays alone, and there is a need for straightforward and unbiased protocols to accurately assess quantitative herbicide resistance. instaGraminoid-a computer vision and statistical analysis package-was developed as an automated and scalable method for quantifying herbicide resistance. The package was tested in rigid ryegrass (Lolium rigidum), the most noxious and highly resistant weed in Australia and the Mediterranean region. This method provides quantitative measures of the degree of chlorosis and necrosis of individual plants which was shown to accurately reflect herbicide resistance. We were able to reliably characterise resistance to four herbicides with different sites of action (glyphosate, sulfometuron, terbuthylazine, and trifluralin) in two L. rigidum populations from Southeast Australia. Cross-validation of the method across populations and herbicide treatments showed high repeatability and transferability. Significant positive correlations in resistance of individual plants were observed across herbicides, which suggest either the accumulation of herbicide-specific resistance alleles in single genotypes (multiple stacked resistance) or the presence of general broad-effects resistance alleles (cross-resistance). We used these quantitative estimates of cross-resistance to simulate how resistance development under an herbicide rotation strategy is likely to be higher than expected.

Defenses Against ROS in Crops and Weeds: The Effects of Interference and Herbicides

The antioxidant defense system acts to maintain the equilibrium between the production of reactive oxygen species (ROS) and the elimination of toxic levels of ROS in plants. Overproduction and accumulation of ROS results in metabolic disorders and can lead to the oxidative destruction of the cell. Several stress factors cause ROS overproduction and trigger oxidative stress in crops and weeds. Recently, the involvement of the antioxidant system in weed interference and herbicide treatment in crops and weeds has been the subject of investigation. In this review, we address ROS production and plant mechanisms of defense, alterations in the antioxidant system at transcriptional and enzymatic levels in crops induced by weed interference, and herbicide exposure in crops and weeds. We also describe the mechanisms of action in herbicides that lead to ROS generation in target plants. Lastly, we discuss the relations between antioxidant systems and weed biology and evolution, as well as the interactive effects of herbicide treatment on these factors.

CYP81A P450s are involved in concomitant cross-resistance to acetolactate synthase and acetyl-CoA carboxylase herbicides in Echinochloa phyllopogon

Californian populations of Echinochloa phyllopogon have evolved multiple-herbicide resistance (MHR), posing a threat to rice production in California. Previously, we identified two CYP81A cytochrome P450 genes whose overexpression is associated with resistance to acetolactate synthase (ALS) inhibitors from two chemical groups. Resistance mechanisms to other herbicides remain unknown. We analyzed the sensitivity of an MHR line to acetyl-CoA carboxylase (ACCase) inhibitors from three chemical groups, followed by an analysis of herbicide metabolism and segregation of resistance of the progenies in sensitive (S) and MHR lines. ACCase herbicide metabolizing function was investigated in the two previously identified P450s. MHR plants exhibited resistance to all the ACCase inhibitors by enhanced herbicide metabolism. Resistance to the ACCase inhibitors segregated in a 3 : 1 ratio in the F₂ generation and completely co-segregated with ALS inhibitor resistance in F₆ lines. Expression of the respective P450 genes conferred resistance to the three herbicides in rice, which is in line with the detection of hydroxylated herbicide metabolites in vivo in transformed yeast. CYP81As are super P450s that metabolize multiple herbicides from five chemical classes, and concurrent overexpression of the P450s induces metabolism-based resistance to the three ACCase inhibitors in MHR E. phyllopogon, as it does to ALS inhibitors.

Target-site and non-target-site-based resistance to tribenuron-methyl in multiply-resistant Myosoton aquaticum L

Myosoton aquaticum L., a widespread and competitive winter weed of wheat in China, has evolved resistance to many classes of herbicides. In one M. aquaticum population (AH03), collected from Anhui Province, where tribenuron-methyl and florasulam had been used to control this weed resistance to both herbicides had evolved. Compared with the sensitive population, HN03(S), the resistant (R) population, AH03, was highly resistant to tribenuron-methyl, flucarbazone-Na and pyroxsulam, moderately resistant to pyrithiobac‑sodium, and florasulam, and had low resistance to diflufenican. AH03 was still controlled by imazethapyr, 2,4-D butylate, fluroxypyr-meptyl, and isoproturon. Pretreatment with the P450 inhibitor malathion reduced the GR₅₀ value of tribenuron-methyl by 43% in the R population, and by 25% in the S population. This indicates that P450-mediated enhanced metabolism is one likely mechanism for tribenuron-methyl resistance in M. aquaticum. Glutathione-S-transferase (GST) activity could be induced by tribenuron-methyl in both the R and S populations. However, both the basal and induced GST activity of the R population was lower than that of the S population. The in vitro ALS assay confirmed that the ALS from the R plants showed a high resistance (52.93-fold) to tribenuron-methyl. ALS gene sequencing revealed a Pro197Ala substitution in the R plants. Based on the ALS gene sequence analysis, molecular markers were also developed to identify the specific Pro197Ala mutation. This population of M. aquaticum has multiple resistance and target-site (ALS Pro197Ala) and non-target-site resistance mechanisms contribute to tribenuron-methyl resistance.

Characterization of three glyphosate resistant Parthenium hysterophorus populations collected in citrus groves from Mexico

Continuous use of glyphosate in citrus groves in the Gulf of Mexico region has selected for resistant Parthenium hysterophorus L. populations. In this study, the target-site and non-target-site resistance mechanisms were characterized in three putative glyphosate-resistant (GR) P. hysterophorus populations, collected in citrus groves from Acateno, Puebla (GR1 and GR2) and Martínez de la Torre, Veracruz (GR3), and compared with a susceptible population (GS). Based on plant mortality, the GR populations were 9.2-17.3 times more resistant to glyphosate than the GS population. The low shikimate accumulation in the GR population confirmed this resistance. Based on plant mortality and shikimate accumulation, the GR3 population showed intermediate resistance to glyphosate. The GR populations absorbed 15-28% less 14C-glyphosate than the GS population (78.7% absorbed from the applied) and retained 48.7-70.7% of 14C-glyphosate in the treated leaf, while the GS population translocated ~68% of absorbed herbicide to shoots and roots. The GR3 population showed the lowest translocation and absorption rates, but was found to be susceptible at the target site level. The 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene sequence of the GR1 and GR2 populations showed the Pro106-Ser mutation, conferring 19- and 25-times more resistance in comparison to the GS population, respectively. Reduced absorption and impaired translocation conferred glyphosate resistance on the GR3 population, and contributed partially to the resistance of the GR1 and GR2 populations. Additionally, the Pro-106-Ser mutation increased the glyphosate resistance of the last two P. hysterophorus populations.

Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen

We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the transcriptional profiling against glyphosate resistance in giant ragweed. Assembly and genic features show a normal angiosperm quadripartite plastome structure with no signatures of deviation in gene directionality. Comparative analysis revealed large inversions across the plastome of giant ragweed and the previously sequenced members of the plant family. Asteraceae plastid genomes contain two inversions of 22.8 and 3.3 kb; the former is located between trnS-GCU and trnG-UCC genes, and the latter between trnE-UUC and trnT-GGU genes. The plastid genome sequences of A. trifida and the related species, Ambrosia artemisiifolia, are identical in gene content and arrangement, but they differ in length. The phylogeny is well-resolved and congruent with previous hypotheses about the phylogenetic relationship of Asteraceae. Transcriptomic analysis revealed divergence in the relative expressions at the exonic and intronic levels, providing hints toward the ecological adaptation of the genus. Giant ragweed shows various levels of glyphosate resistance, with introns displaying higher expression patterns at resistant time points after the assumed herbicide treatment.

Metribuzin Resistance in a Wild Radish ( Raphanus raphanistrum) Population via Both psbA Gene Mutation and Enhanced Metabolism

There have been many studies on target-site resistance (TSR) to PSII-inhibiting herbicides, but only a few on the non-target-site resistance (NTSR). Here, we reported both TSR and NTSR to metribuzin in a wild radish population. Dose-response studies revealed a higher level of resistance to metribuzin in the resistant (R) compared to the susceptible (S) population. Sequencing of the target psbA gene revealed the known Ser-264-Gly mutation in R plants. In addition, a higher level of [¹⁴C]-metribuzin metabolism and, consequently, a lower level of [¹⁴C] translocation were also detected in the R plants. These results demonstrated that both psbA gene mutation and enhanced metabolism contribute to metribuzin resistance in this wild radish population. Furthermore, this resistant population showed resistance to ALS-inhibiting herbicides due to multiple ALS gene mutations. This is the first report in wild radish of metabolic herbicide resistance, in addition to the target-site psbA gene mutation.

Reduced Absorption and Impaired Translocation Endows Glyphosate Resistance in Amaranthus palmeri Harvested in Glyphosate-Resistant Soybean from Argentina

Amaranthus palmeri S. Watson is probably the worst glyphosate-resistant (GR) weed worldwide. The EPSPS (5-enolpyruvylshikimate-3-phosphate-synthase) gene amplification has been reported as the major target-site-resistance (TSR) mechanism conferring resistance to glyphosate in this species. In this study, TSR and non-target-site-resistance (NTSR) mechanisms to glyphosate were characterized in a putative resistant A. palmeri population (GRP), harvested in a GR soybean crop from Argentina. Glyphosate resistance was confirmed for the GRP population by dose-response assays. No evidence of TSR mechanisms, as well as glyphosate metabolism, was found in this population. Moreover, a susceptible population (GSP) that absorbed about 10% more herbicide than the GRP population was evaluated at different periods after treatment. The GSP population translocated about 20% more glyphosate to the remainder of the shoots and roots at 96 h after treatment than the control, while the GRP population retained 62% of herbicide in the treated leaves. This is the first case of glyphosate resistance in A. palmeri involving exclusively NTSR mechanisms.

HRGPred: Prediction of herbicide resistant genes with k-mer nucleotide compositional features and support vector machine

Herbicide resistance (HR) is a major concern for the agricultural producers as well as environmentalists. Resistance to commonly used herbicides are conferred due to mutation(s) in the genes encoding herbicide target sites/proteins (GETS). Identification of these genes through wet-lab experiments is time consuming and expensive. Thus, a supervised learning-based computational model has been proposed in this study, which is first of its kind for the prediction of seven classes of GETS. The cDNA sequences of the genes were initially transformed into numeric features based on the k-mer compositions and then supplied as input to the support vector machine. In the proposed SVM-based model, the prediction occurs in two stages, where a binary classifier in the first stage discriminates the genes involved in conferring the resistance to herbicides from other genes, followed by a multi-class classifier in the second stage that categorizes the predicted herbicide resistant genes in the first stage into any one of the seven resistant classes. Overall classification accuracies were observed to be ~89% and >97% for binary and multi-class classifications respectively. The proposed model confirmed higher accuracy than the homology-based algorithms viz., BLAST and Hidden Markov Model. Besides, the developed computational model achieved ~87% accuracy, while tested with an independent dataset. An online prediction server HRGPred (http://cabgrid.res.in:8080/hrgpred) has also been established to facilitate the prediction of GETS by the scientific community.

High [CO2] and Temperature Increase Resistance to Cyhalofop-Butyl in Multiple-Resistant Echinochloa colona

Changes in the environment, specifically rising temperature and increasing atmospheric carbon dioxide concentration [CO₂], can alter the growth and physiology of weedy plants. These changes could alter herbicide efficacy, crop-weed interaction, and weed management. The objectives of this research were to quantify the effects of increased atmospheric [CO₂] and temperature on absorption, translocation and efficacy of cyhalofop-butyl on multiple-resistant (MR) and susceptible (S) Echinochloa colona genotypes. E. colona, or junglerice, is a troublesome weed in rice and in agronomic and horticultural crops worldwide. Cyhalofop-butyl is a grass herbicide that selectively controls Echinochloa spp. in rice. Maximum ¹⁴C-cyhalofop-butyl absorption occurred at 120 h after herbicide treatment (HAT) with >97% of cyhalofop-butyl retained in the treated leaf regardless of [CO₂], temperature, or genotype. Neither temperature nor [CO₂] affected herbicide absorption into the leaf. The translocation of herbicide was slightly reduced in the MR plants vs. S plants either under elevated [CO₂] or high temperature. Although plants grown under high [CO₂] or high temperature were taller than those in ambient conditions, neither high [CO₂] nor high temperature reduced the herbicide efficacy on susceptible plants. However, herbicide efficacy was reduced on MR plants grown under high [CO₂] or high temperature about 50% compared to MR plants at ambient conditions. High [CO₂] and high temperature increased the resistance level of MR E. colona to cyhalofop-butyl. To mitigate rapid resistance evolution under a changing climate, weed management practitioners must implement measures to reduce the herbicide selection pressure. These measures include reduction of weed population size through reduction of the soil seedbank, ensuring complete control of current infestations with multiple herbicide modes of action in mixture and in sequence, augmenting herbicides with mechanical control where possible, rotation with weed-competitive crops, use of weed-competitive cultivars, use of weed-suppressive cover crops, and other practices recommended for integrated weed management.

Alterations in Life-History Associated With Non-target-site Herbicide Resistance in Alopecurus myosuroides

The evolution of resistance to herbicides is a classic example of rapid contemporary adaptation in the face of a novel environmental stress. Evolutionary theory predicts that selection for resistance will be accompanied by fitness trade-offs in environments where the stress is absent. Alopecurus myosuroides, an autumn-germinating grass weed of cereal crops in North-West Europe, has evolved resistance to seven herbicide modes-of-action, making this an ideal species to examine the presence and magnitudes of such fitness costs. Here, we use two contrasting A. myosuroides phenotypes derived from a common genetic background, one with enhanced metabolism resistance to a commercial formulation of the sulfonylurea (ALS) actives mesosulfuron and iodosulfuron, and the other with susceptibility to these actives (S). Comparisons of plant establishment, growth, and reproductive potential were made under conditions of intraspecific competition, interspecific competition with wheat, and over a gradient of nitrogen deprivation. Herbicide dose response assays confirmed that the two lines had contrasting resistance phenotypes, with a 20-fold difference in resistance between them. Pleiotropic effects of resistance were observed during plant development, with R plants having a greater intraspecific competitive effect and longer tiller lengths than S plants during vegetative growth, but with S plants allocating proportionally more biomass to reproductive tissues during flowering. Direct evidence of a reproductive cost of resistance was evident in the nitrogen deprivation experiment with R plants producing 27% fewer seed heads per plant, and a corresponding 23% reduction in total seed head length. However, these direct effects of resistance on fecundity were not consistent across experiments. Our results demonstrate that a resistance phenotype based on enhanced herbicide metabolism has pleiotropic impacts on plant growth, development and resource partitioning but does not support the hypothesis that resistance is associated with a consistent reproductive fitness cost in this species. Given the continued difficulties associated with unequivocally detecting costs of herbicide resistance, we advocate future studies that adopt classical evolutionary quantitative genetics approaches to determine genetic correlations between resistance and fitness-related plant life history traits.

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.

Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

BACKGROUND

Water chickweed (Myosoton aquaticum (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides.

RESULTS

We identified a M. aquaticum population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to CYP734A1, CYP76C1, and CYP86B1) and one ABC transporter gene (with homology to ABCC10) were highly expressed in all resistant plants.

CONCLUSION

The mechanism of TM resistance in M. aquaticum is controlled by NTSR rather than TSR. Four genes, CYP734A1, CYP76C1, CYP86B1, and ABCC10 could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in M. aquaticum using the Illumina platform. Our data provide resource for M. aquaticum biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.

Optimizing RNA-seq studies to investigate herbicide resistance

Transcriptomic profiling, specifically via RNA sequencing (RNA-seq), is becoming one of the more commonly used methods for investigating non-target site resistance (NTSR) to herbicides due to its high throughput capabilities and utility in organisms with little to no previous sequence information. A review of the weed science RNA-seq literature revealed some basic principles behind generating quality data from these types of studies. First, studies that included more replicates per biotype and took steps to control for genetic background had significantly better control of false positives and, consequently, shorter lists of potential resistance genes to sift through. Pooling of biological replicates prior to sequencing was successful in some cases, but likely contributed to an overall increase in the false discovery rate. Although the inclusion of herbicide-treated samples was common across most of the studies, it ultimately introduced difficulties in interpretation of the final results due to challenges in capturing the right sampling window after treatment and to the induction of stress responses in the injured herbicide-sensitive plants. RNA-seq is an effective tool for NTSR gene discovery, but careful consideration should be given to finding the most powerful and cost-effective balance between replicate number, sequencing depth and treatment number. © 2017 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.

Metabolism of 2,4-dichlorophenoxyacetic acid contributes to resistance in a common waterhemp (Amaranthus tuberculatus) population

BACKGROUND

Synthetic auxins such as 2,4-dichlorophenoxyacetic acid (2,4-D) have been widely used for selective control of broadleaf weeds since the mid-1940s. In 2009, an Amaranthus tuberculatus (common waterhemp) population with 10-fold resistance to 2,4-D was found in Nebraska, USA. The 2,4-D resistance mechanism was examined by conducting [¹⁴ C] 2,4-D absorption, translocation and metabolism experiments.

RESULTS

No differences were found in 2,4-D absorption or translocation between resistant and susceptible A. tuberculatus plants. Resistant plants metabolized [¹⁴ C] 2,4-D more rapidly than did susceptible plants. The half-life of [¹⁴ C] 2,4-D in susceptible plants was 105 h, compared with 22 h in resistant plants. Pretreatment with the cytochrome P450 inhibitor malathion inhibited [¹⁴ C] 2,4-D metabolism in resistant plants and reduced the 2,4-D dose required for 50% growth inhibition (GR₅₀ ) of resistant plants by 7-fold to 27 g ha^-1 , similar to the GR₅₀ for susceptible plants in the absence of malathion.

CONCLUSION

Our results demonstrate that rapid 2,4-D metabolism is a contributing factor to resistance in A. tuberculatus, potentially mediated by cytochrome P450. Metabolism-based resistance to 2,4-D could pose a serious challenge for A. tuberculatus control because of the potential for cross-resistance to other herbicides. © 2017 Society of Chemical Industry.

Gene expression in response to glyphosate treatment in fleabane (Conyza bonariensis) - glyphosate death response and candidate resistance genes

BACKGROUND

This study takes a whole-transcriptome approach to assess gene expression changes in response to glyphosate treatment in glyphosate-resistant fleabane. We assessed gene expression changes in both susceptible and resistant lines so that the glyphosate death response could be quantified, and constitutively expressed candidate resistance genes identified. There are three copies of the glyphosate target site (5-enolpyruvylshikimate-3-phosphate; EPSPS) gene in Conyza and because Conyza bonariensis is allohexaploid, there is a baseline nine copies of the gene in any individual.

RESULTS

Many genes were differentially expressed in response to glyphosate treatment. Known resistance mutations are present in EPSPS2 but they are present in a glyphosate-susceptible line as well as resistant lines and therefore not sufficient to confer resistance. EPSPS1 is expressed four times more than EPSPS2, further reducing the overall contribution of these mutations.

CONCLUSION

We demonstrate that glyphosate resistance in C. bonariensis is not the result of EPSPS mutations or overexpression, but due to a non-target-site mechanism. A large number of genes are affected by glyphosate treatment. We present a list of candidate non-target-site-resistance (NTSR) genes in fleabane for future studies into these mechanisms. © 2017 Society of Chemical Industry.

Carbon (δ13C) and Nitrogen (δ15N) Stable Isotope Composition Provide New Insights into Phenotypic Plasticity in Broad Leaf Weed Rumex acetosa under Allelochemical Stress

Phenolic compounds, hydroquinone and cinnamic acid derivatives have been identified as major allelochemicals with known phytotoxicity from allelopathic plant Acacia melanoxylon R. Br. Several phenolic compounds such as ferulic acid (FA), p-hydroxybenzoic acid (pHBA) and flavonoid (rutin, quercetin) constituents occur in the phyllodes and flowers of A. melanoxylon and have demonstrated inhibitory effects on germination and physiological characteristics of lettuce and perennial grasses. However, to date, little is known about the mechanisms of action of these secondary metabolites in broad-leaved weeds at ecophysiological level. The objective of this study was to determine the response of Rumex acetosa carbon isotope composition and other physiological parameters to the interaction of plant secondary metabolites (PSM) (FA and pHBA) stress and the usefulness of carbon isotope discrimination (Δ¹³C) as indicative of the functional performance of intrinsic water use efficiency (iWUE) at level of plant leaf. R. acetosa plant were grown under greenhouse condition and subjected to PSM stress (0, 0.1, 0.5, 1.0, and 1.5 mM) for six days. Here, we show that FA and pHBA are potent inhibitors of Δ¹³C that varied from 21.0‰ to 22.9‰. Higher pHBA and FA supply enhanced/retard the N_leaf and increased the C_leaf while ratio of intercellular CO₂ concentration from leaf to air (Ci/Ca) was significantly decreased as compared to control. Leaf water content and leaf osmotic potential were decreased following treatment with both PSM. The Ci/Ca decreased rapidly with higher concentration of FA and pHBA. However, iWUE increased at all allelochemical concentrations. At the whole plant level, both PSM showed pronounced growth-inhibitory effects on PBM and C and N concentration, root fresh/dry weight, leaf fresh/dry weight, and root, shoot length of C₃ broad leaf weed R. acetosa. Carbon isotope discrimination (Δ) was correlated with the dry matter to transpiration ratio (transpiration efficiency) in this C₃ species, but its heritability and relationship to R. acetosa growth are less clear. Our FA and pHBA compounds are the potent and selective carbon isotope composition (δ¹³C) inhibitors known to date. These results confirm the phytotoxicity of FA and pHBA on R. acetosa seedlings, the reduction of relative water content and the induction of carbon isotope discrimination (Δ) with lower plant biomass.

Enhanced Herbicide Metabolism and Metabolic Resistance Genes Identified in Tribenuron-Methyl Resistant Myosoton aquaticum L

The evolved resistance of Myosoton aquaticum L. to acetolactate synthase (ALS) inhibitors is well established, but most research has focused on target-site resistance, while nontarget-site resistance remains neglected. Here, we investigated mechanisms of the latter. The pretreatment with the P450 inhibitor malathion significantly increased the sensitivity of resistant plants to tribenuron-methyl. The rapid P450-mediated tribenuron-methyl metabolism in resistant plants was confirmed by LC-MS/MS analysis. Besides, GST activity was higher among resistant than susceptible individuals. The next transcriptome analysis generated 544,102,236 clean reads from RNA sequencing libraries. De novo assembly yielded 102,529 unigenes with an average length of 866 bp, annotated across seven databases. Digital gene expression selected 25 differentially expressed genes, further validated with qRT-PCR. Three P450 genes, two GST genes, two glucosyltransferase genes, four ABC transporter genes, and four additional contigs were constitutively up-regulated in resistant individuals. Overall, our research confirmed that enhanced herbicide metabolism drives tribenuron-methyl resistance in M. aquaticum.

The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.)

BACKGROUND

Weed management is critical to global crop production and is complicated by rapidly evolving herbicide resistance in weeds. New sources of herbicide resistance are needed for crop plants so that applied herbicides can be rotated or combined to thwart the evolution of resistant weeds. The diverse family of cytochrome P450 proteins has been suggested to be a source of detoxifying herbicide metabolism in both weed and crop plants, and greater understanding of these genes will offer avenues for crop improvement and novel weed management practices.

RESULTS

Here, we report the identification of CYP749A16 (Gh_D10G1401) which is responsible for the natural tolerance exhibited by most cotton, Gossypium hirsutum L., cultivars to the herbicide trifloxysulfuron sodium (TFS, CGA 362622, commercial formulation Envoke). A 1-bp frameshift insertion in the third exon of CYP749A16 results in the loss of tolerance to TFS. The DNA marker designed from this insertion perfectly co-segregated with the phenotype in 2145 F₂ progeny of a cross between the sensitive cultivar Paymaster HS26 and tolerant cultivar Stoneville 474, and in 550 recombinant inbred lines of a multi-parent advanced generation inter-cross population. Marker analysis of 382 additional cotton cultivars identified twelve cultivars containing the 1-bp frameshift insertion. The marker genotypes matched perfectly with phenotypes in 188 plants from the selected twelve cultivars. Virus-induced gene silencing of CYP749A16 generated sensitivity in the tolerant cotton cultivar Stoneville 474.

CONCLUSIONS

CYP749A16 located on chromosome D10 is required for TFS herbicide tolerance in cotton. This finding should add to the repertoire of tools available to farmers and breeders for the advancement of agricultural productivity.

Inheritance of 4-hydroxyphenylpyruvate dioxygenase inhibitor herbicide resistance in an Amaranthus tuberculatus population from Iowa, USA

Waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) is a weed prevalent in the Midwest United States and can cause yield losses up to 74% in maize (Zea mays L.) and 56% in soybean (Glycine max (L.) Merr.). An important adaptive trait commonly found in waterhemp is the ability to evolve herbicide resistance and waterhemp populations have evolved resistance to six herbicide sites of action. In 2011, two waterhemp populations were discovered resistant to p-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicides. We reciprocally crossed a known HPPD-resistant waterhemp population with a known HPPD-susceptible waterhemp population and then intermated the F₁ families to established a pseudo-F₂ generation. We challenged the parent, F₁ and pseudo-F₂ generations against four HPPD-inhibiting herbicide rates (mesotrione). Our results suggest the HPPD-resistance trait is polygenic. Furthermore, the number of genes involved with the herbicide resistance increase at higher herbicide rates. These data indicated at least one dominant allele at each major locus is required to confer HPPD herbicide resistance in waterhemp. Using different waterhemp populations and methodologies, this study confirms the reported "complex" HPPD resistance inheritance while providing new information in the response of HPPD-resistant waterhemp to HPPD herbicides.

Mechanisms of glyphosate resistance and response to alternative herbicide-based management in populations of the three Conyza species introduced in southern Spain

BACKGROUND

In perennial crops, the most common method of weed control is to spray herbicides, and glyphosate has long been the first choice of farmers. Three species of the genus Conyza are among the most problematic weeds for farmers, exhibiting resistance to glyphosate. The objectives of this study were to evaluate resistance levels and mechanisms, and to test chemical control alternatives in putative resistant (R) populations of Conyza bonariensis, Conyza canadensis and Conyza sumatrensis.

RESULTS

Plants from the three R populations of Conyza spp. survived high doses of glyphosate compared with plants from susceptible (S) populations. The rate of movement of 14 C glyphosate out of treated leaves in plants from S populations was higher than in plants from R populations. Only plants from the R population of C. sumatrensis contained the known target site 5-enolpyruvylshikimate-3-phosphate synthase mutation Pro106-Thr. Field responses to the different alternative herbicide treatments tested indicated injury and high effectiveness in most cases.

CONCLUSIONS

The results indicate that non-target site resistant (NTSR) mechanisms explain resistance in C. bonariensis and C. canadensis, whereas both NTSR and target site resistant (TSR) mechanisms contribute to resistance in C. sumatrensis. The results obtained in the field trials suggest that the resistance problem can be solved through integrated weed management. © 2018 Society of Chemical Industry.

Stress-induced evolution of herbicide resistance and related pleiotropic effects

Herbicide-resistant weeds, especially those with resistance to multiple herbicides, represent a growing worldwide threat to agriculture and food security. Natural selection for resistant genotypes may act on standing genetic variation, or on a genetic and physiological background that is fundamentally altered because of stress responses to sublethal herbicide exposure. Stress-induced changes include DNA mutations, epigenetic alterations, transcriptional remodeling, and protein modifications, all of which can lead to herbicide resistance and a wide range of pleiotropic effects. Resistance selected in this manner is termed systemic acquired herbicide resistance, and the associated pleiotropic effects are manifested as a suite of constitutive transcriptional and post-translational changes related to biotic and abiotic stress adaptation, representing the evolutionary signature of selection. This phenotype is being investigated in two multiple herbicide-resistant populations of the hexaploid, self-pollinating weedy monocot Avena fatua that display such changes as well as constitutive reductions in certain heat shock proteins and their transcripts, which are well known as global regulators of diverse stress adaptation pathways. Herbicide-resistant populations of most weedy plant species exhibit pleiotropic effects, and their association with resistance genes presents a fertile area of investigation. This review proposes that more detailed studies of resistant A. fatua and other species through the lens of plant evolution under stress will inform improved resistant weed prevention and management strategies. © 2018 Society of Chemical Industry.

Metabolic Resistance to Acetolactate Synthase Inhibiting Herbicide Tribenuron-Methyl in Descurainia sophia L. Mediated by Cytochrome P450 Enzymes

Descurainia sophia is one of the most notorious broadleaf weeds in China and has evolved extremely high resistance to acetolactate synthase (ALS)-inhibiting herbicide tribenuron-methyl. The target-site resistance due to ALS gene mutations was well-known, while the non-target-site resistance is not yet well-characterized. Metabolic resistance, which is conferred by enhanced rates of herbicide metabolism, is the most important NTSR. To explore the mechanism of metabolic resistance underlying resistant (R) D. sophia plants, tribenuron-methyl uptake and metabolism levels, qPCR reference gene stability, and candidate P450 genes expression patterns were investigated. The results of liquid chromatography-mass spectrometry (LC-MS) analysis indicated that the metabolic rates of tribenuron-methyl in R plants was significantly faster than in susceptible (S) plants, and this metabolism differences can be eliminated by P450 inhibitor malathion. The genes for 18S rRNA and TIP41-like were identified as the most suitable reference genes using programs of BestKeeper, NormFinder, and geNorm. The P450 gene CYP96A146 constitutively overexpressed in R plants compared to S plants; this overexpression in R plants can be suppressed by malathion. Taken together, a higher expression level of P450 genes, leading to higher tribenuron-methyl metabolism, appears to be responsible for metabolic resistance to tribenuron-methyl in R D. sophia plants.

The rise and future of glyphosate and glyphosate-resistant crops

Glyphosate and glyphosate-resistant crops had a revolutionary impact on weed management practices, but the epidemic of glyphosate-resistant (GR) weeds is rapidly decreasing the value of these technologies. In areas that fully adopted glyphosate and GR crops, GR weeds evolved and glyphosate and glyphosate traits now must be combined with other technologies. The chemical company solution is to combine glyphosate with other chemicals, and the seed company solution is to combine glyphosate resistance with other traits. Unfortunately, companies have not discovered a new commercial herbicide mode-of-action for over 30 years and have already developed or are developing traits for all existing herbicide types with high utility. Glyphosate mixtures and glyphosate trait combinations will be the mainstays of weed management for many growers, but are not going to be enough to keep up with the capacity of weeds to evolve resistance. Glufosinate, auxin, HPPD-inhibiting and other herbicide traits, even when combined with glyphosate resistance, are incremental and temporary solutions. Herbicide and seed businesses are not going to be able to support what critics call the chemical and transgenic treadmills for much longer. The long time without the discovery of a new herbicide mode-of-action and the epidemic of resistant weeds is forcing many growers to spend much more to manage weeds and creating a worst of times, best of times predicament for the crop protection and seed industry. © 2016 Society of Chemical Industry.

Glyphosate resistance in Ambrosia trifida: Part 2. Rapid response physiology and non-target-site resistance

BACKGROUND

The glyphosate-resistant rapid response (GR RR) resistance mechanism in Ambrosia trifida is not due to target-site resistance (TSR) mechanisms. This study explores the physiology of the rapid response and the possibility of reduced translocation and vacuolar sequestration as non-target-site resistance (NTSR) mechanisms.

RESULTS

GR RR leaf discs accumulated hydrogen peroxide within minutes of glyphosate exposure, but only in mature leaf tissue. The rapid response required energy either as light or exogenous sucrose. The combination of phenylalanine and tyrosine inhibited the rapid response in a dose-dependent manner. Reduced glyphosate translocation was observed in GR RR, but only when associated with tissue death caused by the rapid response. Nuclear magnetic resonance studies indicated that glyphosate enters the cytoplasm and reaches chloroplasts, and it is not moved into the vacuole of GR RR, GR non-rapid response or glyphosate-susceptible A. trifida.

CONCLUSION

The GR RR mechanism of resistance is not associated with vacuole sequestration of glyphosate, and the observed reduced translocation is likely a consequence of rapid tissue death. Rapid cell death was inhibited by exogenous application of aromatic amino acids phenylalanine and tyrosine. The mechanism by which these amino acids inhibit rapid cell death in the GR RR phenotype remains unknown, and it could involve glyphosate phytotoxicity or other agents generating reactive oxygen species. Implications of these findings are discussed. The GR RR mechanism is distinct from the currently described glyphosate TSR or NTSR mechanisms in other species. © 2017 Society of Chemical Industry.