Evolving understanding of the evolution of herbicide resistance

A greater number of, and more varied, modes of resistance have evolved in weeds than in other pests because the usage of herbicides is far more extensive than the usage of other pesticides, and because weed seed output is so great. The discovery and development of selective herbicides are more problematic than those of insecticides and fungicides, as these must only differentiate between plant and insect or pathogen. Herbicides are typically selective between plants, meaning that before deployment there are already some crops possessing natural herbicide resistance that weeds could evolve. The concepts of the evolution of resistance and the mechanisms of delaying resistance have evolved as nature has continually evolved new types of resistance. Major gene target‐site mutations were the first types to evolve, with initial consideration devoted mainly to them, but slowly ‘creeping’ resistance, gradually accruing increasing levels of resistance, has become a major force owing to an incremental accumulation of genetic changes in weed populations. Weeds have evolved mechanisms unknown even in antibiotic as well as other drug and pesticide resistances. It is even possible that cases of epigenetic ‘remembered’ resistances may have appeared. Copyright © 2009 Society of Chemical Industry     

The sodium channel gene in Tetranychus cinnabarinus (Boisduval): identification and expression analysis of a mutation associated with pyrethroid resistance

BACKGROUND: The carmine spider mite (CSM), Tetranychus cinnabarinus, is the most harmful mite pest of various crops and vegetable plants. Pyrethroid insecticide fenpropathrin has been used to control insects and mites worldwide, but CSM has developed resistance to this compound. RESULTS: Three synergists together eliminated about 50% resistance against fenpropathrin in the CSM. A point mutation was identified from the sodium channel gene of fenpropathrin‐resistant CSM (FeR) by comparing cDNA sequences between FeR and susceptible (S) sodium channel genes, which caused a phenylalanine (F) to isoleucine (I) change at amino acid 1538 position in IIIS6 of the sodium channel and has been proven to confer strong resistance to pyrethroid in other species. The mRNA expression of the sodium channel gene in the FeR and abamectin‐resistant strain (AbR), which was included as a control, were both relatively lower than in the S. CONCLUSION: These results demonstrate that a mutation (F1538I) is present in the sodium channel gene in FeR of CSM, likely playing an important role in fenpropathrin resistance in T. cinnabarinus, but that decrease in the abundance of sodium channel did not confer this resistance. The F1538I mutation could be used as a molecular marker for detecting kdr resistance in Arachnida populations. Copyright © 2011 Society of Chemical Industry     

Mechanism of resistance to carpropamid in Magnaporthe grisea

The inhibitory activity of carpropamid on scytalone dehydratase (SDH) extracted from a carpropamid-resistant strain of Magnaporthe grisea (Hebert) Barr was dramatically reduced in comparison with that on SDH extracted from the sensitive strain. A single-point mutation (G to A) located at the upstream region (233 bp downstream from the ATG codon) resulting in a one-amino-acid substitution (valine [GTG] 75 to methionine [ATG]: V75M) was found in the resistant strain. To examine whether the V75M mutation is the primary reason for decreasing the sensitivity of SDH to carpropamid, the SDH cDNAs of both the sensitive and the resistant strain were cloned into a GST-fused protein expression vector-system. The recombinant SDHs of both strains exhibited the same sensitivities to carpropamid as those extracted from the mycelia of the respective strains. These data clearly revealed that the V75M mutation causes the low sensitivities of the SDHs of the carpropamid-resistant strains, and strongly suggests that the V75M mutation confers resistance of these strains to carpropamid.     

Isolation and expression of genes for acetolactate synthase and acetyl-CoA carboxylase in Echinochloa phyllopogon, a polyploid weed species

BACKGROUND: Target‐site resistance is the major cause of herbicide resistance to acetolactate synthase (ALS)‐ and acetyl‐CoA carboxylase (ACCase)‐inhibiting herbicides in arable weeds, whereas non‐target‐site resistance is rarely reported. In the Echinochloa phyllopogon biotypes resistant to these herbicides, target‐site resistance has not been reported, and non‐target‐site resistance is assumed to be the basis for resistance. To explore why target‐site resistance had not occurred, the target‐site genes for these herbicides were isolated from E. phyllopogon, and their expression levels in a resistant biotype were determined. RESULTS: Two complete ALS genes and the carboxyltransferase domain of four ACCase genes were isolated. The expression levels of ALS and ACCase genes were higher in organs containing metabolically active meristems, except for ACC4, which was not expressed in any organ. The differential expression among examined organs was more prominent for ALS2 and ACC2 and less evident for ALS1, ACC1 and ACC3. CONCLUSION: E. phyllopogon has multiple copies of the ALS and ACCase genes, and different expression patterns were observed among the copies. The existence of three active ACCase genes and the difference in their relative expression levels could influence the occurrence of target‐site resistance to ACCase inhibitors in E. phyllopogon. Copyright © 2012 Society of Chemical Industry     

Distribution of herbicide‐resistant acetyl‐coenzyme A carboxylase alleles in Lolium rigidum across grain cropping areas of South Australia

Resistance to the acetyl‐coenzyme A carboxylase (ACCase)‐inhibiting herbicides in Lolium rigidum is widespread in grain cropping areas of South Australia. To better understand the occurrence and spread of resistance to these herbicides and how it has changed with time, the carboxyl transferase (CT) domain of the ACCase gene from resistant L. rigidum plants, collected from both random surveys of the mid‐north of Southern Australia over 10 years as well as stratified surveys in individual fields, was sequenced and target site mutations characterised. Amino acid substitutions occurring as a consequence of these target site mutations, at seven positions in the ACCase gene previously correlated with herbicide resistance, were identified in c. 80% of resistant individuals, indicating target site mutation is a common mechanism of resistance in L. rigidum to this herbicide mode of action. Individuals containing multiple amino acid substitutions (two, and in two cases, three substitutions) were also found. Substitutions at position 2041 occurred at the highest frequency in all years of the large area survey, while substitutions at position 2078 were most common in the single farm analysis. This study has shown that target site mutations leading to amino acid substitutions in ACCase of L. rigidum are widespread across South Australia and that these mutations have likely evolved independently in different locations. The results indicate that seed movement, both within and between fields, may contribute to the spread of resistance in a single field. However, over a large area, the independent appearance and selection of target site mutations conferring resistance through herbicide use is the most important factor.     

Molecular characterisation of resistance to ALS-inhibiting herbicides in Hordeum leporinum biotypes

BACKGROUND: The acetolactate synthase (ALS)-inhibiting herbicide sulfosulfuron is registered in Australia for the selective control of Hordeum leporinum Link. in wheat crops. This herbicide failed to control H. leporinum on two farms in Western Australia on its first use. This study aimed to determine the level of resistance of three H. leporinum biotypes, identify the biochemical and molecular basis and develop molecular markers for diagnostic analysis of the resistance. RESULTS: Dose-response studies revealed very high level (>340-fold) resistance to the sulfonylurea herbicides sulfosulfuron and sulfometuron. In vitro ALS assays revealed that resistance was due to reduced sensitivity of the ALS enzyme to herbicide inhibition. This altered ALS sensitivity in the resistant biotypes was found to be due to a mutation in the ALS gene resulting in amino acid proline to serine substitution at position 197. In addition, two- to threefold higher ALS activities were consistently found in the resistant biotypes, compared with the known susceptible biotype. Two cleaved amplified polymorphic sequence (CAPS) markers were developed for diagnostic testing of the resistant populations. CONCLUSION: This study established the first documented case of evolved ALS inhibitor resistance in H. leporinum and revealed that the molecular basis of resistance is due to a Pro to Ser mutation in the ALS gene.     

A SNaPshot assay for the rapid and simple detection of known point mutations conferring resistance to ACCase‐inhibiting herbicides in Lolium spp.

Evolution of resistance to herbicides in weeds is becoming an increasing problem worldwide. To develop effective strategies for weed control, a thorough knowledge of the basis of resistance is required. Although non‐target‐site‐based resistance is widespread, target site resistance, often caused by a single nucleotide change in the gene encoding the target enzyme, is also a common factor affecting the efficacies of key herbicides. Therefore, fast and relatively simple high‐throughput screening methods to detect target site resistance mutations will represent important tools for monitoring the distribution and evolution of resistant alleles within weed populations. Here, we present a simple and quick method that can be used to simultaneously screen for up to 10 mutations from several target site resistance‐associated codons in a single reaction. As a proof of concept, this SNaPshot multiplex method was successfully applied to the genotyping of nine variable nucleotide positions in the CT domain of the chloroplastic ACCase gene from Lolium multiflorum plants from 54 populations. A total of 10 nucleotide substitutions at seven of these nine positions (namely codons 1781, 1999, 2027, 2041 2078, 2088 and 2096) are known to confer resistance to ACCase‐inhibiting herbicides. This assay has several advantages when compared with other methods currently in use in weed science. It can discriminate between different nucleotide changes at a single locus, as well as screening for SNPs from different target sites by pooling multiple PCR products within a single reaction. The method is scalable, allowing reactions to be carried out in either 96‐ or 384‐well plate formats, thus reducing work time and cost.     

The choice of target site is crucial in artificial miRNA-mediated virus resistance in transgenic Nicotiana tabacum

MicroRNAs (miRNAs) are negative regulators of gene expression via mRNA degradation or translational repression. The potential of artificial miRNAs (amiRNAs) as antiviral agents has been used in plant biotechnology. In this study, we designed eight amiRNAs derived from Potato Virus Y (PVY) Coat Protein RNA sequences and generated transgenic tobacco plants to express these amiRNAs to confer virus resistance against PVY. Together with transient assays, the hairpin amiRcp precursors that mimic natural miRNA precursor molecules proved to be effective in expressing amiRcps and silencing the target gene. Virus resistance assay revealed that not all amiRcps targeting viral CP sequence are equally effective in preventing PVY infection. Plants with amiRcp-8 targeting the 3′ end (nt735–nt754) region exhibited high virus resistance up to 64.69%. The amiRcp-6 harboring RNA sequence (nt567–nt586) induced the lowest percentages with only 17.05%. Besides, northern blots showed that there was a correlation between the resistance level and the accumulation of amiRNA expression. Furthermore, we used bioinformatics approach to predict the mRNA structure and found that targeting sequences of loose structure benefit to improve the virus resistance level. Our results indicate that the selection of appropriate target sequence is crucial for transgenic plant against virus and provide useful guideline for the design of pathogen-derived amiRNAs.     

First glyphosate‐resistant Lolium spp. biotypes found in a European annual arable cropping system also affected by ACCase and ALS resistance

In Europe, glyphosate‐resistant weeds have so far only been reported in perennial crops. Following farmers' complaints of poor herbicide efficacy, resistance to glyphosate as well as to ACCase and ALS inhibitors was investigated in 11 populations of Lolium spp. collected from annual arable cropping systems in central Italy. Field histories highlighted that farmers had relied heavily on glyphosate, often at low rates, as well as in a non‐registered crop. The research aimed at elucidating the resistance status, including multiple resistance, of Lolium spp. populations through glasshouse screenings and an outdoor dose–response experiment. Target‐site resistance mechanism was also investigated for the substitutions already reported for EPSPs, ALS and ACCase genes. Three different resistant patterns were identified: glyphosate resistant only, multiple resistant to glyphosate and ACCase inhibitors and multiple resistant to glyphosate and ALS inhibitors. Amino acid substitutions were found at position 106 of the EPSPs gene, at position 1781, 2088 and 2096 of the ACCase gene and at position 197 and 574 of the ALS gene. Not all populations displayed amino acid substitutions, suggesting the presence of non‐target‐site‐mediated resistance mechanisms. After 39 years of commercial availability of glyphosate, this is the first report of multiple resistance involving glyphosate selected in annual arable crops in Europe. Management implications and options are discussed.     

Biochemical mechanisms of cross-resistance to aryloxyphenoxypropionate and cyclohexanedione herbicides in populations of Avena spp.

Aryloxyphenoxypropionate (APP) and cyclohexanedione (CHD) herbicides are used extensively in the UK to control grass weeds, including Avena spp. (wild-oats). Reports of resistance to APP and CHD herbicides are a particular concern for the agricultural community. In this study, the responses of four UK Avena populations were characterized towards the APP herbicides fenoxaprop-P-ethyl and fluazifop-P-butyl, and towards the CHD herbicides cycloxydim and tralkoxydim. An A. sterilis ssp. ludoviciana population (T/41) was found to be highly resistant to fenoxaprop-P-ethyl and fluazifop-P-butyl, but did not show cross-resistance to cycloxydim and tralkoxydim. In contrast, one A. sterilis ssp. ludoviciana (T/11) and one A. fatua population (Dorset) showed partial resistance to both APP herbicides and also showed cross-resistance to the CHD herbicide tralkoxydim, but not to cycloxydim. Before this study, the biochemical mechanisms that confer resistance to the APP and CHD herbicides in UK Avena populations were unknown. Results from the present study show that an enhanced rate of metabolism of fenoxaprop-P-ethyl was found to confer resistance in the two partially resistant Avena populations (T/11 and Dorset), and the presence of an insensitive form of the target enzyme, ACCase, was responsible for target site resistance to fenoxaprop-P-ethyl and fluazifop-P-butyl in the highly resistant population T/41. Cross-resistance to the CHD herbicide tralkoxydim in the T/11 and Dorset populations was not conferred by insensitive ACCase, and was most probably caused by enhanced metabolism. This is the first report that resistance to fenoxaprop-P-ethyl can be conferred by enhanced metabolism in Avena spp.