Point mutations including a novel Pro-197-Phe mutation confer cross-resistance to acetolactate synthase (ALS) inhibiting herbicides in Lactuca serriola in Australia

BACKGROUND

Control of prickly lettuce has become increasingly difficult for lentil growers in southern Australia because of widespread resistance to common herbicides, a lack of alternative herbicide options and the prolific production of highly mobile seed. This study aimed to quantify acetolactate synthase (ALS)-inhibiting herbicide resistance in the Mid North (MN) and Yorke Peninsula (YP) of South Australia, characterize the resistance mutations present and investigate population structure and gene flow in this species.

RESULTS

Resistance was identified in all populations tested, with average survival of 92% to chlorsulfuron and 95% to imazamox + imazapyr. Five different amino acid substitutions were identified at proline 197 of the ALS gene. There was no significant difference in the median lethal dose (LD₅₀) between plants with these five different substitutions when treated with metsulfuron-methyl; however, the imidazolinone resistance level was higher in plants with a phenylalanine substitution and lower in plants with a serine. Population structure based on 701 single nucleotide polymorphisms and 271 individuals provided evidence for both independent evolution of the same mutation in different populations, as well as frequent short- to medium-distance dispersal accompanied by occasional long-distance dispersal events. The overall inbreeding coefficient (F_IS) was calculated at 0.5174, indicating an intermediate level of outcrossing despite the cross-pollination experiment showing only low outcrossing. In the structure analyses, most individuals from YP were assigned to a single cluster, whereas most individuals from MN were assigned 50% to each of two clusters, indicating some genetic differences between these two regions, but also evidence for dispersal between them.

CONCLUSIONS

Use of imidazolinone herbicides has selected for mutations conferring higher levels of resistance, such as the Pro-197-Phe mutation, and resulted in further spread of resistance in this species. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

Efficacy of cultural control methods for combating herbicide-resistant Lolium rigidum

Herbicide-resistant populations of annual ryegrass (Lolium rigidum) are estimated to affect crop production on about 5000 farms in southern Australia. In order to manage resistant populations, some farmers have adopted a two-to-three-year pasture phase which allows use of grazing by sheep, and non-selective herbicides to deplete the weed seed-bank. However, in low-to-medium rainfall zones, where financial returns from pastures are relatively low, farmers have generally combined cultural practices for weed management with the use of alternative herbicides, mainly trifluralin. Used singly, none of the currently available cultural techniques provides an adequate level of weed control. However, when used in carefully planned combinations, extremely effective ryegrass control can be achieved. Some of the important cultural practices for ryegrass control include delayed sowing (sometimes in conjunction with a shallow autumn cultivation); stubble burning; cutting the crop for hay or green manure, increased crop density and capture of weed seeds at harvest. Selection of crop species and cultivars with superior weed suppression potential is also receiving considerable attention. ©1997 SCI     

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.     

Monitoring the temporal changes in herbicide-resistant Amaranthus tuberculatus: a landscape-scale probability-based estimation in Iowa

Background

A landscape-scale probability-based sampling of Iowa soybean [Glycine max (L.) Merr.] fields was conducted in 2013 and 2019; Amaranthus tuberculatus [Moq.] J.D. Sauer seed was collected from 97 random geospatial selected fields. The objectives were to evaluate the prevalence and distribution of herbicide-resistant A. tuberculatus (waterhemp) in soybean fields and evaluate temporal changes over 6 years. Amaranthus tuberculatus seedlings were evaluated for resistance to imazethapyr, atrazine, glyphosate, lactofen and mesotrione at 1× and 4× label rates.

Results

Resistance to imazethapyr, glyphosate, lactofen and mesotrione at the 1× rate increased significantly from 2013 to 2019 and was found in 99%, 97%, 16% and 15% of Iowa A. tuberculatus populations in 2019, respectively. Resistance to atrazine at the 4× rate increased over time; atrazine resistance was found in 68% of populations in 2019. Three-way multiple herbicide-resistant A. tuberculatus was the most frequent and increased significantly to 4× rates from 16% in 2013 to 43% of populations in 2019. All A. tuberculatus populations resistant to HPPD-inhibitor herbicides also were resistant to atrazine.

Conclusion

To the best of our knowledge, this is the first probability-based study that presented evolution of A. tuberculatus herbicide resistance over time. The results demonstrated that imazethapyr, atrazine and glyphosate resistance in Iowa A. tuberculatus populations was frequent whereas resistance to lactofen and mesotrione was less frequent. Most Iowa A. tuberculatus populations evolved resistance to multiple sites of action over time. The results of our study are widely applicable given the similarities in weed management practices throughout the Midwest United States. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

北京市及河北省小麦赤霉病菌群体遗传结构及生物学特性

本文分析了北京市与河北省小麦赤霉病菌群体遗传结构以及基础生物学特性。结果表明所有菌株均为禾谷镰刀菌(Fusarium graminearum),属于一个大的单一群体,群体内具有较高的遗传多样性。毒素化学型测定表明,北京与河北地区小麦真菌毒素污染的主要风险为DON与15ADON毒素。表型测定显示,与F.asiaticum群体相比,F.graminearum具有较高的产孢能力,而生长速率和产毒能力较低。该群体对主要杀菌剂多菌灵、戊唑醇和氰烯菌酯均无抗药性。     

油茶暹罗刺盘孢菌群体遗传结构分析

暹罗刺盘孢菌是油茶炭疽病病原之一,在我国多个油茶产区均有分布。研究油茶暹罗刺盘孢菌群体遗传结构可为全面、有效防治油茶炭疽病害提供理论依据。本研究对分离自海南、江西、湖南、广西4省(自治区)6个地区暹罗刺盘孢菌菌株的ITS、CAL和GAPDH 3个基因的序列进行群体遗传结构分析。根据拼接的上述3个基因的序列,57个暹罗刺盘孢菌菌株可定义为13个单倍型,其中单倍型H7为主要单倍型,分布于本研究所涉及的所有地区。病菌不同地理种群间的遗传分化较大,AMOVA分析显示,遗传变异主要发生在种群内,病菌未经历过大规模的种群扩张。研究结果表明油茶炭疽病原暹罗刺盘孢菌种群具有丰富的遗传多样性。     

Population genetic diversity and structure of the pecan scab pathogen,Venturia effusa,on cv. Desirable and native seedlings,and the impact of marker number

Scab (Venturia effusa) is the major cause of economic loss in pecan in the south-eastern USA. We explored population genetic diversity and structure among orchards of cv. Desirable and native seedlings, and within-orchard variability among trees of all cultivars sampled. We compared the ability of 30, 15 and 7 previously developed microsatellites to characterize the population genetic diversity and structure of V. effusa. Analyses of molecular variance (AMOVA) provided little evidence of structure dependent on cultivar, but there was some evidence of structure between orchards of a cultivar based on distance. Individual orchard AMOVA showed that three of 11 orchards had between-tree population structure. Among six populations from cv. Desirable, a Mantel test showed that geographic distance was related to the pairwise genetic divergence (R² = 0.84). Among 11 orchards of various cultivars there was little difference in diversity using 30, 15 or 7 markers, or population structure based on AMOVA. Some minor differences in population structure were seen based on discriminant analysis of principal components, or dendrograms. Thus, depending on the objectives, future studies may use as few as 15 or 7 markers without losing ability to discern population genetic diversity or structure. More populations exhibited linkage disequilibrium when using 15 or 30 markers compared to when using seven markers. Knowledge of population genetics of V. effusa in relation to host genotype is needed to understand pathogen population interactions and gene flow, knowledge that will help underpin future breeding efforts to develop durable resistance in this long-lived orchard tree.     

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.     

Genetic diversity of herbicide-resistant and -susceptible Avena fatua populations in North Dakota and Minnesota

Genetic diversity within and among 20 herbicide-resistant (HR) and 16 herbicide-susceptible (HS) Avena fatua multi-field populations was determined using 82 polymorphic loci resulting from two intersimple sequence repeat (ISSR) primers and one long-primer random amplified polymorphic DNA (LP-RAPD) primer. Collections from the Red River Valley of North Dakota and Minnesota, sampled in 1964 and 2000, represented A. fatua populations before and after intensive exposure to herbicides. A 1995 collection from south-west North Dakota represented A. fatua exposed to low herbicide selection. Despite differences in years of herbicide exposure among collections, both HR and HS populations from every collection maintained nearly similar levels of ISSR and RAPD diversity. Genetic differentiation among populations (G_ST) varied from 11% to 13% among HR populations and from 9% to 16% among HS populations, indicating that 84–91% of total variation remained within HS or within HR populations. Minimal difference in gene diversity between HR and HS is consistent with multiple origins of resistance, where HR A. fatua most likely evolved from diverse founding individuals.     

Germination,emergence, and persistence of Sonchus oleraceus,a major crop weed in subtropical Australia

Sonchus oleraceus (common sowthistle) is a dominant weed and has increased in prevalence in conservation cropping systems of the subtropical grain region of Australia. Four experiments were undertaken to define the environmental factors that favor its germination, emergence, and seed persistence. Seeds were germinated at constant temperatures between 5 and 35°C and water potentials between 0 and ?1.4 MPa. The maximum germination rate of 86–100% occurred at 0 and ?0.2 MPa, irrespective of the temperature when exposed to light (12 h photoperiod light/dark), but the germination rate was reduced by 72% without light. At water potentials of ?0.6 to ?0.8 MPa, the germination rate was reduced substantially by higher temperatures; no seed germinated at a water potential >?1.0 MPa. Emergence and seed persistence were measured over 30 months following seed burial at 0 (surface), 1, 2, 5, and 10 cm depths in large pots that were buried in a south‐eastern Queensland field. Seedlings emerged readily from the surface and 1 cm depth, with no emergence from below the 2 cm depth. The seedlings emerged during any season following rain but, predominantly, within 6 months of planting. Seed persistence was short‐term on the soil surface, with 2% of seeds remaining after 6 months, but it increased with the burial depth, with 12% remaining after 30 months at 10 cm. Thus, a minimal seed burial depth with reduced tillage and increased surface soil water with stubble retention has favored the proliferation of this weed in any season in a subtropical environment. However, diligent management without seed replenishment will greatly reduce this weed problem within a short period.     

海南橡胶树暹罗刺盘孢菌群体遗传结构分析

暹罗刺盘孢菌Colletotrichum siamense是引起海南橡胶树炭疽病的重要病原之一,为了明确海南橡胶树暹罗刺盘孢菌群体的遗传结构,本研究对海南5个市(县)的橡胶树暹罗刺盘孢菌的ITS序列进行分析。结果表明,58个病菌样品可推导出11种单倍型,其中单倍型H11包含样品数最多且在5个市(县)均有分布,其次为单倍型H4,在4个市(县)有分布。遗传分化指数(Fst)表明保亭种群与其他种群的遗传分化较大。AMOVA分析显示,遗传变异主要发生在种群内,占总变异的93.9%。对所有地理种群病原菌ITS序列的核苷酸不配对进行分析,表明病菌未经历过大规模的种群扩张。系统发育分析表明,来自相同地区的病菌单倍型并没有聚在一起。研究结果表明海南橡胶树暹罗刺盘孢菌种群具有丰富的遗传多样性。     

Genetic variation and population structure of Fusarium oxysporum f.sp. vasinfectum in Australia

Genetic variation among 348 isolates of Fusarium oxysporum f.sp. vasinfectum (Fov) collected from diseased cotton plants in 31 fields in six cotton-growing regions in New South Wales and Queensland in 2002 and 2004 was analysed using amplified fragment length polymorphisms (AFLPs). Twenty-eight haplotypes were identified based on 146 polymorphic bands generated with four Eco RI and Mse I and four Hind III and Mse I primer combinations. The haplotypes separated into two distinct groups (37% similarity), with 21 in group I and seven in group II. The two unique vegetative compatibility groups of Fov known to occur in Australia (VCG 01111 and VCG 01112) were correlated to the two AFLP groups, with both VCG 01111 reference isolates being included in group I and both VCG 01112 reference isolates in group II. Group I was widespread, occurring in all regions sampled and all but one of the fields, while group II was limited to three fields in the Boggabilla region. Group I was further divided into two subgroups. The two haplotypes in subgroup I-B (I-20 and I-21) may represent the emergence of a new form of Fov based on their marked genetic discrimination from the subgroup I-A haplotypes. No spatial population differentiation was discernible at the national level, as only 3·9% of total genetic variation was attributed to differences among regions ( P =  0·4868). When each region was analysed separately, clear differentiation was found in the Boggabilla region, with 86·3% of total genetic variation resulting from differences among fields ( P <  0·0001).     

海南橡胶树白粉菌的群体遗传结构研究

白粉病是海南橡胶树上发生最严重的叶部病害,为了明确海南橡胶树白粉菌群体的遗传结构,本研究对海南7个市(县)的橡胶树白粉菌的ITS序列进行分析。结果表明,95个病菌样品可推导出5种单倍型,其中单倍型H1包含样品数为88个,且在7个市(县)均有分布;三亚种群的单倍型多样性和核苷酸多样性最高。总体和各地理群体的中性检验结果显示,群体扩张遵循中性进化,群体大小保持相对稳定。遗传分化指数(Fst)表明三亚种群与白沙、儋州、海口和琼中等四市(县)种群的遗传分化较大。AMOVA分析显示,遗传变异主要发生在种群内,占总变异的89.66%。因此海南橡胶树白粉菌菌株间虽存在一定的遗传分化,但整体遗传多样性偏低。     

Modelling binary mixtures of herbicides in populations resistant to one of the components: evaluation for resistance management

BACKGROUND: Herbicide mixtures are commonly proposed to delay the selection of herbicide resistance in susceptible populations (called the SM strategy). However, in practice, herbicide mixtures are often used when resistance to one of the two active ingredients has already been detected in the targeted population (called the RM strategy). It is doubtful whether such a practice can select against resistance, as the corresponding selection pressure is still exerted. As a consequence, the effect of mixtures on the evolution of an already detected resistance to one of the herbicides in the combination remains largely unexplored. In the present work, a simple model was developed to explore further the necessary and sufficient conditions under which a binary RM strategy might stabilise or even reduce resistance frequency. RESULTS: Covering the hypothetical largest range of parameters, 39% of 9000 random simulations attest that the RM strategy might theoretically reduce resistance frequency. When strong enough, high genetic cost of resistance, negative cross‐resistance between the herbicides associated in the mixture and reduced selection differential between resistant and susceptible plants can counterbalance the resistance advantage to one of the two applied herbicides. However, the required conditions for an RM strategy to ensure resistance containment in natural conditions seldom overlap with experimental parameter estimates given in the literature. CONCLUSION: It is concluded that the sufficient conditions for an RM strategy to be effective would rarely be encountered. As a consequence, the strategy of formulating mixtures with herbicides for which resistance has already been detected should be avoided. Copyright © 2008 Society of Chemical Industry     

Population structure and possible origin of Amylostereum areolatum in South Africa

The woodwasp, Sirex noctilio , and its symbiotic fungus, Amylostereum areolatum , cause extensive damage to pine plantations in the Southern Hemisphere. S. noctilio was first reported from South Africa in 1994. In this study, the population diversity of A. areolatum isolates from South Africa, South America, Australasia and Europe was determined by vegetative incompatibility testing. All 108 South African and 26 South American isolates belonged to the same vegetative compatibility group (VCG). This VCG showed a weak incompatibility reaction with the single Tasmanian and single New Zealand isolates tested. This VCG differed from VCGs from Europe. It also differed from isolates associated with the biocontrol nematode, Deladenus siricidicola , which is produced in Australia. It is concluded that the South African and South American populations of A. areolatum share a common origin .     

The impact of altered herbicide residues in transgenic herbicide-resistant crops on standard setting for herbicide residues

The global area covered with transgenic (genetically modified) crops has rapidly increased since their introduction in the mid-1990s. Most of these crops have been rendered herbicide resistant, for which it can be envisaged that the modification has an impact on the profile and level of herbicide residues within these crops. In this article, the four main categories of herbicide resistance, including resistance to acetolactate-synthase inhibitors, bromoxynil, glufosinate and glyphosate, are reviewed. The topics considered are the molecular mechanism underlying the herbicide resistance, the nature and levels of the residues formed and their impact on the residue definition and maximum residue limits (MRLs) defined by the Codex Alimentarius Commission and national authorities. No general conclusions can be drawn concerning the nature and level of residues, which has to be done on a case-by-case basis. International residue definitions and MRLs are still lacking for some herbicide-crop combinations, and harmonisation is therefore recommended.     

Microsatellite variability of sulfonylurea‐resistant and susceptible populations of Schoenoplectus juncoides (Cyperaceae) in Kinki,Japan

Schoenoplectus juncoides is one of the most harmful weeds found in East Asian paddy fields. Recent emergence of biotypes that are resistant to the herbicide sulfonylurea (SU) has made weed control difficult. To examine the effect of the evolution of this herbicide resistance on genetic diversity within local populations, we investigated microsatellite variability within and among paddy field populations of S. juncoides in Kinki, Japan. In vivo assay of acetolactate synthase activity and root elongation assay in the presence of SU revealed that of 21 populations, five were sulfonylurea‐susceptible (SU‐S) and eight were completely sulfonylurea‐resistant (SU‐R). The remaining eight populations were a mixture of SU‐S and SU‐R individuals. The average gene diversity for SU‐R populations (H_S = 0.168) was lower than those for SU‐S (H_S = 0.256) and mixed (H_S = 0.209) populations, but the difference was not significant. This indicates that positive selection for SU‐R phenotype did not cause a genome‐wide reduction in genetic diversity. Genetic differentiation among S. juncoides populations was higher than that observed for most weed species studied previously. Although populations in neighbouring paddy fields showed a high level of differentiation, Bayesian clustering analyses suggested that some level of gene flow occurs among them and that the genetic exchange or colonisation between neighbouring populations could contribute to the geographical expansion of the resistant allele.