Evolutionary-thinking in agricultural weed management

Does weed diversity mitigate yield losses?

While intensive control of weed populations plays a central role in current agriculture, numerous studies highlight the multifaceted contribution of weeds to the functionality and resilience of agroecosystems. Recent research indicates that increased evenness within weed communities may mitigate yield losses in contrast to communities characterized by lower diversity, since weed species that strongly affect crop yields, also dominate weed communities, with a concurrent reduction of evenness. If confirmed, this observation would suggest a paradigm shift in weed management towards promoting higher community diversity. To validate whether the evenness of weed communities is indeed linked to higher crop productivity, we conducted two field experiments: one analyzing the effects of a natural weed community in an intercrop of faba bean and oat, and the other analyzing the effects of artificially created weed communities, together with the individual sown weed species, in faba bean, oats and an intercrop of both crops. The evenness of the weed communities ranged from 0.2 to 0.9 in the natural weed community, from 0.2 to 0.7 in faba bean, from 0 to 0.8 in the intercrop and from 0.3 to 0.9 in oats. Neither the natural nor the artificial weed community showed significant effects of evenness on crop grain yield or crop biomass. The results of this study do not validate a positive relationship of crop productivity and weed evenness, possibly due to low weed pressure and the absence of competitive effects but suggest that also less diverse weed communities may be maintained without suffering yield losses. This is expected to have far reaching implications, since not only diverse weed communities, but also higher abundances of few weed species may contribute to ecosystem functions and may support faunal diversity associated with weeds.

Current status of community resources and priorities for weed genomics research

Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.

A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.)

BACKGROUND

Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved.

RESULTS

A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments.

CONCLUSION

Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.

Changes in the herbicide sensitivity and competitive ability of Abutilon theophrasti over 28 years: Implications for hormesis and weed evolution

BACKGROUND

The potential of weed species to respond to selection forces affecting the evolution of weedy traits such as competitive ability is poorly understood. This research characterized evolutionary growth changes in a single Abutilon theophrasti Medik. population comparing multiple generations collected from 1988 to 2016. A competition study was performed to understand changes in competitive ability, and a herbicide dose-response study was carried out to assess changes in sensitivity to acetolactate synthase-inhibiting herbicides and glyphosate over time.

RESULTS

When grown in monoculture, A. theophrasti biomass production per plant increased steadily across year-lines while leaf number decreased. In replacement experiments, A. theophrasti plants from newer year-lines were more competitive and produced more biomass and leaf area than the oldest year-line. No clear differences in sensitivity to imazamox were observed among year-lines. However, starting in 1995, this A. theophrasti population exhibited a progressive increase in growth in response to a sublethal dose of glyphosate (52 g a.e. ha-1 ), with the 2009 and 2016 year-lines having more than 50% higher biomass than the nontreated control.

CONCLUSION

This study demonstrates that weeds can rapidly evolve increased competitive ability. Furthermore, the results indicate the possibility of changes in glyphosate hormesis over time. These results highlight the importance of the role that rapid (i.e., subdecadal) evolution of growth traits might have on the sustainability of weed management strategies. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Assessment of ACC and P450 Genes Expression in Wild Oat (Avena ludoviciana) in Different Tissues Under Herbicide Application

Target-site resistance (TSR) and non-target-site resistance (NTSR) to herbicides in arable weeds are increasing rapidly all over the world and threatening universal food safety. Resistance to herbicides that inhibit ACCase activity has been identified in wild oat. In this study, expression of ACC1, ACC2, CYP71R4 and CYP81B1 genes under herbicide stress conditions were studied in two TSR (resistant in the residue Ile1781-Leu and Ile2041-Asn of ACCase) biotypes, two NTSR biotypes and one susceptible biotype of A. ludoviciana for the first time. Treated and untreated biotypes with ACCase-inhibitor clodinafop propargyl herbicide were sampled from the stem and leaf tissues at 24 h after treatment. Our results showed an increase in gene expression levels in different tissues of both types of resistance biotypes that occurred under herbicide treatment compared with non-herbicide treatment. In all samples, the expression levels of leaf tissue in all studied genes were higher than in stem tissue. The results of ACC gene expression showed that the expression level of ACC1 was significantly higher than that of ACC2. Also, expression levels of TSR biotypes were higher than NTSR biotypes for the ACC1 gene. For both CYP71R4 and CYP81B1 genes, the expression ratio increased significantly in TSR and NTSR biotypes in different tissues after herbicide treatment. In contrast, the expression levels of CYP genes in NTSR biotypes were higher than in TSR biotypes. Our results support the hypothesis that the reaction of plants to herbicide is carried out through a different regulation of genes, which can be the result of the interaction of resistance type in the target or non-target-site.

Early growth, development and allometry of glyphosate-resistant and susceptible Amaranthus palmeri in response to current and elevated temperature and CO2

This study aimed to evaluate the influence of CO2 and temperature on glyphosate-resistant and susceptible biotypes of Amaranthus palmeri (Palmer amaranth) in terms of morphological development. Height (cm), stem diameter (cm), leaf area (cm2), number of leaves, leaf, stem, and root dry matter, plant volume (m3), as well as shoot-to-root allometry were evaluated. The Palmer amaranth biotypes were grown under four different scenarios: 1-low temperature (23/33 °C) and CO2 (410 ± 25 ppm); 2-low temperature (23/33 °C) and high CO2 (750 ± 25 ppm); 3-high temperature (26/36 °C) and low CO2 (410 ± 25 ppm); and 4-high temperature (26/36 °C) and CO2 (750 ± 25 ppm). Between CO2 and temperature, the majority of differences observed were driven by CO2 levels. Palmer amaranth grown under 750 ppm of CO2 was 15.5% taller, displayed 10% more leaf area (cm2), 18% more stem dry matter, and had a 28.4% increase in volume (m3) compared to 410 ppm of CO2. GA2017 and GA2020 were 18% and 15.5% shorter, respectively. The number of leaves was 27% greater for GA2005. Plant volume decreased in GA2017 (35.6%) and GA2020 (23.8%). The shoot-to-root ratio was isomeric, except at 14 and 21 DAT, where an allometric growth towards shoot development was significant. Palmer amaranth biotypes responded differently to elevated CO2, and the impacts of temperature need further investigation on weed physiology. Thus, environmental and genetic background may affect the response of glyphosate-resistant and susceptible populations to climate change scenarios.

Research Progress of Benzothiazole and Benzoxazole Derivatives in the Discovery of Agricultural Chemicals

Benzoxazole and benzothiazole have a broad spectrum of agricultural biological activities, such as antibacterial, antiviral, and herbicidal activities, which are important fused heterocyclic scaffold structures in agrochemical discovery. In recent years, great progress has been made in the research of benzoxazoles and benzothiazoles, especially in the development of herbicides and insecticides. With the widespread use of benzoxazoles and benzothiazoles, there may be more new products containing benzoxazoles and benzothiazoles in the future. We systematically reviewed the application of benzoxazoles and benzothiazoles in discovering new agrochemicals in the past two decades and summarized the antibacterial, fungicidal, antiviral, herbicidal, and insecticidal activities of the active compounds. We also discussed the structural-activity relationship and mechanism of the active compounds. This work aims to provide inspiration and ideas for the discovery of new agrochemicals based on benzoxazole and benzothiazole.

Convergent Adaptation of Multiple Herbicide Resistance to Auxin Mimics and ALS- and EPSPS-Inhibitors in Brassica rapa from North and South America

Herbicide-resistant weeds have been identified and recorded on every continent where croplands are available. Despite the diversity of weed communities, it is of interest how selection has led to the same consequences in distant regions. Brassica rapa is a widespread naturalized weed that is found throughout temperate North and South America, and it is a frequent weed among winter cereal crops in Argentina and in Mexico. Broadleaf weed control is based on glyphosate that is used prior to sowing and sulfonylureas or mimic auxin herbicides that are used once the weeds have already emerged. This study was aimed at determining whether a convergent phenotypic adaptation to multiple herbicides had occurred in B. rapa populations from Mexico and Argentina by comparing the herbicide sensitivity to inhibitors of the acetolactate synthase (ALS), 5-enolpyruvylshikimate-3-phosphate (EPSPS), and auxin mimics. Five B. rapa populations were analyzed from seeds collected in wheat fields in Argentina (Ar1 and Ar2) and barley fields in Mexico (Mx1, Mx2 and MxS). Mx1, Mx2, and Ar1 populations presented multiple resistance to ALS- and EPSPS-inhibitors and to auxin mimics (2,4-D, MCPA, and fluroxypyr), while the Ar2 population showed resistance only to ALS-inhibitors and glyphosate. Resistance factors ranged from 947 to 4069 for tribenuron-methyl, from 1.5 to 9.4 for 2,4-D, and from 2.7 to 42 for glyphosate. These were consistent with ALS activity, ethylene production, and shikimate accumulation analyses in response to tribenuron-methyl, 2,4-D, and glyphosate, respectively. These results fully support the evolution of the multiple- and cross-herbicide resistance to glyphosate, ALS-inhibitors, and auxinic herbicides in B. rapa populations from Mexico and Argentina.

Distinct hormonal and morphological control of dormancy and germination in Chenopodium album dimorphic seeds

Dormancy and heteromorphism are innate seed properties that control germination timing through adaptation to the prevailing environment. The degree of variation in dormancy depth within a seed population differs considerably depending on the genotype and maternal environment. Dormancy is therefore a key trait of annual weeds to time seedling emergence across seasons. Seed heteromorphism, the production of distinct seed morphs (in color, mass or other morphological characteristics) on the same individual plant, is considered to be a bet-hedging strategy in unpredictable environments. Heteromorphic species evolved independently in several plant families and the distinct seed morphs provide an additional degree of variation. Here we conducted a comparative morphological and molecular analysis of the dimorphic seeds (black and brown) of the Amaranthaceae weed Chenopodium album. Freshly harvested black and brown seeds differed in their dormancy and germination responses to ambient temperature. The black seed morph of seedlot #1 was dormant and 2/3^rd of the seed population had non-deep physiological dormancy which was released by after-ripening (AR) or gibberellin (GA) treatment. The deeper dormancy of the remaining 1/3^rd non-germinating seeds required in addition ethylene and nitrate for its release. The black seeds of seedlot #2 and the brown seed morphs of both seedlots were non-dormant with 2/3^rd of the seeds germinating in the fresh mature state. The dimorphic seeds and seedlots differed in testa (outer seed coat) thickness in that thick testas of black seeds of seedlot #1 conferred coat-imposed dormancy. The dimorphic seeds and seedlots differed in their abscisic acid (ABA) and GA contents in the dry state and during imbibition in that GA biosynthesis was highest in brown seeds and ABA degradation was faster in seedlot #2. Chenopodium genes for GA and ABA metabolism were identified and their distinct transcript expression patterns were quantified in dry and imbibed C. album seeds. Phylogenetic analyses of the Amaranthaceae sequences revealed a high proportion of expanded gene families within the Chenopodium genus. The identified hormonal, molecular and morphological mechanisms and dormancy variation of the dimorphic seeds of C. album and other Amaranthaceae are compared and discussed as adaptations to variable and stressful environments.

Glyphosate affects the susceptibility of non-target native plant species according to their stage of development and degree of exposure in the landscape

Unsustainable agriculture is producing a great socio-ecological transformation in Latin America because it has expanded into areas occupied by native forests. Glyphosate is the most widely used herbicide, with severe ecotoxicological effects on non-target organisms. The aim of this study was to determine the effects of glyphosate on seedlings of 24 non-target herbaceous and non-herbaceous plant species present in forest relicts of Argentine Chaco. The effects of a gradient of glyphosate doses (525, 1050, 2100, 4200, and 8400 g ai/ha) were measured in seedlings of each species under greenhouse conditions. Seedlings were grown from seeds collected from native forest fragments of different sizes (assuming three different degrees of historical exposure to glyphosate in the landscape). Doses were applied at different stages of seedling development (five- and ten-weeks after emergence), and phytotoxicity, growth reduction, and sensitivity were measured. Glyphosate produced lethal or sublethal effects in all 24 species, some of which were very sensitive (>60 % of the species presented strong to severe growth reduction with ¼ of the dose used on crops). The greatest toxicological effects were related to early stage of development, herbaceous species, and low historical exposure to glyphosate. According to the species sensitivity distribution, the drift-dose to protect 95 % of the plant species that occur in larger forest fragments should not exceed 5 % of the dose commonly used on crops. These results suggest that the current weed management linked to glyphosate-resistant crops could lead to a gradual loss of biodiversity in the landscape. Concurrently, selection of glyphosate-tolerant biotypes in some non-target species could represent a very problematic cycle for the current model of industrial agriculture. Some alternatives for weed control are proposed.

Penoxsulam-resistant barnyardgrass-mediated rhizosphere microbial communities affect the growth of rice

BACKGROUND

The incidence of herbicide-resistant barnyardgrass is escalating in paddy fields, yet the interactions between resistant weeds and rice are largely unknown. The microbiota of herbicide-resistant barnyardgrass rhizosphere soil is critical for both barnyardgrass and rice fitness.

RESULTS

Rice has different biomass allocation and root traits in the presence of penoxsulam-resistant versus penoxsulam-susceptible barnyardgrass or in their conditioned soil. Compared to susceptible barnyardgrass, resistant barnyardgrass led to an allelopathic increase in rice root, shoot, and whole-plant biomasses. Resistant barnyardgrass recruited distinct core and unique microbes in rhizosphere soil compared to susceptible barnyardgrass. In particular, resistant barnyardgrass assembled more Proteobacteria and Ascomycota to enhance plant stress tolerance. Furthermore, the root exudates from resistant and susceptible barnyardgrass were responsible for the assembly and establishment of the root microbial structure. Importantly, (-)-loliolide and jasmonic acid in root exudates were correlated with the core microbes in the rhizosphere soil.

CONCLUSION

The interference of barnyardgrass with rice can be mediated by rhizosphere microbial communities. Biotype-specific variation in the ability to generate soil microbial communities appears to ameliorate the negative consequences for rice growth, providing an intriguing possibility for modulation of the rhizosphere microbiota to increase crop productivity and sustainability. © 2023 Society of Chemical Industry.

The blackgrass genome reveals patterns of non-parallel evolution of polygenic herbicide resistance

Globally, weedy plants are a major constraint to sustainable crop production. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated management of agroecosystems. Alopecurus myosuroides (blackgrass) is a widespread and impactful weed affecting agriculture in Europe. Here we report a chromosome-scale genome assembly of blackgrass and use this reference genome to explore the genomic/genetic basis of non-target site herbicide resistance (NTSR). Based on our analysis of F2 seed families derived from two distinct blackgrass populations with the same NTSR phenotype, we demonstrate that the trait is polygenic and evolves from standing genetic variation. We present evidence that selection for NTSR has signatures of both parallel and non-parallel evolution. There are parallel and non-parallel changes at the transcriptional level of several stress- and defence-responsive gene families. At the genomic level, however, the genetic loci underpinning NTSR are different (non-parallel) between seed families. We speculate that variation in the number, regulation and function of stress- and defence-related gene families enable weedy species to rapidly evolve NTSR via exaptation of genes within large multi-functional gene families. These results provide novel insights into the potential for, and nature of plant adaptation in rapidly changing environments.

Discrepancies between the drivers of alpha and beta plant diversity in arable field margins

Field margins are major habitats for biodiversity conservation and ecosystem functioning in agricultural landscapes, but biotic homogenization of plant communities threatens their ecological and agronomic functions. Our objective is to determine the drivers of plant diversity in field margins for conservation and restoration purposes. To do so, we assessed the effects of field margin structure and long-term management over 20 years (1995-2015) on the taxonomic and functional α- and β-diversity, and the functional composition of herbaceous plant communities. In 2015, we surveyed 302 field margins in bocage landscapes of Brittany, northwestern France. Results were very similar between taxonomic and functional diversity but revealed important discrepancies between the drivers of α- and β-diversity. Deep ditches, mowing and grazing increased α-diversity but did not affect β-diversity. Denser hedgerows had lower α-diversity than other field margins but strongly contributed to β-diversity by harbouring more unique sets of species or life strategies. Long-term herbicide spraying in field margins and cropping intensity in adjacent habitats did not affect α-diversity, but had more complex effects on β-diversity and selected for common weeds. All in all, preservation of dense hedgerows, abandonment of herbicide spraying, and protection against agrochemical drifts are key measures to prevent the establishment of common weeds and biotic homogenization of herbaceous plant communities in field margins. Above all, our study shows how important it is to go beyond α-diversity to make robust conservation and restoration decisions.

Synthesis and Phytotoxic Evaluation of Isatin Derivatives Supported by 3D-QSAR Study

Concerned about weed infestation, a major threat to food production and herbicide resistance that interferes in the mechanism of action of the main herbicides, we have synthesized eight isatin derivatives using the "Click Chemistry" approach through copper-catalyzed azide-alkyne cycloadditions (CuAAC). Sixteen isatin derivatives were evaluated for their phytotoxic activity against the seed culture of the model plants, Lactuca sativa and Allium cepa. Six of them showed phytotoxic activity similar to the positive control, trifluralin. Hypocotyl length measurement analysis in L. sativa revealed that triazole derivative 8 is more active than trifluralin. For A. cepa, root length measurement analyses revealed that 3, 10, 14, 16, and 17 were similar to the positive control trifluralin. Three-dimensional quantitative structure-activity relationship (3D-QSAR) comparative molecular field analysis (CoMFA) model construction using the acetolactate synthase (ALS) crystallographic structure displayed pk_i values of predicted inhibitory activity and contour maps revealing sterically bulky groups for 11, the CF₃ group in ortho, and for 17, Br in ortho, favoring the inhibitory ALS activity.

Up-regulation of bZIP88 transcription factor is involved in resistance to three different herbicides in both Echinochloa crus-galli and E. glabrescens

The resistance of weeds to herbicides poses a major threat to agricultural production, and non-target-site resistance (NTSR) is often a serious problem as its mechanisms can in some cases confer resistance to herbicides with different modes of action. In this study, we hypothesized that bZIP transcription factors (TFs), which regulate abiotic stress responses in many plants, play a regulatory role in NTSR. Whole-plant assays indicated that the wild grasses Echinochloa crus-galli and E. glabrescens are resistant to the herbicides penoxsulam, cyhalofop-butyl, and quintrione. Transcriptome sequencing then identified 101 and 49 bZIP TFs with differential expression following penoxsulam treatment in E. crus-galli and E. glabrescens, respectively. Twelve of these genes had >60% homology with rice genes. The expression of bZIP88 was considerably up-regulated 6 h after treatment with the three different herbicides, and it was similar between resistant and susceptible populations; however, the relative expression levels before herbicide treatment and 24 h after were the same. We used rice (Oryza sativa ssp. japonica cv Nipponbare) as a model system for functional validation and found that CRISPR-Cas9-knockout of the rice bZIP88 ortholog increased the sensitivity to herbicide, whereas overexpression reduced it. The OsbZIP88 protein was localized to the nucleus. Using ChIP coupled with high-throughput sequencing, OsbZIP88 was found to form a network regulatory center with other TFs such as bZIP20/52/59 to regulate OsKS1, OsCOE1, and OsIM1, which are related to auxin, abscisic acid, brassinosteroids, and gibberellic acid. Based on these results, we have established a database of bZIP TFs corresponding to herbicide stress, and resolved the mechanisms of the positive regulation of herbicide resistance by bZIP88, thereby providing new insights for NTSR.

Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations

Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 19 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size estimate of 8 x 10⁷. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show extreme parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. Two such forces are intra- and inter-locus allelic interactions; we report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.

Non-Target-Site Resistance Mechanisms Endow Multiple Herbicide Resistance to Five Mechanisms of Action in Conyza bonariensis

The repeated use of herbicides can lead to the selection of multiple resistance weeds. Some populations of Conyza bonariensis occurring in olive groves from southern Spain have developed resistance to various herbicides. This study determined the resistance levels to 2,4-D, glyphosate, diflufenican, paraquat, and tribenuron-methyl in a putative resistant (R) C. bonariensis population, and the possible non-target-site resistance (NTSR) mechanisms involved were characterized. Resistance factors varied as follows: glyphosate (8.9), 2,4-D (4.8), diflufenican (5.0), tribenuron-methyl (19.6), and paraquat (85.5). Absorption of ¹⁴C-glyphosate was up to 25% higher in the susceptible (S) population compared to the R one, but ¹⁴C-paraquat absorption was similar (up to 70%) in both populations. S plants translocated more than 60% of both ¹⁴C-glyphosate and ¹⁴C-paraquat toward shoots and roots, while R plants translocated less than 10%. The R population was able to metabolize 57% of the 2,4-D into nontoxic metabolites and 68% of the tribenuron-methyl into metsulfuron-methyl (10%), metsulfuron-methyl-hydroxylate (18%), and conjugate-metsulfuron-methyl (40%). Among the NTSR mechanisms investigated, absorption and translocation could be involved in glyphosate resistance, but only translocation for paraquat. Proofs of the presence of enhanced metabolism as a resistance mechanism were found for tribenuron-methyl and 2,4-D, but not for diflufenican. This research informs the first occurrence of multiple resistance to five herbicide classes (acetolactate synthase inhibitors, 5-enolpyruvylshikimate-3-phosphate synthase inhibitors, photosystem I electron diverters, photosystem II inhibitors, and synthetic auxin herbicides) in C. bonariensis.

The Genomic Architecture of Competitive Response of Arabidopsis thaliana Is Highly Flexible Among Plurispecific Neighborhoods

Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.

The influence of rainfall and tillage on wheat yield parameters and weed population in monoculture versus rotation systems

Extreme climate events (ECEs) of drought are becoming common in Mediterranean areas and farmers need adapt agricultural practices to achieve sustainability. This field study took place in to gain insight into the effects of seasonal rainfall, tillage and crop systems on wheat yield and weed parameters. Conventional (CT), minimum (MT) and no-tillage (NT) systems in wheat monoculture and rotation cropping systems were tested during 3 years of study (2014–2015, 2015–2016 and 2016–2017). Growing Season Rainfall (GSR) was the most influential factor on yield parameters and weed population. In 2016–2017, categorized as an extreme climate event by drought, the GSR accounted for 43.4% of the historical average. This year, the wheat yield (373 kg ha⁻¹) and harvest index (0.18) were the lowest. In 2015–2016, scarcer autumn rainfall (44 mm) affected the weed germination period, reducing the density (17 plants m⁻²) and diversity of weed species (3 species m⁻²) while yield was favoured by high winter and spring rainfall (247 mm). Our study revealed that tillage effects was not significant on wheat yield, but NT systems consistently showed higher weed density and diversity than CT and MT despite the irregular GSR during this study. The rotation system presented higher values of wheat grain yield (781 kg/ha) and dry straw biomass (1803 kg/ha) but also weed biomass (48.54 g m⁻²) compared to monoculture (27.50 g m⁻²). NT and rotation combined increased the weed community although did not reduce the wheat yield compare to conventional systems even with an ECE of drought.

Target site mutations and cytochrome P450s-involved metabolism confer resistance to nicosulfuron in green foxtail (Setaria viridis)

Green foxtail [Setaria viridis (L.) P.Beauv.] is a troublesome grass weed that is widely distributed in maize (Zea mays L.) fields across China. Many populations of S. viridis have evolved resistance to the acetolactate synthase (ALS)-inhibiting herbicide nicosulfuron. The objectives of this research were to confirm nicosulfuron resistance in these populations and to investigate the basis of nicosulfuron resistance. Whole-plant dose-response experiments showed 6 out of 13 S. viridis populations were highly resistance (20-30 times) to nicosulfuron. Sequencing of the ALS gene revealed two amino acid mutations, Asp-376-Glu and Pro-197-Ala, in the nicosulfuron-resistant populations. A malathion pretreatment study revealed that the R376 and R197 subpopulations might have cytochrome P450s-mediated herbicide metabolic resistance. The resistant populations were cross-resistant to imazethapyr but sensitive to topramezone and quizalofop-p-ethyl. This is the first report of resistance to ALS inhibitors conferred by target site mutations (Asp-376-Glu or Pro-197-Ser) and possible cytochrome P450s-involved metabolism in S. viridis.

The genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus

Much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, despite the increasingly recognized importance of polygenic resistance. Little work has been done to characterize the broader genomic basis of herbicide resistance, including the number and distribution of genes involved, their effect sizes, allele frequencies and signatures of selection. In this work, we implemented genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate (Round-up) resistance in the problematic agricultural weed Amaranthus tuberculatus. A GWA was able to correctly identify the known target-gene but statistically controlling for two causal target-site mechanisms revealed an additional 250 genes across all 16 chromosomes associated with non-target-site resistance (NTSR). The encoded proteins had functions that have been linked to NTSR, the most significant of which is response to chemicals, but also showed pleiotropic roles in reproduction and growth. Compared to an empirical null that accounts for complex population structure, the architecture of NTSR was enriched for large effect sizes and low allele frequencies, suggesting the role of pleiotropic constraints on its evolution. The enrichment of rare alleles also suggested that the genetic architecture of NTSR may be population-specific and heterogeneous across the range. Despite their rarity, we found signals of recent positive selection on NTSR-alleles by both window- and haplotype-based statistics, and an enrichment of amino acid changing variants. In our samples, genome-wide single nucleotide polymorphisms explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, even in a collection of individuals where 80% of resistant individuals have large-effect TSR mutations, indicating an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.

Can new herbicide discovery allow weed management to outpace resistance evolution?

While herbicides are the most effective and widely adopted weed management approach, the evolution of multiple herbicide resistance in damaging weed species threatens the yield and profitability of many crops. Weeds accumulate multiple resistance mechanisms through sequential selection and/or gene flow, with long-range and international transport of herbicide-resistant weeds proving to be a serious issue. Metabolic resistance mechanisms can confer resistance across multiple sites of action and even to herbicides not yet discovered. When a new site of action herbicide is introduced to control a key driver weed, it likely will be one of very few effective available herbicide options for that weed in a specific crop due to the continuous use of herbicides over the years and the resulting accumulation of resistance mechanisms, placing it at even higher risk to be rapidly lost to resistance due to the high selection pressure it will experience. The number of available, effective herbicides for certain driver weeds is decreasing over time because the rate of resistance evolution is faster than the rate of new herbicide discovery. Effective monitoring for species movement and diagnostics for resistance should be deployed to rapidly identify emerging resistance to any new site of action. While innovation in herbicide discovery is urgently needed to combat the pressing issue of resistance in weeds, the rate of selection for herbicide resistance in weeds must be slowed through changes in the patterns of how herbicides are used. © 2021 Society of Chemical Industry. © 2021 Society of Chemical Industry.

Agricultural intensification and climate change have increased the threat from weeds

Weeds represent a significant threat to crop yields and global food security. We analysed data on weed competition from the world's longest running agricultural experiment to ask whether potential yield losses from weeds have increased in response to management and environmental change since the advent of the Green Revolution in the 1960s. On plots where inorganic nitrogen fertiliser has been applied, potential yield losses from weeds have consistently increased since 1969. This was explained by a warming climate, measured as air temperature averaged over the growing season for the weeds, and a shift towards shorter crop cultivars. Weeds also reduced yield proportionally more on plots with higher rates of nitrogen which had higher yields when weeds were controlled; the relative benefit of herbicides was, therefore, proportional to potential crop yield. Reducing yield losses from weed competition is increasingly challenging because of the evolution of herbicide resistance. Our results demonstrate that weeds now represent a greater inherent threat to crop production than before the advent of herbicides and integrated, sustainable solutions to weed management are urgently needed to protect the high yield potential of modern crop genotypes.

Adaptation at different points along antibiotic concentration gradients

Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.

Standing genetic variation in laboratory populations of insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance

Insecticides can exert strong selection on insect pest species, including those that vector diseases, and have led to rapid evolution of resistance. Despite such rapid evolution, relatively little is known about standing genetic variation for resistance in insecticide-susceptible populations of many species. To help fill this knowledge gap, we generated genotyping-by-sequencing data from insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis sand flies that survived or died from a sub-diagnostic exposure to either permethrin or malathion using a modified version of the Centers for Disease Control and Prevention bottle bioassay. Multi-locus genome-wide association mapping methods were used to quantify standing genetic variation for insecticide resistance in these populations and to identify specific alleles associated with insecticide survival. For each insecticide treatment, we estimated the proportion of the variation in survival explained by the genetic data (i.e., "chip" heritability) and the number and contribution of individual loci with measurable effects. For all treatments, survival to an insecticide exposure was heritable with a polygenic architecture. Both P. papatasi and L. longipalpis had alleles for survival that resided within many genes throughout their genomes. The implications for resistance conferred by many alleles, as well as inferences made about the utility of laboratory insecticide resistance association studies compared to field observations, are discussed.

In silico local QSAR modeling of bioconcentration factor of organophosphate pesticides

The persistent and accumulative nature of the pesticide of indiscriminate use emerged as ecotoxicological hazards. The bioconcentration factor (BCF) is one of the key elements for environmental assessments of the aquatic compartment. Limitations of prediction accuracy of global model facilitate the use of local predictive models in toxicity modeling of emerging compounds. The BCF data of diverse organophosphate (n = 55) was collected from the Pesticide Properties Database and used as a model data set in the present study to explore physicochemical properties and structural alert concerning BCF. The structures were downloaded from Pubchem, ChemSpider database. Two splitting techniques (biological sorting and structure-based) were used to divide the whole dataset into training and test set compounds. The QSAR study was carried out with two-dimensional descriptors (2D) calculated from PaDEL by applying genetic algorithm (GA) as chemometric tools using QSARINS software. The models were statistically robust enough both internally as well as externally (Q2: 0.709-0.722, Q2 Ext: 0.717-0.903, CCC: 0.857-0.880). Overall molecular mass, presence of fused, and heterocyclic ring with electron-withdrawing groups affect the BCF value. The developed models reflected extended applicability domain (AD) and reliable predictions than the reported models for the studied chemical class. Finally, predictions of unknown organophosphate pesticides and the toxic nature of unknown organophosphate pesticides were commented on. These findings may be useful for the scientific community in prioritizing high potential pesticides of organophosphate class.

Investigating the presence of compensatory evolution in dicamba resistant IAA16 mutated kochia (Bassia scoparia)†

BACKGROUND

Lack of fitness costs has been reported for multiple herbicide resistance traits, but the underlying evolutionary mechanisms are not well understood. Compensatory evolution that ameliorates resistance costs, has been documented in bacteria and insects but rarely studied in weeds. Dicamba resistant IAA16 (G73N) mutated kochia was previously found to have high fecundity in the absence of competition, regardless of significant vegetative growth defects. To understand if costs of dicamba resistance can be compensated through traits promoting reproductive success in kochia, we thoroughly characterized the reproductive growth and development of different G73N kochia biotypes. Flowering phenology, seed production and reproductive allocation were quantified through greenhouse studies, floral (stigma-anthers distance) and seed morphology, as well as resulting mating and seed dispersal systems were studied through time-course microcopy images.

RESULTS

G73N covaried with multiple phenological, morphological and ecological traits that improve reproductive fitness: (i) 16-60% higher reproductive allocation; (ii) longer reproduction phase through early flowering (2-7 days); (iii) smaller stigma-anthers separation (up to 60% reduction of herkogamy and dichogamy) that can potentially promote selfing and reproductive assurance; (iv) 'winged' seeds with 30-70% longer sepals that facilitate long-distance seed dispersal.

CONCLUSION

The current study demonstrates that costs of herbicide resistance can be ameliorated through coevolution of other fitness penalty alleviating traits. As illustrated in a hypothetical model, the evolution of herbicide resistance is an ongoing fitness maximization process, which poses challenges to contain the spread of resistance. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication

Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.

Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides

BACKGROUND

Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance.

RESULTS

Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (F_ST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (F_IS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers.

CONCLUSION

There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry.

Coleorhiza-enforced seed dormancy: a novel mechanism to control germination in grasses

How the biophysical properties of overlaying tissues control growth, such as the embryonic root (radicle) during seed germination, is a fundamental question. In eudicot seeds the endosperm surrounding the radicle confers coat dormancy and controls germination responses through modulation of its cell wall mechanical properties. Far less is known for grass caryopses that differ in tissue morphology. Here we report that the coleorhiza, a sheath-like organ that surrounds the radicle in grass embryos, performs the same role in the grass weed Avena fatua (common wild oat). We combined innovative biomechanical techniques, tissue ablation, microscopy, tissue-specific gene and enzyme activity expression with the analysis of hormones and oligosaccharides. The combined experimental work demonstrates that in grass caryopses the coleorhiza indeed controls germination for which we provide direct biomechanical evidence. We show that the coleorhiza becomes reinforced during dormancy maintenance and weakened during germination. Xyloglucan endotransglycosylases/hydrolases may have a role in coleorhiza reinforcement through cell wall remodelling to confer coat dormancy. The control of germination by coleorhiza-enforced dormancy in grasses is an example of the convergent evolution of mechanical restraint by overlaying tissues.

A dicamba resistance-endowing IAA16 mutation leads to significant vegetative growth defects and impaired competitiveness in kochia (Bassia scoparia)†

BACKGROUND

Precise quantification of the fitness cost of synthetic auxin resistance has been impeded by lack of knowledge about the genetic basis of resistance in weeds. Recent elucidation of a resistance-endowing IAA16 mutation (G73N) in the key weed species kochia (Bassia scoparia), allows detailed characterization of the contribution of resistance alleles to weed fitness, both in the presence and absence of herbicides. Different G73N genotypes from a segregating resistant parental line (9425) were characterized for cross-resistance to dicamba, 2,4-d and fluroxypyr, and changes on stem/leaf morphology and plant architecture. Plant competitiveness and dominance of the fitness effects was quantified through measuring biomass and seed production of three F₂ lines in two runs of glasshouse replacement series studies.

RESULTS

G73N confers robust resistance to dicamba but only moderate to weak resistance to 2,4-D and fluroxypyr. G73N mutant plants displayed significant vegetative growth defects: (i) they were 30-50% shorter, with a more tumbling style plant architecture, and (ii) they had thicker and more ovate (versus lanceolate and linear) leaf blades with lower photosynthesis efficiency, and 40-60% smaller stems with less-developed vascular bundle systems. F₂ mutant plants had impaired plant competitiveness, which can lead to 80-90% less biomass and seed production in the replacement series study. The pleiotropic effects of G73N were mostly semidominant (0.5) and fluctuated with the environments and traits measured.

CONCLUSION

G73N is associated with significant vegetative growth defects and reduced competitiveness in synthetic auxin-resistant kochia. Management practices should target resistant kochia's high vulnerability to competition in order to effectively contain the spread of resistance.

RNA-Seq transcriptome analysis to identify candidate genes involved in non-target site-based mesosulfuron-methyl resistance in Beckmannia syzigachne

American sloughgrass (Beckmannia syzigachne Steud.) has become a dominant weed in fields with rice-wheat rotation. Moreover, herbicide resistance has rendered weed control difficult. We identified a biotype showing resistance to ALS inhibitor mesosulfuron-methyl with a resistant index 3.3, but without any ALS mutation. This study aims to identify and confirm the factors associated with non-target site resistance of this biotype to mesosulfuron-methyl using RNA-Seq. 118,111 unigenes were assembled, and 50.9% of these were annotated across seven databases. Eleven contigs related to metabolic resistance were identified based on differential expression via RNA-Seq which include a novel resistance-related transcription factor (MYC3) and two disease resistance proteins were also identified (At1g58602 and At1g15890). Fold changes in expression of these genes in comparison M-R vs. M-S ranged from 3.9 to 11.6, as confirmed by qPCR. The expression of a contig annotated as cytochrome P450 (CYP86B1) in resistant individuals was over 3 times higher than that in sensitive individuals at 0-72 h after mesosulfuron-methyl treatment. A similar trend was noted for three other genes annotated as glutathione S-transferase (GST), namely GST-T3, GST-U6, and GST-U14; the expression of GST-U6 in resistant individuals was up to 142.3 times higher than that in sensitive individuals at 24 h after mesosulfuron-methyl treatment. In addition, GST activity in resistant individuals was 2.1 to 5.3 times higher than that in sensitive individuals. The GR₅₀ of resistant biotype decreased from 24.4 to 11.3 g a.i. ha^-1 after P450 inhibitor malathion treatment. This study identified a cytochrome P450 gene CYP86B1 and three GST genes GST-T3, GST-U6, and GST-U14 that have higher expression in mesosulfuron-methyl resistant B. syzigachne, suggesting that both P450- and GST-based activities could be involved in resistance.

Evolution of Glyphosate-Resistant Weeds

Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.

Loss of trifluralin metabolic resistance in Lolium rigidum plants exposed to prosulfocarb recurrent selection

BACKGROUND

Resistance to the dinitroaniline herbicide trifluralin in Lolium rigidum (annual ryegrass) often is mediated by the enhanced capacity to metabolize the herbicide to less toxic polar conjugates and/or by functionally recessive target-site mutations in α-tubulin.

RESULTS

In two L. rigidum populations possessing enhanced trifluralin metabolism, resistance was largely reversed by recurrent selection with the thiocarbamate herbicide prosulfocarb (i.e. plant survival was two- to >20-fold lower). Their ability to metabolize trifluralin was significantly decreased (by ≈2.3-fold) following recurrent prosulfocarb selection, to levels comparable to those observed in susceptible plants or when trifluralin metabolism was inhibited by treatment with the insecticide phorate.

CONCLUSIONS

This study provides evidence that trait(s) enabling efficient trifluralin metabolism in L. rigidum are purged from the population under prosulfocarb recurrent selection. The level of trifluralin metabolism in vitro and its inhibition caused by phorate action on trifluralin-metabolizing enzyme(s) is equivalent to the effect produced by prosulfocarb selection. The hypothetical link between the two phenomena is that the putative monooxygenase(s) conferring trifluralin metabolic resistance also mediate the activation of prosulfocarb to its toxic sulfoxide. Thus, we speculate that survival to prosulfocarb via a lack of metabolic herbicide activation, and survival to trifluralin conferred by enhanced herbicide metabolism, are mutually exclusive. These findings not only open up a new research direction in terms of the interaction between different herbicide resistance mechanisms in L. rigidum, but also offer strategies for immediate management of the population dynamics of metabolism-based resistance in the field. © 2020 Society of Chemical Industry.

Current outlook and future research needs for harvest weed seed control in North American cropping systems

Harvest weed seed control (HWSC) comprises a set of tools and tactics that prevents the addition of weed seed to the soil seed bank, attenuating weed infestations and providing a method to combat the development and spread of herbicide-resistant weed populations. Initial HWSC research efforts in North America are summarized and, combined with the vast area of crops suitable for HWSC, clearly indicate strong potential for this technology. However, potential limitations exist that are not present in Australian cropping systems where HWSC was developed. These include rotations with crops that are not currently amenable to HWSC (e.g. corn), high moisture content at harvest, untimely harvest, and others. Concerns about weeds becoming resistant to HWSC (i.e. adapting) exist, as do shifts in weed species composition, particularly with the diversity of weeds in North America. Currently the potential of HWSC vastly outweighs any drawbacks, necessitating further research. Such expanded efforts should foremost include chaff lining and impact mill commercial scale evaluation, as this will address potential limitations as well as economics. Growers must be integrated into large-scale, on-farm research and development activities aimed at alleviating the problems of using HWSC systems in North America and drive greater adoption subsequently. © 2020 Society of Chemical Industry.

The Evolution and Ecology of Resistance in Cancer Therapy

Despite the continuous deployment of new treatment strategies and agents over many decades, most disseminated cancers remain fatal. Cancer cells, through their access to the vast information of the human genome, have a remarkable capacity to deploy adaptive strategies for even the most effective treatments. We note there are two critical steps in the clinical manifestation of treatment resistance. The first, which is widely investigated, requires molecular machinery necessary to eliminate the cytotoxic effect of the treatment. However, the emergence of a resistant phenotype is not in itself clinically significant. That is, resistant cells affect patient outcomes only when they succeed in the second step of resistance by proliferating into a sufficiently large population to allow tumor progression and treatment failure. Importantly, proliferation of the resistant phenotype is by no means certain and, in fact, depends on complex Darwinian dynamics governed by the costs and benefits of the resistance mechanisms in the context of the local environment and competing populations. Attempts to target the molecular machinery of resistance have had little clinical success largely because of the diversity within the human genome-therapeutic interruption of one mechanism simply results in its replacement by an alternative. Here we explore evolutionarily informed strategies (adaptive, double-bind, and extinction therapies) for overcoming treatment resistance that seek to understand and exploit the critical evolutionary dynamics that govern proliferation of the resistant phenotypes. In general, this approach has demonstrated that, while emergence of resistance mechanisms in cancer cells to every current therapy is inevitable, proliferation of the resistant phenotypes is not and can be delayed and even prevented with sufficient understanding of the underlying eco-evolutionary dynamics.

Resistance to Fomesafen, Imazamox and Glyphosate in Euphorbia heterophylla from Brazil

Euphorbia heterophylla is a species of weed that was previously controlled by fomesafen, imazamox and glyphosate, but continued use of these herbicides has selected resistant populations from the Rio Grande do Sul (Brazil). One resistant (R) strain and one susceptible (S) strain to fomesafen, imazamox and glyphosate were compared, the latter by recurrent selection. Dose-response tests showed multiple resistance to these herbicides. The required imazamox concentration to inhibit ALS by 50% was approximately 16 times greater in the R population than in the S population. Based on the EPSPS activity results, the R population was 10 fold less sensitive to glyphosate than the S counterpart. In addition, basal EPSPS activity from R plants was 3.3 fold higher than the level detected on S plants. The Proto IX assays showed high resistance to fomesafen in the R population that accumulated less Proto IX than the S population. Malathion assays showed the participation of CytP450 in fomesafen resistance, but a molecular mechanism could also be involved. To our knowledge, this is the first characterisation of multiple resistance to these three groups of herbicides in E. heterophylla in the world.

Investigation of resistant level to tribenuron-methyl, diversity and regional difference of the resistant mutations on acetolactate synthase (ALS) isozymes in Descurainia sophia L. from China

Descurainia sophia L. is one of the most notorious broadleaf weeds in winter wheat fields of China. In this study, 95 out of 163 (58.3%) D. sophia populations which were collected from provinces of Hebei, Shandong, Henan, Shanxi, Shaanxi and Jiangsu, have evolved resistance to tribenuron-methyl. The als1 and als2 were cloned in all test D. sophia populations, while als3 and als4 were identified only in some of the populations. Resistant mutations of Pro-197-Ser/Thr/Leu/His/Ala/Arg, Asp-376-Glu and Trp-574-Leu were identified in tribenuron-methyl-resistant (TR) D. sophia plants, while the Pro-197-Arg was first identified in D. sophia in this study. These resistant mutations displayed no preference between ALS1 and ALS2. However, Pro-197-Ser/Thr and Trp-574-Leu were identified in all ALS isozymes, while the other mutations were not. In addition, some resistant mutations displayed regional differences, the frequency of Pro-197-Ser in Shandong and Trp-574-Leu in Shanxi province is much higher than that in other provinces.

Agricultural adaptation in the native North American weed waterhemp, Amaranthus tuberculatus (Amaranthaceae)

There is increasing interest in documenting adaptation of weedy plant species to agricultural ecosystems, beyond the evolution of herbicide resistance. Waterhemp (Amaranthus tuberculatus) is a native plant of the Midwestern U.S. that began infesting agricultural fields in the 20th century within the central portion of its range. We hypothesized that the vegetative growth and reproductive traits of waterhemp from this heavily infested central region provide differential fitness benefits in agricultural environments. We collected seeds from across the species' native range, representing regions with varying degrees of waterhemp infestation, and planted them together in common garden soybean plots. A 2010 common garden experiment was conducted within the range of agriculturally weedy waterhemp (in Missouri), and a 2011 common garden experiment was conducted outside of this range (in Ohio). Days to flowering and flowering plant height, mature plant size data (height, number of branches, and length of the longest branch), and above-ground biomass were measured to estimate relative fitness. In both common garden locations, plants from regions where waterhemp occurs as an agricultural weed - including those from the heavily infested Mississippi Valley region (Iowa, Illinois, and Missouri) and the less severely infested Plains region (Nebraska, Kansas, and Oklahoma) - had higher relative performance in almost all fitness-related measures than plants from the Northeast region (Ohio, Michigan, and Ontario), which had little to no agriculturally weedy waterhemp at the time of our study. Further analysis revealed that fewer days to flowering in the Northeast populations can be largely accounted for by latitude of origin, suggesting a strong genetic influence on this reproductive trait. These findings suggest intraspecific variation in agricultural adaptation in a native U.S. weed, and support the use of agricultural weeds to study adaptation.

Italian weedy rice-A case of de-domestication?

Weedy rice is a representative of the extensive group of feral weeds that derive from crops, but has returned to the lifestyle of a wild species. These weeds develop either from a hybridization of crops with wild relatives (exoferality), or by mutation of crops to weedy forms (endoferality). Due to the close relation of weed and crop, the methods for weed-targeted containment are limited to date. A deeper understanding of the development of such weeds might help to design more efficient and sustainable approaches for weed management. Weedy rice poses a serious threat to rice yields worldwide. It is widely accepted that weedy rice has originated independently in different regions all over the world. However, details of its evolution have remained elusive. In the current study, we investigated the history of weedy rice in northern Italy, the most important rice-growing area in Europe. Our approach was to analyze genes related to weedy traits (SD1, sh4, Rc) in weedy rice accessions compared to cultivars, and to integrate these results with phenotypic and physiological data, as well as historical information about rice farming in Italy. We arrive at a working model for the timeline of evolution of weedy rice in Italy indicating that both exoferality and endoferality acted as forces driving the development of the diverse weedy rice populations found in the region today. Models of weed evolution can help to predict the direction which weed development might take and to develop new, sustainable methods to control feral weeds.

Exploiting evolutionary steering to induce collateral drug sensitivity in cancer

Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased fecundity or increased sensitivity to another drug. These evolutionary trade-offs can be exploited using 'evolutionary steering' to control the tumour population and delay resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here, we present an approach for evolutionary steering based on a combination of single-cell barcoding, large populations of 108-109 cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary steering in a lung cancer model, showing that it shifts the clonal composition of the tumour in our favour, leading to collateral sensitivity and proliferative costs. Genomic profiling revealed some of the mechanisms that drive evolved sensitivity. This approach allows modelling evolutionary steering strategies that can potentially control treatment resistance.

Evolving Multiple Resistance to EPSPS, GS, ALS, PSI, PPO, and Synthetic Auxin Herbicides in Dominican Republic Parthenium hysterophorus Populations. A Physiological and Biochemical Study

Two Parthenium hysterophorus populations resistant (R) and susceptible (S) harvested in banana crop from the Dominican Republic were studied. All S plants died when the herbicides were applied at field dose, except with paraquat. For the R population, the order of plant survival was as follows: glyphosate and paraquat > flazasulfuron > glufosinate > fomesafen > 2,4-D. The resistance factors obtained in the dose–response assays showed a high resistance to glyphosate, flazasulfuron, and fomesafen, medium resistance to glufosinate and 2,4-D, and a natural tolerance to paraquat (resistance factor (RF) = 1.0). The I50 values obtained in the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), acetolactate synthase (ALS), and glutamine synthetase (GS) activity studies with glyphosate, flazasulfuron, and glufosinate, respectively, were greater in R than in S. The effect of fomesafen was measured by the Proto IX levels, obtaining five times more Proto IX in the S than in the R population. The resistance to 2,4-D in the R was determined by the lower accumulation of ethylene compared to the S population. The studies with 14C-paraquat conclude that the lower absorption and translocation in both the R and S populations would explain the natural tolerance of P. hysterophorus. This is the first case of multiple resistance to herbicides with different mechanisms of action confirmed in P. hysterophorus.

Dormancy, a critical trait for weed success in crop production systems

Agricultural practices exert selective forces on weed populations. As these practices change over time, weed adaptive traits also evolve, allowing weeds to persist in the new environment. However, only weeds having individuals showing the trait with adaptive significance will be able to cope with these changes, thus allowing a sub-population to be selected for persistence. In addition, changes in agricultural practices can select new weed species showing functional traits with characteristics adaptive to the modified system. Seed dormancy has long been recognized as a trait with enormous adaptive value to adjust weed biology to cropping systems. In this paper, we illustrate with examples of success and failure, the value of seed dormancy as a functional trait to cope with long-term changes in crop production systems. We show that successful outcomes are mostly related to the existence of sufficient variability for the functioning of physiological mechanisms that control dormancy characteristics as influenced by the agricultural environment. Presented examples illustrate how knowledge about the relationship that exists between agricultural practices and their selective pressure on seed dormancy can be instrumental in predicting changes in weed biotype dormancy characteristics or foreseeing the appearance of new weed species in future agricultural scenarios. © 2019 Society of Chemical Industry.

Synthesis of new tetronamides displaying inhibitory activity against bloom-forming cyanobacteria

BACKGROUND

The increasing frequency and intensity of cyanobacterial blooms pose a serious threat to aquatic ecosystems. These blooms produce potent toxins that can contaminate drinking water and endanger the life of wild and domestic animals as well as humans. Consequently, the development of effective methods for their control is a matter of high priority. We have previously shown that some γ-benzylidenebutenolides, related to the rubrolide family of natural products, are capable of inhibiting the photosynthetic electron transport chain (Hill reaction), a target of commercial herbicides. Here we report the synthesis and biological properties of a new class of rubrolide-inspired molecules featuring a tetronamide motif.

RESULTS

A total of 47 N-aryl tetronamides, including 38 aldol adducts, were prepared bearing phenyl, biphenyl, naphthyl, aliphatic and heteroaromatic groups. Some of the aldol adducts were dehydrated to the corresponding γ-benzylidenetetronamides, although satisfactory yields were obtained in only three cases (52-97%). None of the synthesized compounds were capable of blocking the Hill reaction. This notwithstanding, several aldol adducts equipped with a biphenyl substituent displayed excellent inhibitory activity against Synechococcus elongatus and other cyanobacterial strains (IC₅₀  = 1-5 μM). Further, these tetronamides were found to be essentially inactive against eukaryotic microorganisms.

CONCLUSION

Several newly synthesized biphenyl-containing tetronamides were shown to display potent and selective inhibitory activity against cyanobacteria. These compounds appear to exert their biological effects without interfering with the Hill reaction. As such, they represent novel leads in the search of environmentally benign agents for controlling cyanobacterial blooms. © 2019 Society of Chemical Industry.

Eco-evolutionary agriculture: Host-pathogen dynamics in crop rotations

Since its origins, thousands of years ago, agriculture has been challenged by the presence of evolving plant pathogens. Temporal rotations of host and non-host crops have helped farmers to control epidemics among other utilities, but further efforts for strategy assessment are needed. Here, we present a methodology for developing crop rotation strategies optimal for control of pathogens informed by numerical simulations of eco-evolutionary dynamics in one field. This approach can integrate agronomic criteria used in crop rotations—soil quality and cash yield—and the analysis of pathogen evolution in systems where hosts are artificially selected. Our analysis shows which rotation patterns perform better in maximising crop yield when an unspecified infection occurs, with yield being dependent on both soil quality and the strength of the epidemic. Importantly, the use of non-host crops, which both improve soil quality and control the epidemic results in similar rational rotation strategies for diverse agronomic and infection conditions. We test the repeatability of the best rotation patterns over multiple decades, an essential end-user goal. Our results provide sustainable strategies for optimal resource investment for increased food production and lead to further insights into the minimisation of pesticide use in a society demanding ever more efficient agriculture.

The invention of agriculture is a major evolutionary transition in the social evolution of the human race. Transforming the lifestyle from nomadic to sedentary, agriculture provided humankind with the stability necessary to make rapid advancements. However, agriculture, as we know it, is now in danger. While agriculture is a grand artificial selection experiment, it is in a constant battle with the brute force of natural selection, generating highly infectious plant pathogens. Traditional techniques such as slash-burn techniques are not sustainable for feeding the ever-increasing population. Crop rotation, on the other hand, has been developed over thousands of years as a sustainable method. We provide a computational model of how crop rotations can be used to tackle pathogen infection and what properties of rotation patterns make them sustainable in the long run. We hope that this study, together with other sustainable methods such as minimal pesticide use and biocontrol, can make agriculture more efficient.

Cytochrome P450 Herbicide Metabolism as the Main Mechanism of Cross-Resistance to ACCase- and ALS-Inhibitors in Lolium spp. Populations From Argentina: A Molecular Approach in Characterization and Detection

Knowledge about the mechanisms of herbicide resistance provide valuable insights into evolving weed populations in response to selection pressure and should be used as a basis for designing management strategies for herbicide-resistant weeds. The selection pressure associated with reactive management against glyphosate-resistant Lolium spp. populations would have favored the herbicide resistance to ACCase- and ALS-inhibitors. This work was aimed to determine the sensitivity of 80 Argentinean Lolium spp. populations to ALS- and ACCase-inhibitor herbicides for use in wheat or barley and to study the mechanisms of resistance involved. Sensitivity to pinoxaden and iodosulfuron-mesosulfuron were positively correlated (r = 0.84), even though both affect different target sites. Inhibitors of cytochrome P450 monooxygenases (P450s) increased the sensitivity to pinoxaden and iodosulfuron-mesosulfuron in 94% of herbicide-resistant populations and target-site ACCase resistance mutations were detected only in two cases. Polymorphic variants were obtained with a pair primer designed on P450 sequences, cluster analysis discriminated around 80% of susceptible and P450-metabolic resistant plants sampled from a single population or different populations. Five markers corresponding to herbicide sensitivity were identified to be significantly associated with phenotypic variance in plants. Resistance to ALS- and ACCase-inhibitor herbicides were closely related, challenging the rotation of herbicides of both sites of action as a practice against resistance. In that sense, the use of pinoxaden and iodosulfuron-mesosulfuron would have provoked a selection on P450 genes that conduced a convergence of P450-metabolism based resistant Lolium spp. populations, which was detected by markers in a contribution to elucidate the molecular basis of this type of resistance.

Fitness of Herbicide-Resistant Weeds: Current Knowledge and Implications for Management

Herbicide resistance is the ultimate evidence of the extraordinary capacity of weeds to evolve under stressful conditions. Despite the extraordinary plant fitness advantage endowed by herbicide resistance mutations in agroecosystems under herbicide selection, resistance mutations are predicted to exhibit an adaptation cost (i.e., fitness cost), relative to the susceptible wild-type, in herbicide untreated conditions. Fitness costs associated with herbicide resistance mutations are not universal and their expression depends on the particular mutation, genetic background, dominance of the fitness cost, and environmental conditions. The detrimental effects of herbicide resistance mutations on plant fitness may arise as a direct impact on fitness-related traits and/or coevolution with changes in other life history traits that ultimately may lead to fitness costs under particular ecological conditions. This brings the idea that a “lower adaptive value” of herbicide resistance mutations represents an opportunity for the design of resistance management practices that could minimize the evolution of herbicide resistance. It is evident that the challenge for weed management practices aiming to control, minimize, or even reverse the frequency of resistance mutations in the agricultural landscape is to “create” those agroecological conditions that could expose, exploit, and exacerbate those life history and/or fitness traits affecting the evolution of herbicide resistance mutations. Ideally, resistance management should implement a wide range of cultural practices leading to environmentally mediated fitness costs associated with herbicide resistance 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.

Evolutionary epidemiology predicts the emergence of glyphosate resistance in a major agricultural weed

The evolution of resistance to herbicides is a striking example of rapid, human-directed adaptation with major consequences for food production. Most studies of herbicide resistance are performed reactively and focus on post hoc determination of resistance mechanisms following the evolution of field resistance. If the evolution of resistance can be anticipated, however, pro-active management to slow or prevent resistance traits evolving can be advocated. We report a national-scale study that combines population monitoring, glyphosate sensitivity assays, quantitative genetics and epidemiological analyses to pro-actively identify the prerequisites for adaptive evolution (directional selection and heritable genetic variation) to the world's most widely used herbicide (glyphosate) in a major, economically damaging weed species, Alopecurus myosuroides. Results highlighted pronounced, heritable variability in glyphosate sensitivity amongst UK A. myosuroides populations. We demonstrated a direct epidemiological link between historical glyphosate selection and current population-level sensitivity, and show that current field populations respond to further glyphosate selection. This study provides a novel, pro-active assessment of adaptive potential for herbicide resistance, and provides compelling evidence of directional selection for glyphosate insensitivity in advance of reports of field resistance. The epidemiological approach developed can provide a basis for further pro-active study of resistance evolution across pesticide resistance disciplines.