Bayer CropScience
  • Monheim am Rhein, Germany
Recent publications
Key message The integration of known and latent environmental covariates within a single-stage genomic selection approach provides breeders with an informative and practical framework to utilise genotype by environment interaction for prediction into current and future environments. Abstract This paper develops a single-stage genomic selection approach which integrates known and latent environmental covariates within a special factor analytic framework. The factor analytic linear mixed model of Smith et al. (2001) is an effective method for analysing multi-environment trial (MET) datasets, but has limited practicality since the underlying factors are latent so the modelled genotype by environment interaction (GEI) is observable, rather than predictable. The advantage of using random regressions on known environmental covariates, such as soil moisture and daily temperature, is that the modelled GEI becomes predictable. The integrated factor analytic linear mixed model (IFA-LMM) developed in this paper includes a model for predictable and observable GEI in terms of a joint set of known and latent environmental covariates. The IFA-LMM is demonstrated on a late-stage cotton breeding MET dataset from Bayer CropScience. The results show that the known covariates predominately capture crossover GEI and explain 34.4% of the overall genetic variance. The most notable covariates are maximum downward solar radiation (10.1%), average cloud cover (4.5%) and maximum temperature (4.0%). The latent covariates predominately capture non-crossover GEI and explain 40.5% of the overall genetic variance. The results also show that the average prediction accuracy of the IFA-LMM is $$0.02-0.10$$ 0.02 - 0.10 higher than conventional random regression models for current environments and $$0.06-0.24$$ 0.06 - 0.24 higher for future environments. The IFA-LMM is therefore an effective method for analysing MET datasets which also utilises crossover and non-crossover GEI for genomic prediction into current and future environments. This is becoming increasingly important with the emergence of rapidly changing environments and climate change.
Shinyshval: A User-Friendly Shiny implementation of the EFSA SHVAL tool for the use in the European pollinator risk assessment, by Szöcs et al. A shiny implementation of the SHVAL pollinator risk assessment tool to evaluate plant protection products is practical and user-friendly, and can inspire the design of future computational regulatory tools, employing best practices for scientific computing.
Background: Afoxolaner is a novel representative of the isoxazolines, a class of ectoparasiticides which has been commercialised for the control of tick and flea infestations in dogs. In this study, the biological efficacy of afoxolaner against the two-spotted spider mite Tetranychus urticae was evaluated. Furthermore, as isoxazolines are known inhibitors of γ-aminobutyric acid-gated chloride channels (GABACls), the molecular mode of action of afoxolaner on T. urticae GABACls (TuRdls) was studied using functional expression in Xenopus oocytes followed by two-electrode voltage-clamp (TEVC) electrophysiology and results were compared with inhibition by fluralaner, fipronil and endosulfan. To examine the influence of known GABACl resistance mutations, H301A, I305T and A350T substitutions in TuRdl1 and a S301A substitution in TuRdl2 were introduced. Results: Bioasassays revealed excellent efficacy of afoxolaner against all developmental stages and no cross-resistance was found in a panel of strains resistant to most currently used acaricides. Laboratory selection over a period of 3 years did not result in resistance. TEVC revealed clear antagonistic activity of afoxolaner and fluralaner for all homomeric TuRdl1/2/3 channels. The introduction of single, double or triple mutations to TuRdl1 and TuRdl2 did not lower channel sensitivity. Contrastingly, both endosulfan and fipronil had minimal antagonistic activities against TuRdl1/2/3, and channels carrying single mutations while the sensitivity of double and triple TuRdl1 mutants was significantly increased. Conclusions: Our results demonstrate that afoxolaner is a potent antagonist of GABACls of T. urticae and has a powerful mode of action to control spider mites. This article is protected by copyright. All rights reserved.
The present agrochemical safety evaluation paradigm is long-standing and anchored in well-established testing and evaluation procedures. However, it does not meet the present-day challenges of rapidly growing populations, food insecurity, and pressures from climate change. To transform the current framework and apply modern evaluation strategies that better support sustainable agriculture, the Health and Environmental Sciences Institute (HESI) assembled a technical committee to reframe the safety evaluation of crop-protection products. The committee is composed of international experts from regulatory agencies, academia, industry, and non-governmental organizations. Their mission is to establish a framework that supports the development of fit-for-purpose agrochemical safety evaluation that is applicable to changing global, as well as local needs and regulatory decisions, and incorporates relevant evolving science. This will be accomplished through the integration of state-of-the-art scientific methods, technologies, and data sources, to inform safety and risk decisions, and adapt them to evolving local and global needs. The project team will use a systems-thinking approach to develop the tools that will implement a problem formulation and exposure driven approach to create sustainable, safe, and effective crop protection products, and reduce, replace, and refine animal studies with fit-for-purpose assays. A new approach will necessarily integrate the most modern tools and latest advances in chemical testing methods to guarantee the robust human and environmental safety and risk assessment of agrochemicals. This article summarizes the challenges associated with the modernization of agrochemical safety evaluation, proposes a potential roadmap, and seeks input and engagement from the broader community to advance this effort. Pest Management Science-Perspective
ABSTRACT The use of ultra-coarse droplets for herbicide application reduces the risk of drift but may compromise the coverage and efficacy of the treatment. The objective of this work was to evaluate the use of ultra-coarse droplets, in different spray volumes, in the application of dicamba herbicide in association with glyphosate, for the control of weeds in two field trials. The first trial was conducted in a 5 x 2 factorial design, with five spray volumes (58, 72, 96, 144, and 177 L ha-1) and two air induction flat-fan spray tips (MUG 110015 - MagnoJet and TTI 110015 - Teejet). The control efficiency of Commelina benghalensis and the spray deposition on the target were evaluated by detecting a tracer using spectrophotometry. The second was conducted in a 2 x 2 factorial scheme, using two volumes (100 and 125 L ha-1) and two tips (MUG 11002 and TTI 11002). The control efficiency of Conyza spp. and fresh matter were evaluated. The different spray volumes and tips did not differ in relation to the deposition of the tracer. The use of ultra-coarse droplets was adequate for weed control. The TTI and MUG tips gave similar and adequate control performance starting at 96 L ha-1. Increasing the volume above 100 L ha-1 did not result in better control.
Plant-parasitic nematodes (PPN) are responsible for severe yield losses in crop production. Management is challenging as effective and safe means are rare. Recently, it has been discovered that the succinate dehydrogenase (SDH) inhibitor fluopyram is highly effective against PPN while accompanying an excellent safety profile. Here we show that fluopyram is a potent inhibitor of SDH in nematodes but not in mammals, insects and earthworm, explaining the selectivity on molecular level. As a consequence of SDH inhibition, fluopyram impairs ATP generation and causes paralysis in PPN and Caenorhabditis elegans. Interestingly, efficacy differences of fluopyram amongst PPN species can be observed. Permanent exposure to micromolar to nanomolar amounts of fluopyram prevents Meloidogyne spp. and Heterodera schachtii infection and their development at the root. Preincubation of Meloidogyneincognita J2 with fluopyram followed by a recovery period effectively reduces gall formation. However, the same procedure does not inhibit H.schachtii infection and development. Sequence comparison of sites relevant for ligand binding identified amino acid differences in SDHC which likely mediate selectivity, coincidently revealing a unique amino acid difference within SDHC conserved among Heterodera spp. Docking and C.elegans mutant studies suggest that this minute difference mediates altered sensitivity of H.schachtii towards fluopyram.
Historically, end-product quality testing has been costly and required large flour samples and therefore, was generally implemented in late phases of variety development imposing huge cost on the breeding effort and effectiveness. High genetic correlations of end-product quality traits with higher-throughput and non-destructive testing technologies, such as near infra-red (NIR), could enable early-stage testing and effective selection on these highly valuable traits in a multi-trait genomic prediction model. We studied the impact on end-product quality trait accuracy of adding NIR phenotypes as a second trait in genomic best linear unbiased prediction (GBLUP) to increase training population size of six quality traits (crumb yellowness, water absorption, texture hardness, flour yield, grain protein, flour swelling volume). 1400-1900 bread wheat lines were measured during 2012-2019 in laboratory assays along with NIR records of approximately 27,000 lines. All lines were genotyped with the Infinium™ Wheat Barley 40K BeadChip and imputed using exome sequence data. End-product and NIR phenotypes were genetically correlated (0.5–0.83, except for Flour Swelling Volume 0.19). Prediction accuracies of end-product traits ranged between 0.28–0.64 and increased by 30% through inclusion of NIR predicted phenotypes compared to single trait analysis. There was a high correlation between the magnitude of multi-trait prediction accuracy and genetic correlations between end-product and NIR phenotypes (0.69–0.77). Our forward prediction validation revealed a gradual increase in prediction accuracy when adding more years to the multi-trait model. Overall, we achieved genomic prediction accuracies at a level that enables selection for end-product quality traits early in the breeding cycle.
In Europe, the risk assessment for bees on EU or national level has always focussed on potential impacts on honeybees. During the revision of the European Food Safety Authority (EFSA) bee guidance it was explicitly stated that bumblebees and solitary bees should be considered as well and consequently concerns were raised regarding the representativeness of honeybees for these other bee species. These concerns originate from differences in size as well as differences in behavioural and life history traits of other bee species. In response to this concern, the non‐Apis working group of the International Commission for Plant‐Pollinator Relationships (ICP‐PR) initiated a ring test of a semi‐field tunnel study design using the bumblebee Bombus terrestris. Nine laboratories participated, validating and improving the proposed design over a two‐year period. The intention of the ring test experiments was to develop and if possible establish a test protocol to conduct more standardized semi‐field tests with bumblebees. In this paper, the results of the ring tests are summarized and discussed to give recommendations for a promising experimental design. This article is protected by copyright. All rights reserved.
Arbuscular mycorrhizal fungi perform key soil ecosystem services and due to their symbiotic relationship with plant roots, may be exposed to the plant protection products (PPPs) applied to soils and crops. In 2017, the European Food Safety Authority (EFSA) released a Scientific Opinion addressing the state of the science on risk assessment of PPPs for in-soil organisms recommending the inclusion of AMF ecotoxicological testing in the PPP regulatory process. However, it is not clear how this can be implemented in a tiered, robust and ecologically relevant manner. Through a critical review of current literature, we examine the recommendations made within the EFSA report and the methodologies available to integrate AMF into the PPP risk assessment and provide perspective and commentary on their agronomic and ecological relevance. We conclude that considerable research questions remain to be addressed prior to the inclusion of AMF into the in-soil organism risk assessment, many of which stem from the unique challenges associated with including an obligate symbiont within the PPP risk assessment. Finally, we highlight critical knowledge gaps and the further research required to enable to development of relevant, reliable, and robust scientific tests alongside pragmatic and scientifically sound guidance to ensure that any future risk assessment paradigm is adequately protective of the ecosystem services it aims to preserve. This article is protected by copyright. All rights reserved. © 2022 SETAC.
The green leaf area index (GLAI) has been widely used in agriculture, forestry, and environmental sciences for the analysis and modeling of many biophysical processes of vegetation, including the attenuation of light through the canopy, transpiration, photosynthesis, and carbon and nutrient cycles. Nevertheless, its usefulness is hampered by the uncertainty introduced through the lack of quantitative information on leaf biochemistry, particularly leaf chlorophyll content, in its computation. Thus far, this uncertainty has not been properly recognized nor quantified. The main goal of this study was to quantify the uncertainty of GLAI as used in the estimation of key photosynthetic canopy traits, namely canopy chlorophyll content (CCC). This uncertainty was assessed through the evaluation of the relationship between GLAI and CCC in structurally and functionally contrasting crop species (Zea mays L., Glycine max (L.) Merr., and Oryza sativa L). Results show that for the same GLAI value, CCC varied 2- to 3-fold due mainly to the variability of leaf chlorophyll content. Therefore, we suggest using the absorption coefficient in the red-edge region of the electromagnetic spectrum as an alternative to GLAI for the evaluation of CCC and other important photosynthetic canopy traits. The absorption coefficient in this spectral region is particularly suitable as it has been successfully related with the gross primary productivity of vegetation canopies, the quantum yield of photosynthesis, and is sensitive to the repositioning of chloroplasts within leaf cells in response to water stress.
Physiologically based kinetic (PBK) models facilitate chemical risk assessment by predicting in vivo exposure while reducing the need for animal testing. PBK models for mammals have seen significant progress, which has yet to be achieved for avian systems. Here, we quantitatively compare physiological, metabolic and anatomical characteristics between birds and mammals, with the aim of facilitating bird PBK model development. For some characteristics, there is considerable complementarity between avian and mammalian species with identical values for the following: blood hemoglobin and hemoglobin concentrations per unit erythrocyte volume together with relative weights of the liver, heart, and lungs. There are also systematic differences for some major characteristics between avian and mammalian species including erythrocyte volume, plasma concentrations of albumin, total protein and triglyceride together with liver cell size and relative weights of the kidney, spleen, and ovary. There are also major differences between characteristics between sexually mature and sexually immature female birds. For example, the relative weights of the ovary and oviduct are greater in sexually mature females compared to immature birds as are the plasma concentrations of triglyceride and vitellogenin. Both these sets of differences reflect the genetic “blue print” inherited from ancestral archosaurs such as the production of large eggs with yolk filled oocytes surrounded by egg white proteins, membranes and a calciferous shell together with adaptions for flight in birds or ancestrally in flightless birds.
The heavy use of pesticides in agricultural areas often leads to the contamination of nearby mosquito larvae breeding sites. Exposure to complex mixtures of agrochemicals can affect the insecticide sensitivity of mosquito larvae. Our study objective was to determine whether agrochemical residues in Anopheline larval breeding sites can affect the tolerance of adults to commonly used adulticides. We focussed on Fludora® Fusion, a vector control insecticide formulation combining two insecticides (deltamethrin and clothianidin) with different modes of action. An. gambiae larvae were exposed to a sub-lethal dose of a mixture of agrochemical pesticides used in a highly active agricultural area on the Ivory Coast. Comparative bioassays with Fludora Fusion mixture and its two insecticide components (deltamethrin and clothianidin) were carried out between adult mosquitoes exposed or not to the agrochemicals at the larval stage. A transcriptomic analysis using RNA sequencing was then performed on larvae and adults to study the molecular mechanisms underlying the phenotypic changes observed. Bioassays revealed a significantly increased tolerance of adult females to clothianidin (2.5-fold) and Fludora Fusion mixture (2.2-fold) following larval exposure to agrochemicals. Significantly increased tolerance to deltamethrin was not observed suggesting that insecticide exposure affects the adult efficacy of the Fludora Fusion mixture mainly through mechanisms acting on clothianidin. Transcriptomic analysis revealed the potential of agrochemicals to induce various resistance mechanisms including cuticle proteins, detoxification action and altered insecticide sequestration. These results suggest that although the Fludora Fusion mixture is effective for adult vector control, its efficacy may be locally affected by the ecological context. The present study also suggests that, although the complex interactions between the use of agrochemicals and vector control insecticides are difficult to decipher in the field, they still must be considered in the context of insecticide resistance management programmes.
Prediction of complex traits based on genome-wide marker information is of central importance for both animal and plant breeding. Numerous models have been proposed for the prediction of complex traits and still considerable effort has been given to improve the prediction accuracy of these models, because various genetics factors like additive, dominance and epistasis effects can influence of the prediction accuracy of such models. Recently machine learning (ML) methods have been widely applied for prediction in both animal and plant breeding programs. In this study, we propose a new algorithm for genomic prediction which is based on neural networks, but incorporates classical elements of LASSO. Our new method is able to account for the local epistasis (higher order interaction between the neighboring markers) in the prediction. We compare the prediction accuracy of our new method with the most commonly used prediction methods, such as BayesA, BayesB, Bayesian Lasso (BL), genomic BLUP and Elastic Net (EN) using the heterogenous stock mouse and rice field data sets.
The organotin acaricide fenbutatin oxide (FBO) - an inhibitor of mitochondrial ATP-synthase - has been one of the most extensively used acaricides for the control of spider mites, and is still in use today. Resistance against FBO has evolved in many regions around the world but only few studies have investigated the molecular and genetic mechanisms of resistance to organotin acaricides. Here, we found that FBO resistance is polygenic in two genetically distant, highly resistant strains of the spider mite Tetranychus urticae, MAR-AB and MR-VL. To identify the loci underlying FBO resistance, two independent bulked segregant analysis (BSA) based QTL mapping experiments, BSA MAR-AB and BSA MR-VL, were performed. Two QTLs on chromosome 1 were associated with FBO resistance in each mapping experiment. At the second QTL of BSA MAR-AB, several cytochrome P450 monooxygenase (CYP) genes were located, including CYP392E4, CYP392E6 and CYP392E11, the latter being overexpressed in MAR-AB. Synergism tests further implied a role for CYPs in FBO resistance. Subunit c of mitochondrial ATP-synthase was located near the first QTL of both mapping experiments and harbored a unique V89A mutation enriched in the resistant parents and selected BSA populations. Marker-assisted introgression into a susceptible strain demonstrated a moderate but significant effect of the V89A mutation on toxicity of organotin acaricides. The impact of the mutation on organotin inhibition of ATP synthase was also functionally confirmed by ATPase assays on mitochondrial preparations. To conclude, our findings suggest that FBO resistance in the spider mite T. urticae is a complex interplay between cytochrome P450-mediated detoxification and target-site resistance.
In the current scenario of human-driven climate change, extreme weather events will likely affect agricultural production worldwide. Soilless production systems have recently arisen as a solution to optimize the use of natural resources, such as water and soil, and hence will contribute to reducing the environmental impact of agriculture. However, nutritional imbalance due to adverse environmental factors, such as drought, high temperatures, and salinity, might produce calcium-related physiological disorders during plant growth, such as blossom-end rot (BER) in fruits and tipburn (TB) in leaves, which are a serious problem in crop production. Here, we discuss the different agronomic, physiological, and genetic factors that favor the induction of BER in tomato and TB in lettuce and anticipate the use of an integration of breeding and technological approaches to alleviate nutritional disorders in soilless production systems.
The long-term investment in new approach methodologies (NAMs) within the EU and other parts of the world is beginning to result in an emerging consensus of how to use information from in silico, in vitro and targeted in vivo sources to assess the safety of chemicals. However, this methodology is being adopted very slowly for regulatory purposes. Here, we have developed a framework incorporating in silico, in vitro and in vivo methods designed to meet the requirements of REACH in which both hazard and exposure can be assessed using a tiered approach. The outputs from each tier are classification categories, safe doses, and risk assessments, and progress through the tiers depends on the output from previous tiers. We have exemplified the use of the framework with three examples. The outputs were the same or more conservative than parallel assessments based on conventional studies. The framework allows a transparent and phased introduction of NAMs in chemical safety assessment and enables science-based safety decisions which provide the same level of public health protection using fewer animals, taking less time, and using less financial and expert resource. Furthermore, it would also allow new methods to be incorporated as they develop through continuous selective evolution rather than periodic revolution.
The United States Environmental Protection Agency (EPA) has long required both avian sub-acute dietary and acute oral studies to inform risk assessments for pesticides. Recently, the EPA collaborated with People for the Ethical Treatment of Animals to determine whether the results of the acute oral avian toxicity test or the sub-acute dietary toxicity test consistently generated the greatest risk predictions in EPA tier 1 assessments for pesticides first registered between 1998 and 2017. Their study concluded that in 99% of the cases, risk conclusions were driven by the acute oral study (OPPTS 850.2100, OCSPP 850.2100 or similar) because using these data results in higher risk quotients than sub-acute dietary data. Shortly after publishing these results, the EPA released a formal memorandum providing guidance for waiving the sub-acute dietary study for most pesticides. The EPA will, however, retain the option to require sub-acute dietary studies for pesticides with certain chemical properties. However, as the avian sub-acute dietary study has an exposure regimen that is often more representative of how birds are exposed to pesticides under actual use conditions than does the acute oral study (i.e. as part of a dietary item eaten over the course of a day and not a bolus dose), this study can provide useful context for risk assessment, on a case-by-case basis. Decision criteria are needed to determine a path forward that both minimize vertebrate animal testing and positions the avian sub-acute dietary data as an option for risk refinement. Decision criteria are proposed here with recommendations for refining the design of avian sub-acute dietary studies to ensure that the data generated are optimized to support a science-based acute avian risk assessment, supported by a case study demonstrating when and how sub-acute dietary studies may be used in a higher tier risk assessment. This article is protected by copyright. All rights reserved. © 2022 SETAC.
The risk of honey bee (Apis mellifera L.) exposure to pesticide residues while foraging for nectar and pollen is commonly explored in the context of agroecosystems. However, pesticides are also used in urban and suburban areas for vegetation management, vector control, and the management of ornamental plants in public and private landscapes. The extent to which pesticides pose a health risk to honey bees in these settings remains unclear. We addressed this at a landscape scale by conducting pesticide residue screening analyses on 768 nectar and 862 pollen samples collected monthly over 2 years from honey bee colonies located in urban and suburban areas in eight medium to large cities in California, Florida, Michigan, and Texas (USA). A risk assessment was performed using the US Environmental Protection Agency's BeeREX model whenever an oral toxicity value was available for a compound. Chemical analyses detected 17 pesticides in nectar and 60 in pollen samples during the survey. Approximately 73% of all samples contained no detectable pesticide residues. Although the number of detections varied among the sampled regions, fewer pesticides were detected in nectar than in pollen. Per BeeREX, four insecticides showed a potential acute risk to honey bees: imidacloprid, chlorpyrifos, and esfenvalerate in nectar, and deltamethrin in nectar and pollen. In general, exposure of honey bees to pesticides via nectar and pollen collection was low in urban and suburban areas across the United States, and no seasonal or spatial trends were evident. Our data suggest that honey bees are exposed to fewer pesticides in developed areas than in agricultural ones. Environ Toxicol Chem 2022;00:1-13. © 2021 SETAC
It is important to detect and measure specific proteins expressed in transgenic (GM) plants during development, both for quality and regulatory purposes. Immunological assays are well established for the detection of proteins, having been developed in the 1960’s and are well suited for this purpose. The ability of an antibody to specifically bind to an epitope allows protein assays, unlike those for nucleic acids, to be performed on crude extracts. They can provide accurate quantitative measurement of target proteins in plant tissues, or qualitative measurement and a fast and flexible method of identifying material in the seed and grain supply chain. This chapter explores the creation and characterization of various approaches and methods used to apply antibody and other developing technologies to the assay of proteins in Agricultural Biotechnology.
Intact soil food webs are pivotal to maintain essential soil functions such as carbon recycling, sequestering and biomass production. While the functional role of micro‐ (e.g. bacteria and fungi) and macrofauna (e.g. earthworms) is comparatively well established, the importance of the mesofauna community (e.g. abundance and diversity of Acari and Collembola) in maintaining soil functionality is less clear. We investigated this question in a six‐month field experiment in arable soil by actively manipulating mesofauna abundance and biodiversity through the application of two legacy insecticides (lindane and methamidophos) at sufficiently high doses to reduce mesofauna abundance (well above previously registered application rates; 2.5 and 7.5 kg a.s./ha for lindane, and 0.6 and 3 kg a.s./ha for methamidophos) and measure the impact, on organic matter degradation. Our results show that both insecticides had reduced Collembola and Acari abundances by up to 80% over the 6 months study duration. In addition, we observed less pronounced and more complex changes in mesofauna biodiversity over time. These included insecticide‐dependent temporal fluctuations (both reduction and increase) for different estimates (indices) of local (alpha)‐diversity over time and no lasting impact for most estimates after six months. Even at these exceptionally high field rates Collembola and Acari diversity was observed to generally recover by six months. In contrast, considering organic matter breakdown, we found no evidence for a treatment related effect. These results suggest that organic matter breakdown in arable soils is likely driven by other trophic levels (e.g. microorganisms or earthworms) with only a limited influence of the mesofauna community. We discuss these findings with regard to their implications for our current understanding of soil food web function and future European soil risk assessments. This article is protected by copyright. All rights reserved.
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646 members
Tobias Pamminger
  • Crop Protection
Vandna Kukshal
  • Crop Protection
Jeroen Van Rie
  • Bayer CropScience
Marc Lamshöft
  • Regulatory Science - Environmental Safety
Monheim am Rhein, Germany