Hyperspectral measurements of yellow rust and fusarium head blight in cereal crops: Part 1: Laboratory study

This paper assesses the potential use of a hyperspectral camera for measurement of yellow rust and fusarium head blight in wheat and barley canopy under laboratory conditions. Scanning of crop canopy in trays occurred between anthesis growth stage 60, and hard dough growth stage 87. Visual assessment was made at four levels, namely, at the head, at the flag leaves, at 2nd and 3rd leaves, and at the lower canopy. Partial least squares regression (PLSR) analyses were implemented separately on data captured at four growing stages to establish separate calibration models to predict the percentage coverage of yellow rust and fusarium head blight infection. Results showed that the standard deviation between 500 and 650 nm and the squared difference between 650 and 700 nm wavelengths were found to be significantly different between healthy and infected canopy particularly for yellow rust in both crops, whereas the effect of water-stress was generally found to be unimportant. The PLSR yellow rust models were of good prediction capability for 6 out of 8 growing stages, a very good prediction at early milk stage in wheat and a moderate prediction at the late milk development stage in barley. For fusarium, predictions were very good for seven growing stages and of good performance for anthesis growing stage in wheat, with best performing for the milk development stages. However, the root mean square error of predictions for yellow rust were almost half of those for fusarium, suggesting higher prediction accuracies for yellow rust measurement under laboratory conditions

Species matter when considering landscape effects on carabid distributions

Increasing the abundance and diversity of carabid beetles is a common objective of farm habitat management to deliver sustainable pest control. Carabid spatial distributions in relation to crop areas are important to the delivery of this ecosystem service. We used pitfall count data at distances from edge habitats into crop centres, from farm sites across the UK, to determine the effects of in-field and adjacent environmental features on carabid abundance and diversity. Overall carabid abundance increased towards the crop centre, whilst species richness and diversity decreased. The analyses of carabid abundance based on all the species pooled together strongly reflected the behaviour of the most abundant species. Species preferences varied by crop, soil type, and environmental features. For instance, some species were positively associated with habitats such as margins, while others responded negatively. This contrast in individual species models highlights the limitations on pooled models in elucidating responses. Studies informing farm-habitat design should consider individual species’ preferences for effective enhancement of pest control services. Diverse cropping and landscape heterogeneity at the farm scale can benefit the varied preferences of individual species, help build diverse communities and, potentially increase service resilience and stability over time

Facilitating the elicitation of beliefs for use in Bayesian Belief modelling

Expert opinion is increasingly being used to inform Bayesian Belief Networks, in particular to define the conditional dependencies modelled by the graphical structure. The elicitation of such expert opinion remains a major challenge due to both the quantity of information required and the ability of experts to quantify subjective beliefs effectively. In this work, we introduce a method designed to initialise conditional probability tables based on a small number of simple questions that capture the overall shape of a conditional probability distribution before enabling the expert to refine their results in an efficient way. These methods have been incorporated into a software Application for Conditional probability Elicitation (ACE), freely available at https://github.com/KirstyLHassall/ACE Hassall (2019

The contribution of fibre components to water absorption of wheat grown in the UK

Background and objectives The water absorption (WA) of white wheat flour is a major factor affecting processing quality, and millers, therefore, process their wheat to achieve the required level. Although it is likely that WA is determined by the amounts and compositions of three major grain components, starch, protein, and arabinoxylan, the contribution of the latter is not agreed and not recognized in the widely used Farrand equation. Findings We have measured a range of parameters related to fiber amount and composition and tested the ability of these to improve the prediction of WA using a modified Farrand equation. The addition of a range of single fiber traits improved the prediction of WA from a baseline of 82.98% to a maximum of 86.78%, but inclusion of all fiber traits as PCs resulted in a further improvement to 90%. Inclusion of the PCs also accounted for variation in WA between harvest years. The greatest improvement from inclusion of a single trait was observed with β‐glucan, the inclusion of arabinogalactan peptide (AGP) also resulted in improved prediction of WA. Conclusions The study shows that fiber components contribute to variation in WA, including differences between harvest years, but that β‐glucan and AGP have similar or greater impacts than AX. Significance and novelty The study dissects the contributions of AX amount and composition to WA and demonstrates a contribution of b‐glucan for the first time

Spectral soil analysis for fertilizer recommendations by coupling with QUEFTS for maize in East Africa: A sensitivity analysis

Laboratory analysis of soil properties is prohibitively expensive and difficult to scale across the soils in sub-Saharan Africa. This results in a lack of soil-specific fertilizer recommendations, where recommendation can only be provided at a regional scale. This study aims to assess the feasibility of using spectral soil analysis to provide soil-specific fertilizer recommendations. Using a range of spectrometers [NeoSpectra Saucer (NIR), FieldSpec 4 (vis-NIR) with contact probe or mug light interface, FTIR Bruker Tensor 27 (MIR)], 346 archived soil samples (0–20 cm) with known soil chemical properties collected from Ethiopia, Kenya and Tanzania were scanned. Partial least square regression (PLSR) was used to develop prediction models for selected soil properties including pH, soil organic carbon (SOC), total nitrogen, Olsen P, and exchangeable K. These predicted properties, and associated uncertainty, were used to derive fertilizer recommendations for maize using the Quantitative Evaluation of the Fertility of Tropical Soils (QUEFTS) model parameters for sub-Saharan Africa. Most soil properties (pH, SOC, total nitrogen, and exchangeable K) were well predicted (Concordance Correlation Coefficient values between 0.88 and 0.96 and Ratio of Performance to Interquartile values between 1.4 and 5.9) by all the spectrometers but there were performance variations between soil properties and spectrometers. Use of the predicted soil data for the development of fertilizer recommendations gave promising results when compared to the recommendations obtained with the conventional soil analysis. For example, the least performing NeoSpectra Saucer over/under-estimated up to 8 and 24 kg ha-1N and P, respectively, though there was insignificant variation in estimation of P fertilizer among spectrometers. We conclude that spectral technology can be used to determine major soil properties with satisfactory precision, sufficient for specific fertilizer decision making in East Africa, possibly even with portable equipment in the field

Changes in organic carbon to clay ratios in different soils and land uses in England and Wales over time

Realistic targets for soil organic carbon (SOC) concentrations are needed, accounting for differences between soils and land uses. We assess the use of SOC/clay ratio for this purpose by comparing changes over time in (a) the National Soil Inventory of England and Wales, first sampled in 1978–1983 and resampled in 1994–2003, and (b) two long-term experiments under ley-arable rotations on contrasting soils in the East of England. The results showed that normalising for clay concentration provides a more meaningful separation between land uses than changes in SOC alone. Almost half of arable soils in the NSI had degraded SOC/clay ratios ( 1/8, respectively. Given the wide range of soils and land uses across England and Wales in the datasets used to test these targets, they should apply across similar temperate regions globally, and at national to sub-regional scales.Biotechnology and Biological Sciences Research Council (BBSRC): BBS/E/C/000I0310 and BBS/E/C/000 J0300. Lawes Agricultural Trus

N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway

The N-end rule pathway of targeted protein degradation is an important regulator of diverse processes in plants but detailed knowledge regarding its influence on the proteome is lacking.To investigate the impact of the Arg/N-end rule pathway on the proteome of etiolated seedlings, we used terminal amine isotopic labelling of substrates with tandem mass tags (TMT-TAILS) for relative quantification of N-terminal peptides in prt6, an Arabidopsis thaliana N-end rule mutant lacking the E3 ligase PROTEOLYSIS6 (PRT6).TMT-TAILS identified over 4000 unique N-terminal peptides representing c. 2000 protein groups. Forty-five protein groups exhibited significantly increased N-terminal peptide abundance in prt6 seedlings, including cruciferins, major seed storage proteins, which were regulated by Group VII Ethylene Response Factor (ERFVII) transcription factors, known substrates of PRT6. Mobilisation of endosperm a-cruciferin was delayed in prt6 seedlings. N-termini of several proteases were downregulated in prt6, including RD21A. RD21A transcript, protein and activity levels were downregulated in a largely ERFVII-dependent manner. By contrast, cathepsin B3 protein and activity were upregulated by ERFVIIs independent of transcript. We propose that the PRT6 branch of the pathway regulates protease activities in a complex manner and optimises storage reserve mobilisation in the transition from seed to seedling via control of ERFVII action

Linking soil adsorption-desorption characteristics with grain zinc concentrations and uptake by teff, wheat and maize in different landscape positions in Ethiopia

AimZinc deficiencies are widespread in many soils, limiting crop growth and contributing to Zn deficiencies in human diets. This study aimed at understanding soil factors influencing grain Zn concentrations and uptake of crops grown in different landscape positions in West Amhara, Ethiopia.MethodsOn-farm experiments were conducted in three landscape positions, with five farmers’ fields as replicates in each landscape position, and at three sites. Available Zn from the soil (Mehlich 3, M3, Zn) and applied fertilizer (NET_FERT Zn, estimated based on adsorption/desorption characteristics and applied Zn) were related to the actual grain Zn concentration and uptake of teff, wheat, and maize. Zinc fertilizer treatments tested were Zn applied at planting (basal), basal plus side dressing and a control with no Zn applied.ResultsZn treatments had a significant effect on grain Zn concentration (increase by up to 10%) but the effect on grain yield was variable. Differences in crop Zn concentrations along the landscape positions were observed but not at all sites and crops. Trial results showed that soils with higher soil pH and Soil Organic Carbon (SOC) (typical of footslope landscape positions) tended to adsorb more applied Zn (reduce NET_FERT Zn) than soils with lower soil pH and SOC (typical of upslope landscape positions). Zn availability indicators (M3, NET_FERT Zn, clay%) explained 14-52% of the observed variation in grain Zn concentrations, whereas macronutrient indicators (Total N, exchangeable K) together with M3 Zn were better in predicting grain Zn uptake (16 to 32% explained variability). Maize had the lowest grain Zn concentrations but the highest grain Zn uptake due to high yields.ConclusionWe found that the sum of indigenous and fertilizer Zn significantly affects grain Zn loadings of cereals and that the associated soil parameters differ between and within landscape positions. Therefore, knowledge of soil properties and crop characteristics helps to understand where agronomic biofortification can be effective

Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pre-treatments reduced this damage. Ethylene pre-treatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival

The contribution of spatial mass effects to plant diversity in arable fields

International audienceIn arable fields, plant species richness consistently increases at field edges. This potentially makes the field edge an important habitat for the conservation of the ruderal arable flora (or 'weeds') and the invertebrates and birds it supports. Increased diversity and abundance of weeds in crop edges could be owing to either a reduction in agricultural inputs towards the field edge and/or spatial mass effects associated with dispersal from the surrounding landscape. We contend that the diversity of weed species in an arable field is a combination of resident species, that can persist under the intense selection pressure of regular cultivation and agrochemical inputs (typically more ruderal species), and transient species that rely on regular dispersal from neighbouring habitats (characterised by a more 'competitive' ecological strategy). We analysed a large dataset of conventionally managed arable fields in the UK to study the effect of the immediate landscape on in-field plant diversity and abundance and to quantify the contribution of spatial mass effects to plant diversity in arable fields in the context of the ecological strategy of the resulting community. We demonstrated that the decline in diversity with distance into an arable field is highly dependent on the immediate landscape, indicating the important role of spatial mass effects in explaining the increased species richness at field edges in conventionally managed fields. We observed an increase in the proportion of typical arable weeds away from the field edge towards the centre. This increase was dependent on the immediate landscape and was associated with a higher proportion of more competitive species, with a lower fidelity to arable habitats, at the field edge. Synthesis and applications. Conserving the ruderal arable plant community, and the invertebrates and birds that use it as a resource, in conventionally managed arable fields typically relies on the targeted reduction of fertilisers and herbicides in so-called 'conservation headlands'. The success of these options will depend on the neighbouring habitat and boundary. They should be placed along margins where the potential for ingress of competitive species, that may become dominant in the absence of herbicides, is limited. This will enhance ecosystem services delivered by the ruderal flora and reduce the risk of competitive species occurring in the crop