Colin James Alexander

Objective: The objective of this study was to investigate the genetic control of polyphenol accumulation in red raspberry (Rubus idaeus L). Methods: The levels of total anthocyanins and 37 individual polyphenol metabolites were measured over three years in a raspberry biparental mapping population. Quantitative trait loci (QTLs) for these traits were mapped onto a high-density SNP linkage map. Results: At least one QTL was detected for each trait, with good consistency among the years. On four linkage groups (LG), there were major QTLs affecting several metabolites. On LG1, a QTL had large effects on anthocyanins and flavonols containing a rutinoside or rhamnose group. On LG4, a QTL had large effects on several flavonols and on LG5 and LG6 QTLs had large effects on ellagic acid derivatives. Smaller QTLs were found on LG2 and LG3. Conclusion: The identification of robust QTLs for key polyphenols in raspberry provides great potential for marker-assisted breeding for improved levels of potentially health beneficial components.

Plants are a reservoir of high-value molecules with underexplored biomedical applications. With the aim of identifying novel health-promoting attributes in underexplored natural sources, we scrutinized the diversity of (poly)phenols present within the berries of selected germplasm from cultivated, wild, and underutilized Rubus species. Our strategy combined the application of metabolomics, statistical analysis, and evaluation of (poly)phenols’ bioactivity using a yeast-based discovery platform. We identified species as sources of (poly)phenols interfering with pathological processes associated with redox-related diseases, particularly, amyotrophic lateral sclerosis, cancer, and inflammation. In silico prediction of putative bioactives suggested cyanidin–hexoside as an anti-inflammatory molecule which was validated in yeast and mammalian cells. Moreover, cellular assays revealed that the cyanidin moiety was responsible for the anti-inflammatory properties of cyanidin–hexoside. Our findings unveiled novel (poly)phenolic bioactivities and illustrated the power of our integrative approach for the identification of dietary (poly)phenols with potential biomedical applications.

The intensification of arable production since the 1950s has resulted in increases in yield but only at significant cost to the environment, raising serious concerns about long-term consequences for the sustainability of food production systems. While a range of policies and practices have been put in place to mitigate negative effects in terms of pollution, soil degradation and loss of biodiversity, their efficacy has not been properly quantified. Whole-system effects of management change are rarely studied and so trade-offs and conflicts between different components of the agricultural system are poorly understood. A long-term field platform was therefore established in which conventional arable management was compared with a low-input, integrated cropping system designed with the goal to maintain yields whilst enhancing biodiversity and minimizing environmental impact. Over the first rotation, only winter wheat yielded less under integrated management; yield was maintained for the remaining five crops (spring and winter barley, winter oilseed rape, potato and field beans), suggesting a negligible impact on economic returns. Beneficial broad-leaved weeds were significantly more abundant in the integrated management system across all crops whereas grass weeds showed no overall response to treatment. Soil carbon, pH and soil concentrations of the main plant growth-limiting macronutrients were enhanced under the integrated management system. The integrated system was therefore successful in meeting the goals to enhance biodiversity and reduce environmental impact without jeopardizing crop yields.

Denitrification is a key process responsible for the majority of soil nitrous oxide (N₂O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH adjusted soils (ranging from pH 4.2 to pH 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH whilst cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.

The reduction of the environmental footprint of crop production without compromising crop yield and their nutritional value is a key goal for improving the sustainability of agriculture. In 2009, the Balruddery Farm Platform was established at The James Hutton Institute as a long-term experimental platform for cross-disciplinary research of crops using two agricultural ecosystems. Crops representative of UK agriculture were grown under conventional and integrated management systems and analyzed for their water-soluble vitamin content. Integrated management, when compared with the conventional system, had only minor effects on water-soluble vitamin content, where significantly higher differences were seen for the conventional management practice on the levels of thiamine in field beans (p < 0.01), Spring barley (p < 0.05), and Winter wheat (p < 0.05), and for nicotinic acid in Spring barley (p < 0.05). However, for all crops, variety and year differences were of greater importance. These results indicate that the integrated management system described in this study does not significantly affect the water-soluble vitamin content of the crops analyzed here.

Introduction: Collection of volatiles from plant roots poses technical challenges due to difficulties accessing the soil environment without damaging the roots.Objectives: To validate a new non‐invasive method for passive sampling of root volatiles in situ, from plants grown under field conditions, using solid phase micro‐extraction (SPME).Methods: SPME fibres were inserted into perforated polytetrafluoroethene (PTFE) tubes positioned in the soil next to broccoli plants for collection of root volatiles pre‐ and post‐infestation with Delia radicum larvae. After sample analysis by gas chromatography‐mass spectrometry (GC‐MS), principal component analysis (PCA) was applied to determine differences in the profiles of volatiles between samples.Results: GC‐MS analysis revealed that this method can detect temporal changes in root volatiles emitted before and after Delia radicum damage. PCA showed that samples collected pre‐ and post‐infestation were compositionally different due to the presence of root volatiles induced by D. radicum feeding. Sulphur containing compounds, in particular, accounted for the differences observed. Root volatiles emission patterns post‐infestation are thought to follow the feeding and developmental progress of larvae.Conclusion: This study shows that volatiles released by broccoli roots can be collected in situ using SPME fibres within perforated PTFE tubes under field conditions. Plants damaged by Delia radicum larvae could be distinguished from plants sampled pre‐infestation and soil controls on the basis of larval feeding‐induced sulphur‐containing volatiles. These results show that this new method is a powerful tool for non‐invasive sampling of root volatiles below‐ground. Copyright © 2016 John Wiley & Sons, Ltd.

Introduction: Research on plant root chemical ecology has benefited greatly from recent developments in analytical chemistry. Numerous reports document techniques for sampling root volatiles, although only a limited number describe in situ collection.Objectives: To demonstrate a new method for non‐invasive in situ passive sampling using solid phase micro extraction (SPME), from the immediate vicinity of growing roots.Methods: SPME fibres inserted into polyfluorotetrafluoroethylene (PTFE) sampling tubes located in situ which were either perforated, covered with stainless steel mesh or with microporous PTFE tubing, were used for non‐invasive sub‐surface sampling of root volatiles from glasshouse‐grown broccoli. Sampling methods were compared with above surface headspace collection using Tenax TA. The roots were either mechanically damaged or infested with Delia radicum larvae. Principal component analysis (PCA) was used to investigate the effect of damage on the composition of volatiles released by broccoli roots.Results: Analyses by gas chromatography‐mass spectrometry (GC‐MS) with SPME and automated thermal desorption (ATD) confirmed that sulphur compounds, showing characteristic temporal emission patterns, were the principal volatiles released by roots following insect larval damage. Use of SPME with in situ perforated PTFE sampling tubes was the most robust method for out‐of‐lab sampling.Conclusion: This study describes a new method for non‐invasive passive sampling of volatiles in situ from intact and insect damaged roots using SPME. The method is highly suitable for remote sampling and has potential for wide application in chemical ecology/root/soil research. Copyright © 2016 John Wiley & Sons, Ltd.