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Highlights • The response to nitrogen of 4 winter oat varieties in three field trials was analysed. • A novel high-resolution method was developed to profile metabolite changes. • Conditions that enhance yield do not necessarily result in higher nutritional value. • Choice of variety is of equally high importance as the nitrogen levels applied., Oats (Avena sativa L.) are a healthy food, being high in dietary fibre (e.g. β-glucans), antioxidants, minerals, and vitamins. Understanding the effect of variety and crop management on nutritional quality is important. The response of four oat varieties to increased nitrogen levels was investigated across multiple locations and years with respect to yield, grain quality and metabolites (assessed via GC- and LC- MS). A novel high-resolution UHPLC-PDA-MS/MS method was developed, providing improved metabolite enrichment, resolution, and identification. The combined phenotyping approach revealed that, amino acid levels were increased by nitrogen supplementation, as were total protein and nitrogen containing lipid levels, whereas health-beneficial avenanthramides were decreased. Although nitrogen addition significantly increased grain yield and β-glucan content, supporting increasing the total nitrogen levels recommended within agricultural guidelines, oat varietal choice as well as negative impacts upon health beneficial secondary metabolites and the environmental burdens associated with nitrogen fertilisation, require further consideration.

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 (p0.01), Spring barley (p0.05), and Winter wheat (p0.05), and for nicotinic acid in Spring barley (p0.05). 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.

Senescent sweetening results in the accumulation of reducing sugars in potato tubers following extended periods of storage at moderate temperatures used to avoid the separate condition of cold-induced sweetening. It represents a significant problem for the potato processing industry due to the development of dark fry colour and the accumulation of acrylamide in processed products. Previous studies have implicated oxidative stress in the accumulation of reducing sugars in potato tubers over long term storage. However, in the present analysis we found no evidence for a correlation between oxidative stress as estimated from quantification of hydrogen peroxide, lipid peroxidation or activity of redox enzymes and the accumulation of reducing sugars. On the contrary, transcriptional profiling indicated changes in carbohydrate metabolism were associated with the onset of senescent sweetening and qRT-PCR indicated that reduced abundance of transcripts encoding a plastidial glucose-6-phosphate/phosphate translocator was widely observed during sweetening onset in multiple genotypes. Our data suggest that reduction in the capacity of plastids to import glucose-6-phosphate reduces the capacity for starch resynthesis in the stored tuber thereby shifting the metabolic balance towards starch turnover resulting in reducing sugar accumulation.

Potato (Solanum tuberosum L.) cv. Sante was grown over 2 years under both conventional and organic fertiliser and crop protection regimes. The tuber metabolome was analysed using mass-spectrometry (MS) based approaches, principally liquid chromatography (LC)–MS and gas chromatography (GC)–MS. Data were analysed using Principal Components Analysis (PCA) and Analysis of Variance (ANOVA) to assess any differences between production practices. GC–MS analysis of non-polar metabolites did not detect any statistically significant differences, but GC–MS analysis of polar compounds identified 83 metabolites showing significant differences in the metabolome between the fertiliser treatments. Of the 62 metabolites that were less abundant in tuber samples from organic compared with conventionally fertilised crops, consistent year on year differences were dominated by free amino acids. The effect on free amino acids is associated with the lower nitrogen (N) content of the organically grown potatoes in this instance (50 % lower than for conventional production). LC–MS provided indications that levels of certain glycoalkaloids may be lower under the organic fertiliser regime in one growing season. Differences associated with the crop protection measures used were much less consistent, and relatively small, compared with the fertiliser effects found.

Acrylamide is a neurotoxin and possible carcinogen, and concern has been voiced over human exposure to acrylamide in cooked foods. Processed potato products such as crisps and French fries are often cited as being particularly high in acrylamide. In this manuscript a sub-set of clonal progeny from a specific tetraploid potato breeding population has been assessed for acrylamide forming potential in stored tubers processed into crisps. The clone with the lowest acrylamide content in crisps had both low reducing sugars and asparagine contents. Our data show that, in the segregating breeding population used, both asparagine and reducing sugars levels needed to be taken into account to explain most of the variation in acrylamide and that selection for low levels of both metabolites should be targeted for crop improvement.

Analysis of phloem exudates from the fruit of Cucurbitaceae revealed the presence of several compounds with UV-visible absorption spectra identical to that of l-ascorbic acid. In Cucurbita pepo L. (zucchini), the compounds could be isolated from phloem exudates collected from aerial parts of the plant but were not detected in whole tissue homogenates. The compounds isolated from the phloem exudates of C. pepo fruit were eluted from strong anion exchange resin in the same fraction as l-ascorbic acid and were oxidised by ascorbate oxidase (E.C. 1.10.3.3). The major compound purified from C. pepo fruit exudates demonstrated similar redox properties to l-ascorbic acid and synthetic 6-O-glucosyl-l-ascorbic acid (6-GlcAsA) but differed from those of 2-O-glucosyl-l-ascorbic acid (2-GlcAsA) isolated from the fruit of Lycium barbarum L. Parent and fragment ion masses of the compound were consistent with hexosyl-ascorbate in which the hexose moiety was attached to C5 or C6 of AsA. Acid hydrolysis of the major C. pepo compound resulted in the formation of l-ascorbic acid and glucose. The purified compound yielded a proton NMR spectrum that was almost identical to that of synthetic 6-GlcAsA. A series of l-ascorbic acid conjugates have, therefore, been identified in the phloem of Cucurbitaceae and the most abundant conjugate has been identified as 6-GlcAsA. The potential role of such conjugates in the long-distance transport of l-ascorbic acid is discussed.

Bud break in raspberry (Rubus idaeus L.) is often poor and uneven, with many of the subapical buds remaining in a dormant state. In order to determine the dormancy status of raspberry buds, an empirical measure of bud burst in a growth-permissive environment following exposure to chilling (4 degrees C cold storage) was developed. For cv. Glen Ample, percentage bud burst in intact canes and isolated nodes was recorded after 14 d. Isolated nodes (a measure of endodormancy) achieved 100% bud burst after approximately 1500 h chilling whereas buds on intact plants (combined endo- and paradormancy) required an additional 1000 h chilling. A microarray approach was used to follow changes in gene expression that occurred during dormancy transition. The probes for the microarrays were obtained from endodormant and paradormant raspberry bud cDNA libraries. The expression profiles of 5300 clones from these libraries were subjected to principal component analysis to determine the most significant expression patterns. Sequence analysis of these clones, in many cases, enabled their functional categorization and the development of hypotheses concerning the mechanisms of bud dormancy release. Thus a set of novel candidates for key dormancy-related genes from raspberry buds have been identified. Bud dormancy is fundamental to the study of plant developmental processes and, in addition, its regulation is of significant economic importance to fruit and horticultural industries.

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient ‘genetical genomics’ analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

Blackcurrant (Ribes nigrum L.) is a widely grown commercial crop valued for its high vitamin C (l-ascorbic acid, AsA) content. In the present study, a systematic analysis of the mechanism of fruit AsA accumulation was undertaken. AsA accumulation occurred during fruit expansion and was associated with high in situ biosynthetic capacity via the l-galactose pathway and low rates of turnover. Cessation of AsA accumulation was associated with reduced biosynthesis and increased turnover. Translocation of AsA from photosynthetic or vegetative tissues contributed little to fruit AsA accumulation. Manipulation of substrate availability by defoliation had no effect on fruit AsA concentration but significantly reduced fruit yields. Supply of the AsA precursor l-galactono-1,4-lactone to intact, attached fruit transiently increased fruit AsA concentration which rapidly returned to control levels after removal of the compound. These data suggest strong developmental, metabolic and genetic control of AsA accumulation in blackcurrant fruit and indicate the potential for breeding high AsA cultivars.