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The promoting effects of both high nitrogen (N) and exogenous gibberellin (GA) supply on regrowth of Lolium perenne have been widely reported. The mobilisation of carbohydrate reserves in response to N is a critical mechanism for promoting plant regrowth. However, our knowledge about GA regulation of carbohydrate metabolism remains limited. Here, we analysed the effects of both N and exogenous GA on the molecular mechanisms controlling perennial ryegrass regrowth and investigated the similarities and differences. Our analyses show that both high N and exogenous GA supply lead to a decline in the accumulation of carbohydrate reserves, but the regulatory mechanisms responsible for this decline varied between N and GA supply. The effects of elevated N were mainly through declining fructan biosynthesis which results in improving photosynthate use efficiency to promote plant regrowth, whereas the application of exogenous GA resulted in an increase in the hydrolytic activities of fructan exohydrolase and invertases capable of cleaving reserved carbohydrates to release energy sources for plant regrowth.

Liquid chromatography coupled to mass spectrometry (LCMS) is widely used in metabolomics due to its sensitivity, reproducibility, speed and versatility. Metabolites are detected as peaks which are characterised by mass-over-charge ratio (m/z) and retention time (rt), and one of the most critical but also the most challenging tasks in metabolomics is to annotate the large number of peaks detected in biological samples. Accurate m/z measurements enable the prediction of molecular formulae which provide clues to the chemical identity of peaks, but often a number of metabolites have identical molecular formulae. Chromatographic behaviour, reflecting the physicochemical properties of metabolites, should also provide structural information. However, the variation in rt between analytical runs, and the complicating factors underlying the observed time shifts, make the use of such information for peak annotation a non-trivial task. To this end, we conducted Quantitative Structure–Retention Relationship (QSRR) modelling between the calculated molecular descriptors (MDs) and the experimental retention times (rts) of 93 authentic compounds analysed using hydrophilic interaction liquid chromatography (HILIC) coupled to high resolution MS. A predictive QSRR model based on Random Forests algorithm outperformed a Multiple Linear Regression based model, and achieved a high correlation between predicted rts and experimental rts (Pearson’s correlation coefficient = 0.97), with mean and median absolute error of 0.52 min and 0.34 min (corresponding to 5.1 and 3.2 % error), respectively. We demonstrate that rt prediction with the precision achieved enables the systematic utilisation of rts for annotating unknown peaks detected in a metabolomics study. The application of the QSRR model with the strategy we outlined enhanced the peak annotation process by reducing the number of false positives resulting from database queries by matching accurate mass alone, and enriching the reference library. The predicted rts were validated using either authentic compounds or ion fragmentation patterns. Electronic supplementary material The online version of this article (doi:10.1007/s11306-014-0727-x) contains supplementary material, which is available to authorized users.

While the in vitro clonal propagation of peat mosses (Sphagnaceae) in bioreactors has been established since the late 1980s, it has never been possible to regenerate Sphagnum species from isolated protoplasts, which is a key step towards the production of closely defined genetically modified clones. The present study describes an efficient protocol for protoplast isolation and regeneration of Sphagnum fallax. Protoplast survival rates of over 50% and regeneration rates of up to 20% were achieved by using excised capitulum buds as starting material and by co-cultivating Sphagnum protoplasts with protoplasts from a chlorophyll-deficient Solanum hybrid clone. Besides the effects of nutrient components and differential osmotic readjustment of the regenerant cell clusters, the interference of unique Sphagnum phenolics, sphagnum acid and hydroxybutenolide, with protoplast isolation efficiency is demonstrated.