The Plant Ontology facilitates comparisons of plant development stages across species

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution

Dynamics of male meiotic recombination frequency during plant development using Fluorescent Tagged Lines in Arabidopsis thaliana

Meiotic homologous recombination plays a central role in creating genetic variability, making it an essential biological process relevant to evolution and crop breeding. In this study, we used pollenspecific fluorescent tagged lines (FTLs) to measure male meiotic recombination frequency during the development of Arabidopsis thaliana. Interestingly, a subset of pollen grains consistently shows loss of fluorescence expression in tested lines. Using nine independent FTL intervals, the spatio-temporal dynamics of male recombination frequency was assessed during plant development, considering both shoot type and plant age as independent parameters. In most genomic intervals assayed, male meiotic recombination frequency is highly consistent during plant development, showing no significant change between different shoot types and during plant aging. However, in some genomic regions, such as I1a and I5a, a small but significant effect of either developmental position or plant age were observed, indicating that the meiotic CO frequency in those intervals varies during plant development. Furthermore, from an overall view of all nine genomic intervals assayed, both primary and tertiary shoots show a similar dynamics of increasing recombination frequency during development, while secondary and lateral shoots remain highly stable. Our results provide new insights in the dynamics of male meiotic recombination frequency during plant development

From A. rhizogenes RolD to Plant P5CS: Exploiting Proline to Control Plant Development

The capability of the soil bacterium Agrobacterium rhizogenes to reprogram plant development and induce adventitious hairy roots relies on the expression of a few root-inducing genes (rol A, B, C and D), which can be transferred from large virulence plasmids into the genome of susceptible plant cells. Contrary to rolA, B and C, which are present in all the virulent strains of A. rhizogenes and control hairy root formation by affecting auxin and cytokinin signalling, rolD appeared non-essential and not associated with plant hormones. Its role remained elusive until it was discovered that it codes for a proline synthesis enzyme. The finding that, in addition to its role in protein synthesis and stress adaptation, proline is also involved in hairy roots induction, disclosed a novel role for this amino acid in plant development. Indeed, from this initial finding, proline was shown to be critically involved in a number of developmental processes, such as floral transition, embryo development, pollen fertility and root elongation. In this review, we present a historical survey on the rol genes focusing on the role of rolD and proline in plant development

3D modelling of branching in plants

Shoot branching is a key determinant of overall aboveground plant form. During plant development, the number of branches formed strongly influences the amount of light absorbed by the plant, and thus the plant’s competitive strength in terms of light capture in relation to neighbouring plants. Branching is regulated by multiple internal factors which are modulated by different environmental signals. A key environmental signal in the context of a plant population is a low red / far-red intensity ratio (R:FR) of the light reflected by neighbouring plants. For instance, low R:FR results in suppression of branching in favour of elongation growth, which is a key aspect of shade avoidance. Shade avoidance enables plants to anticipate future competition by preventing being shaded, rather than to react to prevailing shade conditions. Internally, branching is regulated by a finely tuned plant hormone network. The interactions within this network are modified by environmental cues such as R:FR which is perceived by specific photoreceptors. Combined, internal and external signals enable regulation of branch formation under the influence of environmental conditions. The different aspects of branching control act at different levels of biological organization (organ, whole plant, plant community). These aspects can be integrated in one modelling approach, called functional-structural plant modelling (FSPM), explicitly considering spatial 3D plant development. An FSP model typically contains detailed information at any moment in development of the plant on the number, size, location and orientation of all organs that make up the plant. In FSP models, physiological and physical processes occur within the plant (e.g. photosynthesis and transport of assimilates), and interaction with the environment occurs at the interface of organ and environment (e.g. light absorption by a leaf). Explicit simulation of absorption and scattering of light at the level of the plant organ is an important aspect of FSPM. In combination with dedicated experiments, this modelling tool can be used to analyse the response of plants to (imminent) competition, simulate the competitive advantage of shade avoidance for plants of different architecture, and predict plant form in various light environments. To assess the effect of plant population density through R:FR signalling on tillering (branching) in spring wheat (Triticum aestivum L.), an FSPM study was conducted (Figure 1). A simple descriptive relationship was used to link R:FR as perceived by the plant to extension growth of tiller buds and probability of a bud to form a tiller. A further study included a complete sub-model of branching regulation, aiming at simulating branching as an emergent property in Arabidopsis (Arabidopsis thaliana) under the influence of R:FR. These and other studies show that FSPM is a promising tool to simulate aspects of plant development, such as branching, under the influence of environmental factors. In close combination with dedicated experiments, FSPM can shape our ideas of the mechanisms controlling plant development, can integrate existing knowledge on plant development, and can predict plant development in untested conditions

The Development of Polyamines throughout Brassica rapa over its Lifecycle

Polyamines are naturally produced chemicals in plants involved in growth, development and stress response. The primary objective of my study is to create a profile of changes in the entire life of the plant, in every organ at all stages of development from seed germination to seed formation. We have analyzed polyamines putrescine, spermidine and spermine in all parts of Brassica rapa, a small, rapid growing plant. Parallel to the polyamines, we will also study changes in the activities of the polyamine biosynthetic enzymes and the expression of their genes in different organs at different times. In the next stage of the study, the expression of selected genes will be inhibited by RNAi constructs, allowing further analysis of their role in growth and stress response. Because polyamines play are important in development and lifecycle of plants, altering their presence may be useful in altering plant growth patterns, such as in seasonal crops

COBRA: a new European research project for organic plant breeding

Development of organic plant breeding and seed production will have a valuable impact on organic plant production. Breeding of plant material adapted for organic agriculture is crucial in order to cope with stresses such as climate change, weeds and seed borne diseases. Conventional varieties may not meet the specific needs of organic agriculture. The use of plant material adapted to conditions of organic agriculture will have a positive effect on the productivity and sustainability of organic crop production

Impact of Biotechnology on Plant Breeding

The application of modern biotechnology to plant breeding is considered to be more efficient and quicker than conventional breeding techniques in the development of new and more resilient crop varieties. To test the impact that biotechnology is having on a industrial plant breeding activities, we relate firm level Plant Variety Protection Certificate (PVPC) applications to corresponding expenditure on research and development (R&D), agricultural biotechnology patents applications, field trials of genetically modified crops, firm structure, as well as industry specific characteristics. Regression results indicate agbiotech activities are directly related to PVP applications, hence the creation of new plant varieties.Crop Production/Industries, Research and Development/Tech Change/Emerging Technologies,

Development of a food antioxidant complex of plant origin

Розроблено антиоксидантний комплекс для використання в оліях, жирах та продуктах харчування, що потребують збагачення біологічно активними речовинами рослинного походження. Досліджено раціональні умови одержан- ня водно-етанольних екстрактів із рослинної сировини: кори дубу, листя евкаліпту та листя зеленого чаю. Отримано антиоксидант, що здатен запобігати окисненню жировмісних продуктів, зберігаючи їх високу поживну цінність. Антиоксидантні речовини природного походження дозволять створювати збалансовані за складом продукти з підвищеним строком придатності із збереженням початкового природного складу та структури компонентів. Також розроблений антиоксидант є додатковим джерелом речовин, що допомагають організму боротися з вільними радикалами, що утворюються внаслідок фізичних та психічних навантажень. До складу антиоксидантів рослинного походжен- ня входять антиоксидантні вітаміни (токофероли та аскорбінова кислота), рослинні феноли та тиолові антиоксиданти (глутатіон, ліпоєва кислота), мікроелементи. Ці складові беруть участь у процесах гальмування окиснення. Також до таких антиоксидантів входять селен, цинк, фолати та інші речовини. Для планування експериментальних досліджень для кожного виду рослинної сировини стосовно антиоксидантної активності виділених речовин використано повний факторний експеримент першого порядку. Виявлено синергізм дії антиоксидантних речовин при одночасному використанні екстрактів з кори дубу, листя евкаліпта, листя зеленого чаю. Розроблений антиоксидант підвищує період індукції модельної речовини (олії соняшникової) у 2,7 рази, тоді як під час використання антиоксидантів окремо з кожного виду рослин найкращий показник збільшення періоду індукції склав 1,9. Отже, розроблений антиоксидант здатен сприяти збереженню якості і безпечності жировмісних продуктів харчування. Використання даного антиоксиданту може бути запропоновано для продуктів харчування людей, що потребують додаткового введення антиоксидантів та біологічно активних речовин до раціону харчування. Зокрема, це важливо для спортсменів

Using a fuzzy inference system to control a pumped storage hydro plant

The paper discusses the development of a fuzzy inference system (FIS) based governor control for a pumped storage hydroelectric plant. The First Hydro Company's plant at Dinorwig in North Wales is the largest of its kind in Europe and is mainly used for frequency control of the UK electrical grid. In previous investigations, a detailed model of the plant was developed using MATLAB(R)/SIMULINK(R) and this is now being used to compare FIS governor operation with the proportional-integral-derivative (PID) controller currently used. The paper describes the development of an FIS governor, and shows that its response to a step increase in load is superior to the PID under certain conditions of load. The paper proceeds to discuss the implications of these results in view of the possible practical application of an FIS governor at the Dinorwig plant

Cytokinin response factors regulate PIN-FORMED auxin transporters

Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development