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

Genome-Wide Identification, Functional Analysis and Expression Profiling of the Aux/IAA Gene Family in Tomato

Auxin is a central hormone that exerts pleiotropic effects on plant growth including the development of roots, shoots, flowers and fruit. The perception and signaling of the plant hormone auxin rely on the cooperative action of several components,among which auxin/indole-3-acetic acid (Aux/IAA) proteins play a pivotal role. In this study, we identified and comprehensively analyzed the entire Aux/IAA gene family in tomato (Solanum lycopersicum), a reference species for Solanaceae plants, and the model plant for fleshy fruit development. Functional characterization using a dedicated single cell system revealed that tomato Aux/IAA proteins function as active repressors of auxin-dependent gene transcription, with, however, different Aux/IAA members displaying varying levels of repression. Phylogenetic analysis indicated that the Aux/IAA gene family is slightly contracted in tomato compared with Arabidopsis, with a lower representation of non-canonical proteins. Sl-IAA genes display distinctive expression pattern in different tomato organs and tissues, and some of them display differential responses to auxin and ethylene, suggesting that Aux/IAAs may play a role in linking both hormone signaling pathways. The data presented here shed more light on Sl-IAA genes and provides new leads towards the elucidation of their function during plant development and in mediating hormone cross-talk

AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling

Background: DNA replication and transcription are dynamic processes regulating plant development that are dependent on the chromatin accessibility. Proteins belonging to the Agenet/Tudor domain family are known as histone modification "readers" and classified as chromatin remodeling proteins. Histone modifications and chromatin remodeling have profound effects on gene expression as well as on DNA replication, but how these processes are integrated has not been completely elucidated. It is clear that members of the Agenet/Tudor family are important regulators of development playing roles not well known in plants. Methods: Bioinformatics and phylogenetic analyses of the Agenet/Tudor Family domain in the plant kingdom were carried out with sequences from available complete genomes databases. 3D structure predictions of Agenet/Tudor domains were calculated by I-TASSER server. Protein interactions were tested in two-hybrid, GST pulldown, semi-in vivo pulldown and Tandem Affinity Purification assays. Gene function was studied in a T-DNA insertion GABI-line. Results: In the present work we analyzed the family of Agenet/Tudor domain proteins in the plant kingdom and we mapped the organization of this family throughout plant evolution. Furthermore, we characterized a member from Arabidopsis thaliana named AIP1 that harbors Agenet/Tudor and DUF724 domains. AIP1 interacts with ABAP1, a plant regulator of DNA replication licensing and gene transcription, with a plant histone modification "reader" (LHP1) and with non modified histones. AIP1 is expressed in reproductive tissues and its down-regulation delays flower development timing. Also, expression of ABAP1 and LHP1 target genes were repressed in flower buds of plants with reduced levels of AIP1. Conclusions: AIP1 is a novel Agenet/Tudor domain protein in plants that could act as a link between DNA replication, transcription and chromatin remodeling during flower development

African botanical heritage for new crop development

The African continent is rather poor in plant biodiversity when compared to other continents on and around the equator. Nevertheless, lots of useful plant species have been domesticated from Sub-Sahara Africa material. Ethnobotanical research offers the possibility to collect information on use and utility of wild plant species from traditional people often living in or close to a challenging natural environment. This type of information then allows us to find new candidates for domestication and subsequent crop development for income generation and increased food security. The case of Gnetum africanum illustrates the practical implications of developing a lesser-known species, and highlights the institutional problems that go together with niche crop development. The latter are subsequently presented and discussed in extenso, and solutions proposed in a second part of this review text

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

UJI EFEKTIFITAS INFUS DAUN SIRIH (Piper betle L) TERHADAP PERTUMBUHAN Colletotrichum gloeosporioides SECARA IN VITRO

There are various disease attacking plant. According to the cause, plant disease divided into two kinds, biotic (parasite) and abiotic (non-parasite). Biotic disease or parasite is disease caused by fungus, bacterial, virus, nematode, another plant or disturbing plant. Abiotic disease or non- parasite is plant disease caused by mineral poisoned, soil deficiency, polution, un-fit environment. Post harvest disease organisme generally caused by fungus or bacterial. Colletorichum sp is a fungi which caused anthraxnose, developed further, caused a brown color in fruit skin. It would made the skin disintegrated, soft, and change its color into brown. The brown spot became larger and darker, and it became rotten. Betel vine infusion, beside has antiseptic ability and anti-oxydant, it also functioned as fungicide, it caused by eugenol in betel vine from phenol which could be useful as disinfectant. This research aimed to find out the influence of betel vine infusion to the growth of Colletotrichum gloeosporioides and also to find out the infusion concentrate which effective in inhibiting the Colletotrichum gloeosporioide development. Parameter used is the diameter of Colletotrichum gloeosporioide development after betel vine infusion. The research was real experiment used Complete Random Design, It was Randomized Control-Group Posttest Design which consist of 8 treatments. They were concentrate 0%, 75%, 80%, 85%, 90%, 95%, 100% and dithane M45 control with 4 times repeat. Subject in this research was Colletotrichum gloeosporioides from Brawijaya University Farming Laboratory. The research was done at Microbiology Division Biology Laboratory University of Muhammadiyah Malang at May 29th to August 10th 2007. Data analysis used one way variant analysis and Duncan’s Test Phase 1%. The research showed that there was influence of betel vine infusion to the development of Colletotrichum gloeosporioides also optimal concentration in inhibiting the development of Colletotrichum gloeosporioides. From Duncan’s phase 1% analysis, could be found that in each concentration showed different aggregate in every treatment and betel vine infusion at concentrate 75% gave the largest effective influence in inhibiting the development of colletotrichum gloeosporioides since the diameter was the smallest

Multispectral Image Processing for Plants

The development of a machine vision system to monitor plant growth and health is one of three essential steps towards establishing an intelligent system capable of accurately assessing the state of a controlled ecological life support system for long-term space travel. Besides a network of sensors, simulators are needed to predict plant features, and artificial intelligence algorithms are needed to determine the state of a plant based life support system. Multispectral machine vision and image processing can be used to sense plant features, including health and nutritional status