Critical Reviews in Plant Sciences

Published by Taylor & Francis
Online ISSN: 1549-7836
Print ISSN: 0735-2689
Publications
Different input signals create their own characteristic Ca2+ fingerprints. These fingerprints are distinguished by frequency, amplitude, duration, and number of Ca2+ oscillations. Ca(2+)-binding proteins and protein kinases decode these complex Ca2+ fingerprints through conformational coupling and covalent modifications of proteins. This decoding of signals can lead to a physiological response with or without changes in gene expression. In plants, Ca(2+)-dependent protein kinases and Ca2+/calmodulin-dependent protein kinases are involved in decoding Ca2+ signals into phosphorylation signals. This review summarizes the elements of conformational coupling and molecular mechanisms of regulation of the two groups of protein kinases by Ca2+ and Ca2+/calmodulin in plants.
 
A revolution is occurring in our thinking about growth and development as we realize the importance of calcium ions in mediating many different processes in plants. During the last several years, there has been a dramatic unfolding of information suggesting that calcium is not simply a macronutrient. It has been found to have major metabolic and developmental control in plants. It is becoming increasingly evident that calcium ions are important intracellular messengers in plants. Recent reports indicate that calcium is involved in coupling primary stimuli such as hormones, light, and gravity to response. Since the discovery of calmo‐dulin, it has become clear that the calcium messages are often relayed by this ubiquitous calcium‐binding protein. Polarity, secretion, growth, cell division, ripening and senescence, and even gene expression are influenced by calcium and calmodulin. This review focuses on recent developments involving calcium and calmodulin as they relate to plant growth and development.
 
An irradiation with visible light can alter the gravitropic responsiveness of shoots and roots. This indicates that light must affect some biochemical process in plant cells which is the same as, or importantly influences, a biochemical process that regulates gravitropism. In many cases, the light receptor for this effect is the pigment phytochrome, which initiates a variety of important photomorphogenic responses in plants. Recent results suggest that both gravistimulation and phytochrome photoactivation result in altered Ca transport into and out of the affected cells. This article reviews the evidence that these Ca fluxes may be the common biochemical process which modulates both gravitropism and photomorphogenesis.
 
Environmental and hormonal signals control diverse physiological processes in plants. The mechanisms by which plant cells perceive and transduce these signals are poorly understood. Understanding biochemical and molecular events involved in signal transduction pathways has become one of the most active areas of plant research. Research during the last 15 years has established that Ca2+ acts as a messenger in transducing external signals. The evidence in support of Ca2+ as a messenger is unequivocal and fulfills all the requirements of a messenger. The role of Ca2+ becomes even more important because it is the only messenger known so far in plants. Since our last review on the Ca2+ messenger system in 1987, there has been tremendous progress in elucidating various aspects of Ca(2+) -signaling pathways in plants. These include demonstration of signal-induced changes in cytosolic Ca2+, calmodulin and calmodulin-like proteins, identification of different Ca2+ channels, characterization of Ca(2+) -dependent protein kinases (CDPKs) both at the biochemical and molecular levels, evidence for the presence of calmodulin-dependent protein kinases, and increased evidence in support of the role of inositol phospholipids in the Ca(2+) -signaling system. Despite the progress in Ca2+ research in plants, it is still in its infancy and much more needs to be done to understand the precise mechanisms by which Ca2+ regulates a wide variety of physiological processes. The purpose of this review is to summarize some of these recent developments in Ca2+ research as it relates to signal transduction in plants.
 
Structural similarity of DNA polymerases 
DNA synthesis fidelity 
Different modes of synthesis during replication and repair 
The primary role of DNA polymerases is to accurately and efficiently replicate the genome in order to ensure the maintenance of the genetic information and its faithful transmission through generations. This is not a simple task considering the size of the genome and its constant exposure to endogenous and environmental DNA damaging agents. Thus, a number of DNA repair pathways operate in cells to protect the integrity of the genome. In addition to their role in replication, DNA polymerases play a central role in most of these pathways. Given the multitude and the complexity of DNA transactions that depend on DNA polymerase activity, it is not surprising that cells in all organisms contain multiple highly specialized DNA polymerases, the majority of which have only recently been discovered. Five DNA polymerases are now recognized in Escherichia coli, 8 in Saccharomyces cerevisiae, and at least 15 in humans. While polymerases in bacteria, yeast and mammalian cells have been extensively studied much less is known about their counterparts in plants. For example, the plant model organism Arabidopsis thaliana is thought to contain 12 DNA polymerases, whose functions are mostly unknown. Here we review the properties and functions of DNA polymerases focusing on yeast and mammalian cells but paying special attention to the plant enzymes and the special circumstances of replication and repair in plant cells.
 
Gravitropism is directed growth of a plant or plant organ in response to gravity and can be divided into the following temporal sequence: perception, transduction, and response. This article is a review of the research on the early events of gravitropism (i.e., phenomena associated with the perception and transduction phases). The two major hypotheses for graviperception are the protoplast-pressure and starch-statolith models. While most researchers support the concept of statoliths, there are suggestions that plants have multiple mechanisms of perception. Evidence supports the hypothesis that the actin cytoskeleton is involved in graviperception/transduction, but the details of these mechanisms remain elusive. A number of recent developments, such as increased use of the molecular genetic approach, magnetophoresis, and laser ablation, have facilitated research in graviperception and have allowed for refinement of the current models. In addition, the entire continuum of acceleration forces from hypo- to hyper-gravity have been useful in studying perception mechanisms. Future interdisciplinary molecular approaches and the availability of sophisticated laboratories on the International Space Station should help to develop new insights into mechanisms of gravitropism in plants.
 
Silicon (Si), aluminum (Al), and iron (Fe) are the three most abundant minerals in soil; however, their effects on plants differ because they are beneficial, toxic, and essential to plant growth, respectively. High accumulation of silicon in the shoots helps some plants to overcome a range of biotic and abiotic stresses. However, plants vary in their ability to take up Si from the soil and load it into the xylem and so the accumulation of silicon varies greatly between plant species. Aluminum toxicity is characterized by a rapid inhibition of root elongation but some species and even genotypes within species can tolerate Al toxicity better than others. While the mechanisms controlling this tolerance in most of the more resistant species are poorly understood, some plants are able to detoxify Al externally and/or internally by complexation with ligands or by pH changes in the rhizosphere. Iron is taken up from the soil by two efficient mechanisms called Strategy I and Strategy II, which operate in distinct phylogenic groups. Strategy I plants increase soil Fe solubility by releasing protons and reductants/chelators, such as organic acids and phenolics, into the rhizosphere, while Strategy II plants are characterized by the secretion of ferric chelating substances (phytosiderophores) coupled with a specific Fe 3+ : chelate uptake system. In this review, the molecular mechanisms underlying root response to Si, Al, and Fe are described.
 
Rapid population growth in the dry climate regions, arable land scarcity, and irrigation expansion limitations direct our interest to possibilities of yield increase in rainfed agriculture. Literature, however, indicates large differences between actual and potential yields, and between yields on farmers' fields and research stations. This article focuses on the determinants of these yield gaps and the windows of opportunity for yield increase on the farmer's field together with the agricultural challenges involved. The study links the conventional approach to estimate crop water requirements and dry spell effects on biomass production to a conceptual Green Water Crop Model. This model addresses the effects on crop yields of the sequential diversions of infiltrating rainfall (rainwater partitioning into runoff, plant available soil water, and deep percolation) and of different relations between nonproductive evaporation flow and productive transpiration flow, defined together as green water flow. Also, the effects of droughts and dry spells are analyzed. The model is used to demonstrate typical situations for semiarid and dry subhumid conditions (lengths of growing period (LGP) of 90 and 179 days, respectively) for maize ( Zea mays (L.)) under on-station agricultural conditions. Based on detailed water flow analysis in a 3-year on-farm case study in the Sahel on pearl millet ( Pennisetum glaucum (L.) Br.), the model is used to clarify the large scope for improved yield levels, achievable through land and water management securing that runoff losses and deep percolation are reduced and nonproductive evaporation losses minimized. The analysis indicates that poor rainwater partitioning and low plant water uptake capacity alone reduces estimated on-farm grain yields to 1/10th of the potential yields. This suggests that lack of water per se not necessarily is the primary constraint to crop growth even in drought prone areas of sub-Saharan Africa. The conclusion is that even a doubling of crop yields would be agro-hydrologically possible with relatively small manipulations of rainwater partitioning in the water balance.
 
Many plants contain carbohydrate-binding proteins that are commonly designated as lectins, agglutinins, or hemagglutinins. Due to the obvious differences in molecular structure, biochemical properties, and carbohydrate-binding specificity, plant lectins are usually considered a complex and heterogeneous group of proteins. Recent advances in the structural analysis of lectins and molecular cloning of lectin genes enable subdividision of plant lectins in a limited number of subgroups of structurally and evolutionary related proteins. Four major lectin families, namely, the legume lectins, the chitin-binding lectins composed of hevein domains, the type 2 ribosome-inactivating proteins, and the monocot mannose-binding lectins comprise the majority of all currently known plant lectins. In addition to these four large families the jacalin-related lectins, the amaranthin family, and the Cucurbitaceae phloem lectins are now recognized as separate subgroups. Each of the above-mentioned lectin families is discussed in detail. The description of the individual lectin families includes (1) a brief historical note, (2) an overview of the occurrence, molecular structure, and primary structure of the lectins, (3) a detailed discussion of the structure of the gene(s) and the biosynthesis and posttranslational processing of the primary translation products, (4) a summary of carbohydrate-binding specificity, (5) if relevant a note on the occurrence of lectin-related proteins, (6) a description of the three-dimensional structure of the lectins and the protomers, (7) a detailed discussion of the molecular evolution, and (8) a critical assessment of the physiological role of each group of lectins. Lectins that cannot be classified into one of the seven groups are discussed separately. General conclusions about the structure, evolution, and function of plant lectins are summarized in the concluding remarks.
 
Major evolutionary lineages of B genes in the phylogeny of some seed plants, and the capacity of the proteins they encode to dimerize. The gene lineages are indicated by different types of lines, as described, and the organismic lineages by grey branches. B proteins and their capacity to homo-or heterodimerize are indicated above the terminal branches. For proteins depicted with bold margins, dimerization specificity was demonstrated by two independent methods (yeast two-hybrid analyses and gel retardation assays). Rough estimates for the separation of the different organismic lineages are indicated at the left margin (in million years ago, MYA); the time point at which the lineage that led to Monocots branched off from the Eudicot lineage is based on molecular rather than fossil evidence. The grey shaded box with a question mark located at the branching point of gymnosperms and angiosperms symbolizes a knowledge gap concerning establishment of the different gene lineages. So far it remains unclear as to whether the duplication that led to the (at least) two different gymnosperm B gene lineages occurred before the split of gymnosperms and angiosperms (with a subsequent gene loss in angiosperms) or within the lineage that led to extant gymnosperms (requiring no gene loss).
Phylogeny of B genes of angiosperms and gymnosperms. A highly simplified phylogenetic tree of the DEF-, GLO-, GGM2-, DAL12-, and CJMADS1-like genes is shown. The tree was rooted by the putative sister group of the B genes, termed GGM13-like (or B sister ) genes. DEF, GLO, and GGM13 symbolize gene clades rather than individual genes. The numbers next to some nodes give bootstrap percentages. Genus names of species from which the gymnosperm B genes were isolated are given in parentheses behind the gene names. Symbols at certain nodes define putative apomorphies, as described in the legend. (Picture taken from Winter et al., 2002a; see there for further details.)  
On the origin of flowers. (a) Two hypothetical scenarios for the origin of hermaphroditic, perianth-less flower precursors out of male or female gymnosperm reproductive cones. Both hypotheses assume that B genes have an ancestral function in specifying male reproductive organs, and that changes in B gene expression played an important role during the origin of flowers. The out-of-male hypothesis assumes that hermaphroditic flower precursors originated by the downregulation of B genes at the top of male cones; the out-of-female hypothesis suggests that ectopic expression of B genes at the bottom of female gymnosperm cones generated hermaphroditic cones that evolved into flowers. (b) Reconstruction of Archaefructus sinensis. Archaefructus is the oldest unambiguous angiosperm known from the fossil record. It had flowers as predicted by the out-of-male/out-of-female scenarios, with female organs (carpels) at the top of reproductive achses, and male organs (stamens) attached underneath, but no perianth whatsoever. (c) Hermaphroditic reproductive cone of the Picea abies mutant 'acrocona' (Fladung et al., 1999); occasionally, this gymnosperm develops hermaphroditic reproductive cones that resemble intermediate stages in the evolution of angiosperm flowers as predicted by the out-of-male and out-of-female hypotheses. ((b) is from Sun et al., 2002; (c) was kindly provided by Matthias Fladung.)  
Class B floral homeotic genes play a key role in specifying the identity of male reproductive organs (stamens) and petals during the development of flowers. Recently, close relatives (orthologues) of these genes have been found in diverse gymnosperms, the sister group of the flowering plants (angiosperms). The fact that such genes have not been found so far, despite considerable efforts, in mosses, ferns or algae, has been taken as evidence to suggest that B genes originated 300–400 million years ago in a lineage that led to extant seed plants. Gymnosperms do not develop petals, and their male reproductive organs deviate considerably from angiosperm stamens. So what is the function of gymnosperm B genes? Recent experiments revealed that B genes from diverse extant gymnosperms are exclusively expressed in male reproductive organs (microsporophylls). At least for some of these genes it has been shown that they can partially substitute for the Arabidopsis B genes AP3 and PI in ectopic expression experiments, or even partially substitute these genes in different class B floral organ identity gene mutants. This functional complementation, however, is restricted to male organ development. These findings strongly suggest that gymnosperm and angiosperm B genes have highly related interaction partners and equivalent functions in the male organs of their different host species. It seems likely that in extant gymnosperms B genes have a function in specifying male reproductive organs. This function was probably established already in the most recent common ancestor of extant gymnosperms and angiosperms (seed plants) 300 million years ago and thus represents the ancestral function of seed plant B genes, from which other functions (e.g., in specifying petal identity) might have been derived. This suggests that the B gene function is part of an ancestral sex determination system in which B gene expression specifies male reproductive organ development, while the absence of B gene expression leads to the formation of female reproductive organs. Such a simple switch mechanism suggests that B genes might have played a central role during the origin of flowers. In the out-of-male and out-of-female hypotheses changes in B gene expression led to the origin of hermaphroditic flower precursors out of male or female gymnosperm reproductive cones, respectively. We compare these hypotheses with other recent molecular hypotheses on the origin of flowers, in which C/D and FLORICAULA/LEAFY-like genes is given a more prominent role, and we suggest how these hypotheses might be tested in the future.
 
Genes conferring resistance to antibiotics have been widely used as markers for the selection of transformed cells in the development of genetically modified (GM) plants. Their presence in GM plants released in the environment or used as food or feed has raised concerns over the past years regarding possible risks for human health and the environment. Although these concerns have not been supported so far by scientific evidence, the implementation of selection approaches avoiding the presence of antibiotic resistance marker genes (ARMGs) in the final GM plant is increasingly considered by GM plant developers, not only to alleviate the above-mentioned concerns, but also to circumvent technical limitations associated with the use of ARMGs. In the current paper, we present the results of a three-step analysis of selectable markers and reporter genes as well as methods aiming at developing marker-free GM plants. First, based on a comprehensive review of the scientific literature, technical developments in this domain are presented. Second, a state-of-the-art of the current use of selection approaches is provided based on publicly available information on GM plants tested in the field or authorized for commercialization. Third, in order to get more insight in the underlying practical, scientific and/or regulatory arguments supporting the choice of selection approaches, we present the results of a survey directed at relevant developers and users of GM plants. The applicability, efficiency, operational access and biosafety of the various selection approaches is discussed and considered in light of their current use, and in perspective to the long history of use of ARMGs in plant biotechnology.
 
This review evaluates evidence of the impact of uncomposted plant residues, composts, manures, and liquid preparations made from composts (compost extracts and teas) on pest and disease incidence and severity in agricultural and horticultural crop production. Most reports on pest control using such organic amendments relate to tropical or and climates. The majority of recent work on the use of organic amendments for prevention and control of diseases relates to container-produced plants, particularly ornamentals. However, there is growing interest in the potential for using composts to prevent and control diseases in temperate agricultural and horticultural field crops and information concerning their use and effectiveness is slowly increasing. The impact of uncomposted plant residues, composts, manures, and compost extracts/teas on pests and diseases is discussed in relation to sustainable temperate field and protected cropping systems. The factors affecting efficacy or such organic amendments in preventing and controlling pests and disease are examined and the mechanisms through which control is achieved are described.
 
Allelopathy in aquatic environments may provide a competitive advantage to angiosperms, algae, or cyanobacteria in their interaction with other primary producers. Allelopathy can influence the competition between different photoautotrophs for resources and change the succession of species, for exarnple, in phytoplankton cornmunities. Field evidence and laboratory studies indicate that allelopathy occurs in all aquatic habitats (marine and freshwater), and that ail prirnary producing organisms (cyanobacteria, micro- and macroalgae as well as angiospenns) are capable of producing and releasing allelopathically active compounds. Although allelopathy also includes positive (stimulating) interactions, the majority of studies describe the inhibitory activity of ailelopathicaily active compounds. Different mechanisms operate depending on whether allelopathy takes place in the Open water (pelagic zone) or is Substrate associated (benthic habitats). Allelopathical interactions are especiaily common in fully aquatic species, such as submersed macrophytes or benthic algae and cyanobacteria. The prevention of shading by epiphytic and planktonic primary producers and the competition for space may be the ultimate cause for allelopathical interactions. Aquatic ailelochemicals often target multiple physiological processes. The inhibition of photosynthesis of competing primary producers seems tobe a frequent mode of action. Multiple biotic and abiotic factors determine the strength of allelopathic interactions. Bacteria associated with the donor or target organism can metabolize excreted aiielochemicals. Frequently, the impact of surplus or limiting nutrients has been shown to affect the overail production of allelochemicals and their effect on target species. Similarities and differences of ailelopathic interactions in marine and freshwater habitats as well as between the different types of producing organisms are discussed.
 
Apomixis in angiosperms is asexual reproduction from seed. Its importance to angiospermous evolution and biodiversity has been difficult to assess mainly because of insufficient taxonomic documentation. Thus, we assembled literature reporting apomixis occurrences among angiosperms and transferred the information to an internet database (http://www.apomixis.uni-goettingen.de). We then searched for correlations between apomixis occurrences and well-established measures of taxonomic diversity and biogeography. Apomixis was found to be taxonomically widespread with no clear tendency to specific groups and to occur with sexuality at all taxonomic levels. Adventitious embryony was the most frequent form (148 genera) followed by apospory (110) and diplospory (68). All three forms are phylogenetically scattered, but this scattering is strongly associated with measures of biodiversity. Across apomictic-containing orders and families, numbers of apomict-containing genera were positively correlated with total numbers of genera. In general, apomict-containing orders, families, and subfamilies of Asteraceae, Poaceae, and Orchidaceae were larger, i.e., they possessed more families or genera, than non-apomict-containing orders, families or subfamilies. Furthermore, many apomict-containing genera were found to be highly cosmopolitan. In this respect, 62% occupy multiple geographic zones. Numbers of genera containing sporophytic or gametophytic apomicts decreased from the tropics to the arctic, a trend that parallels general biodiversity. While angiosperms appear to be predisposed to shift from sex to apomixis, there is also evidence of reversions to sexuality. Such reversions may result from genetic or epigenetic destabilization events accompanying hybridization, polyploidy, or other cytogenetic alterations. Because of increased within-plant genetic and genomic heterogeneity, range expansions and diversifications at the species and genus levels may occur more rapidly upon reversion to sexuality. The significantly-enriched representations of apomicts among highly diverse and geographically-extensive taxa, from genera to orders, support this conclusion.
 
Plants can have constitutive leaf angles that are fixed and do not vary much among different growth environments. Several species, however, have the ability to actively adjust their leaf angles. Active leaf repositioning can be functional in avoiding detrimental environmental conditions, such as avoidance of heat stress and complete submergence, or can be, for example, utilized to maximize carbon gain by positioning the leaves relative to the incoming radiation. In recent years, major advances have been made in the understanding of the molecular mechanisms, and the underlying hormonal regulation of a particular type of leaf movement: hyponastic growth. This differential petiole growth-driven upward leaf movement is now relatively well understood in model systems such as Rumex palustris and Arabidopsis thaliana. In the first part of this review we will discuss the functional consequences of leaf orientation for plant performance. Next, we will consider hyponastic growth and describe how exploitation of natural (genetic) variation can be instrumental in studying the relevance and control of leaf positioning.
 
Nitrogen-fixing bacteria colonize the roots of many gramineous plants from different geographic regions. The discovery that diazotrophs can be isolated from surface-sterilized roots or other plant material led to studies of their potential to inhabit plant tissue. For some diazotrophs, their endophytic character has been documented. This review summarizes current methods to identify endophytes and to characterize the colonization of plants by endophytic bacteria. Taxonomy, occurrence, diversity, and mechanisms of plant infection of Azoarcus spp. is discussed in relation to Herbaspirillum spp. and Acetobacter diazotrophicus. Perspectives how to study their functions and metabolism in association with plants are discussed.
 
As a result of the rapid expansion in international travel and trade over the past few decades, invasive plants have become a problem of global proportions. Plant invasions threaten the existence of endangered species and the integrity of ecosystems, and their ravages cost national economies tens of billions of dollars every year. Strategies for managing the threats posed by plant invasions involve three main tactics: prevention, eradication, and control. The effectiveness of prevention, involving enactment of legislation to prohibit the entry and spread of noxious alien plants, has been questioned. Eradication of all but the smallest, most localized weed infestations generally is not regarded as economically feasible. Conventional weed control techniques, such as mechanical and chemical controls, because they are expensive, energy and labor intensive, and require repeated application, are impractical for managing widespread plant invasions in ecologically fragile conservation areas or low-value habitat, such as rangelands and many aquatic systems. In addition, mechanical means of control disturb the soil and may cause erosion; chemical herbicides have spurred the evolution of resistance in scores of weed species and, further, may pose risks to wildlife and human health. Because of drawbacks associated with conventional weed control methods, classical biological control, the introduction of selective exotic natural enemies to control exotic pests, increasingly is being considered and implemented as a safe, cost-effective alternative to address the invasive plant problem. Worldwide, biological weed control programs have had an overall success rate of 33 percent; success rates have been considerably higher for programs in individual countries. Benefits are several-fold. Biological control is permanent, energy-efficient, nonpolluting, and inexpensive relative to other methods. Economic returns on investment in biological weed control have been spectacular in some cases, and range from an estimated benefit/cost ratio of 2.3 to 4000 or more. Although the risks involved in biological control in general are considered unacceptable by some, biological weed control in particular has had an enviable safety record. Since establishment of the stringent standards and regulatory apparatus currently in place in the United States and elsewhere, there have been no reported cases of biological weed control causing significant harm to nontarget populations or to the environment at large.
 
Glyoxalases are known to play a very important role in abiotic stress tolerance. This two-step pathway detoxifies ubiquitously present cytotoxic metabolite methylglyoxal, which otherwise increases to lethal concentrations under various stress conditions. Methylglyoxal initiates stress-induced signaling cascade via reactive oxygen species, resulting in the modifications of proteins involved in various signal transduction pathways, that eventually culminates in cell death or growth arrest. The associated mechanism of tolerance conferred by over-expression of methylglyoxal-detoxifying glyoxalase pathway mainly involves lowering of methylglyoxal levels, thereby reducing subsequently induced cellular toxicity. Apart from abiotic stresses, expression of glyoxalases is affected by a wide variety of other stimuli such as biotic, chemical and hormonal treatments. Additionally, alterations in cellular milieu during plant growth and development also affect expression of glyoxalases. The multiple stress-inducible nature of these enzymes suggests a vital role for glyoxalases, associating them with plant defense mechanisms. In this context, we have summarized available transcriptome, proteome and genetic engineering- based reports in order to highlight the involvement of glyoxalases as important components of plant stress response. The role of methylglyoxal as signaling molecule is also discussed. Further, we examine the suitability of glyoxalases and methylglyoxal as potential markers for stress tolerance.
 
Summary of principles underlying transgenic whole-cell biosensors. (A) Example of anthocyanin pigmentation on maize anthers. (B) General design of a promoter-reporter biosensor. (C) Example of a lux -output microbial biosensor exposed to increasing concentrations of its target analyte in a 96-well plate, imaged with a photon detection CCD camera. (D) General design of a FRET biosensor. (E) A potential auxotroph biosensor. (F) General design of a riboswitch biosensor. 
Features of potential transgenic whole-cell biosensor reporters
Biosensor engineering design principles
From the soil, plants take up macronutrients (calcium, magnesium, nitrogen, phosphorus, potassium, sulfur) and micronutrients (boron, chloride, cobalt, copper, iron, manganese, molybdenum, nickel, selenium, and zinc). In acidic soils, aluminum can interfere with nutrient uptake. There is a need for improved diagnostic tests for these soil-derived minerals that are inexpensive and sensitive, provide spatial and temporal information in plants and soil, and report bioavailable nutrient pools. A transgenic whole-cell biosensor detects a stimulus inside or outside a cell and causes a change in expression of a visible reporter such as green fluorescent protein, and thus can convert an invisible plant nutrient into a visible signal. Common transgenic whole-cell biosensors consist of promoter-reporter fusions, auxotrophs for target analytes that are transformed with constitutively expressed reporters, riboswitches and reporters based on Forster Resonance Energy Transfer (FRET). Here, we review transgenic plant biosensors that have been used to detect macronutrients and micronutrients. As plant-based biosensors are limited by the requirement to introduce and optimize a transgene in every genotype of interest, we also review microbial biosensor cells that have been used to measure plant or soil nutrients by co-inoculation with their respective extracts. Additionally, we review published transgenic whole-cell biosensors from other disciplines that have the potential to measure plant nutrients, with the goal of stimulating the development of these diagnostic technologies. We discuss current limitations and future improvements needed, and the long-term potential of transgenic whole-cell biosensors to inform plant physiology, improve soil nutrient management, and assist in breeding crops with improved nutrient use efficiency.
 
Selected references on the sources of cadmium contamination
Effect of different chelants on the translocation of Cd in plants; EDTA and HEDTA in sunflower (Helianthus annuus L.) plant, EDDS and NTA in water spinach (Ipomoea aquatica L.) (soil Cd level = 30 mg kg −1 ) (Chen and Cutright, 2001; Hseu et al., 2013).
Selected references on effect of metal toxicity on plant physiology
Cadmium (Cd) is an inorganic mineral in the earth's crust. Cadmium entry into the environment occurs through geogenic and anthropogenic sources. Industrial activities including mining, electroplating, iron and steel plants, and battery production employ Cd during their processes and often release Cd into the environment. When disseminated into soil, Cd can be detrimental to agro-ecosystems because it is relatively mobile and phytotoxic even at low concentrations. Cadmium's phytotoxicity is due to reductions in the rate of transpiration and photosynthesis and chlorophyll concentration resulting in retardation of plant growth, and an alteration in the nutrient concentration in roots and leaves. In response to Cd toxicity, plants have developed protective cellular mechanisms such as synthesis of phytochelatins and metallothioneins, metal compartmentalization in vacuoles, and the increased activity of antioxidant enzymes to neutralize Cd-induced toxicity. While these direct protective mechanisms can help alleviate Cd toxicity, other indirect mechanisms such as microelements (zinc, iron, manganese, and selenium) interfering with Cd uptake may decrease Cd concentration in plants. This comprehensive review encompasses the significance of Cd, portals of contamination and toxicity to plants, and implications for crop production. Various mitigation strategies with the beneficial effects of zinc, iron, manganese, and selenium in activating defence mechanisms against Cd stress are discussed. Furthermore, this review systematically identifies and summarises suitable strategies for mitigating Cd-induced toxicity in plants.
 
Mycorthizae play a critical role in nutrient capture from soils. Arbuscular mycorrhizae (AM) and ectomycorrhizae (EM) are the most important mycorrhizae in agricultural and natural ecosystems. AM and EM fungi use inorganic NH4+ and NO3-, and most EM fungi are capable of using organic nitrogen. The heavier stable isotope N-15 is discriminated against during biogeochemical and biochemical processes. Differences in N-15 (atom%) or delta(15)N (parts per thousand) provide nitrogen movement information in an experimental system. A range of 20 to 50% of one-way N-transfer has been observed from legumes to nonlegumes. Mycorrhizal fungal mycelia can extend from one plant's roots to another plant's roots to form common mycorrhizal networks (CMNs). Individual species, genera, even families of plants can be interconnected by CMNs. They are capable of facilitating nutrient uptake and flux. Nutrients such as carbon, nitrogen and phosphorus and other elements may then move via either AM or EM networks from plant to plant. Both N-15 labeling and N-15 natural abundance techniques have been employed to trace N movement between plants interconnected by AM or EM networks. Fine mesh (25similar to45 mum) has been used to separate root systems and allow only hyphal penetration and linkages but no root contact between plants. In many studies, nitrogen from N-2-fixing mycorrhizal plants transferred to non-N-2-fixing mycorrhizal plants (one-way N-transfer). In a few studies, N is also transferred from non-N-2-fixing mycorrhizal plants to N-2-fixing mycorrhizal plants (two-way N-transfer). There is controversy about whether N-transfer is direct through CMNs, or indirect through the soil. The lack of convincing data underlines the need for creative, careful experimental manipulations. Nitrogen is crucial to productivity in most terrestrial ecosystems, and there are potential benefits of management in soil-plant systems to enhance N-transfer. Thus, two-way N-transfer warrants further investigation with many species and under field conditions.
 
Due to limited availability of arable land and high market demand for off-season vegetables, cucurbits (plants in the family Cucurbitaceae) are continuously cultivated under unfavorable conditions in some countries. These conditions include environments that are too cold, wet, or dry, or are cool low-light winter greenhouses. Successive cropping can increase salinity, the incidence of cucurbit pests, and soilborne diseases like fusarium wilt caused by Fusarium spp. These conditions cause various physiological and pathological disorders leading to severe crop loss. Chemical pest control is expensive, not always effective, and can harm the environment. Grafting can overcome many of these problems. In fact, in many parts of the world, grafting is a routine technique in continuous cropping systems. It was first commonly used in Japan during the late 1920s by grafting watermelon [Citrullus lanatus (Thunb.) Matsum. and Nakai] onto pumpkin [Cucurbita moschata Duchesne ex. Poir] rootstocks. Soon after, watermelons were grafted onto bottle gourd [Lagenaria siceraria (Molina) Standl.] rootstocks. This practice helped control declining yield due to soilborne diseases. China produces more than half the world's watermelons and cucumbers (Cucumis sativus L.), and approximately 20% of these are grafted. Use of rootstocks can enhance plant vigor through vigorous attainment of soil nutrients, avoidance of soil pathogens and tolerance of low soil temperatures, salinity, and wet-soil conditions. The type of rootstock affects cucurbit plant growth, yield, and fruit quality. Cucurbit grafting is rare in the United States, but with continued loss of quality disease-free farmland along with the phase-out of methyl bromide, the U.S. cucurbit industry sees grafting as an attractive option. Some seed companies now offer watermelon transplants grafted onto squash or bottle gourd rootstocks, and some transplant facilities offer grafting services. There have been thorough analyses of cucurbit grafting in other countries, but the literature in English is limited. This review summarizes the state of the cucurbit grafting industry on a global level, translating work published in many languages.
 
Reliable, precise and accurate estimates of disease severity are important for predicting yield loss, monitoring and forecasting epidemics, for assessing crop germplasm for disease resistance, and for understanding fundamental biological processes including co-evolution. Disease assessments that are inaccurate and/or imprecise might lead to faulty conclusions being drawn from the data, which in turn can lead to incorrect actions being taken in disease management decisions. Plant disease can be quantified in several different ways. This review considers plant disease severity assessment at the scale of individual plant parts or plants, and describes our current understanding of the sources and causes of assessment error, a better understanding of which is required before improvements can be targeted. The review also considers how these can be identified using various statistical tools. Indeed, great strides have been made in the last thirty years in identifying the sources of assessment error inherent to visual rating, and this review highlights ways that assessment errors can be reduced—particularly by training raters or using assessment aids. Lesion number in relation to area infected is known to influence accuracy and precision of visual estimates—the greater the number of lesions for a given area infected results in more overestimation. Furthermore, there is a widespread tendency to overestimate disease severity at low severities (
 
Successful reproduction of flowering plants requires the appropriate timing of the floral transition, as triggered by environmental and internal cues and as regulated by multiple signaling modules. Among these modules, microRNAs (miRNAs), the evolutionarily conserved regulators, respond to environmental and internal cues and network with other integrators of flowering cues. Moreover, miRNA signaling modules affect the timing of flowering in many plant species. Here, we comprehensively review recent progress in understanding the function of miRNAs and their target genes in flowering time regulation in diverse plant species. We focus on the role of the miRNA-target gene modules in various flowering pathways and their conserved and divergent functions in flowering plants. We also examine, in depth, the crosstalk by sequential activity of miR156 and miR172, two of the most-studied and evolutionarily conserved miRNAs in both annual and perennial plants.
 
Reductions in grain yield in wheat caused by drought stress Growth stage Stress type Yield reduction Reference 
Potential traits/characters for screening wheat for drought tolerance 
QTLs identified for drought tolerance in wheat Trait Species Chromosome location Reference Water-soluble carbohydrate Bread wheat 1A, 1D, 2D, 4A, 6B, 7B, 7D Yang et al. (2007) 
Drought is a major environmental stress threatening wheat productivity worldwide. Global climate models predict changed precipitation patterns with frequent episodes of drought. Although drought impedes wheat performance at all growth stages, it is more critical during the flowering and grain-filling phases (terminal drought) and results in substantial yield losses. The severity and duration of the stress determine the extent of the yield loss. The principal reasons for these losses are reduced rates of net photosynthesis owing to metabolic limitations—oxidative damage to chloroplasts and stomatal closure—and poor grain set and development. A comprehensive understanding of the impact of terminal drought is critical for improving drought resistance in wheat, with marker-assisted selection being increasingly employed in breeding for this resistance. The limited success of molecular breeding and physiological strategies suggests a more holistic approach, including interaction of drought with other stresses and plant morphology. Furthermore, integration of physiological traits, genetic and genomic tools, and transgenic approaches may also help to improve resistance against drought in wheat. In this review, we describe the influence of terminal drought on leaf senescence, carbon fixation, grain set and development, and explain drought resistance mechanisms. In addition, recent developments in integrated approaches such as breeding, genetics, genomics, and agronomic strategies for improving resistance against terminal drought in wheat are discussed.
 
Many proteins from plant pathogens affecting the interaction with the host plant have dual functions: they promote virulence on the host species and they function as avirulence determinants by eliciting defense reactions in host cultivars expressing the appropriate resistance genes. In viruses all proteins encoded by the small genomes can be expected to be essential for viral development in the host. However, in different plants surveillance systems have evolved that are able to recognize most of these proteins. Bacteria and fungi have specialized pathogenicity and virulence genes. Many of the latter were originally identified through the resistance gene-dependent elicitor activity of their products. Their role in virulence only became apparent when they were inactivated or transferred to different microbes or after their ectopic expression in host plants. Many microbes appear to maintain these genes despite their disadvantageous effect, introducing only few mutations to abolish the interaction of their products with the plant recognition system. This has been interpreted as been indicative of a virulence function of the gene products that is not impaired by the mutations. Alternatively, in particular in bacteria there is now evidence that pathogenicity was acquired through horizontal gene transfer. Genes supporting virulence in the donor organism's original host appear to have traveled along. Being gratuitous in the new situation, they may have been inactivated without loss of any beneficial function for the pathogen.
 
Trace elements (TEs) occur at low concentrations (<1000 mg kg-1) in organisms, yet they have a large biological effect, both as essential nutrients and environmental contaminants. Phytomanagement describes the manipulation of soil-plant systems to affect the fluxes of TEs in the environment with the goal of remediating contaminated soils, recovering valuable metals, or increasing micronutrient concentrations in crops. Phytomanagement includes all biological, chemical, and physical technologies employed on a vegetated site. Successful phytomanagement should either cost less than other remediation or fortification technologies, or be a profitable operation, by producing valuable plant biomass products. This may include bioenergy or timber production on contaminated land, a practice that does not reduce food production. We review the components of phytomanagement and the underlying biogeochemical processes, with a view to elucidating situations where this technology may be successfully applied and identifying future research needs. Many full-scale operations have proved the efficacy of plants to reduce contaminant mobility in soils (phytostabilization), particularly when used in combination with other technologies. As a stand-alone technology, the oft-touted use of plants to extract TEs from contaminated soils (phytoextraction) or low-grade ore bodies (phytomining) is unsuitable for most, if not all, sites due to low-extraction rates and problems caused by site heterogeneity, the limited rooting depth of plants and the presence of contaminant mixtures. Unsubstantiated claims about phytoextraction have tarnished the reputation of all “phyto” technologies. Nevertheless, phytoextraction, as part of a larger environmental toolkit, has a role in phytomanagement. The growth, or lack thereof, of profitable companies that provide phytomanagement will indicate its value. A critical knowledge gap in phytomanagement is the integration of the processes that affect plant-TE interactions and the biophysical processes affecting TE fluxes in the root zone, especially the effect of roots on contaminant fluxes.
 
The subject of this review is the development of the plant embryo. Plant embryo-genesis is a unique process in the sense that it can be started not only from the fertilized egg but can also be initiated from other cells of the reproductive apparatus and even from somatic cells. One of the challenges of this field is therefore to unravel the molecular mechanisms that lead to the formation of a cell destined to form an embryo. A second important area of research is to determine the molecular basis of pattern formation in the embryo, a process that results in a stereotyped organization of a seedling. On the one hand, the pattern formation process has to establish precisely arranged tissue organization, but on the other hand sufficient flexibility during plant development has to be maintained to allow continuous formation of new organs from meristems.
 
The U.S. livestock industry has evolved to confine a large number of animals on a few farms in concentrated areas in many states. The trend to fewer, larger operations coupled with highly intensive production methods has resulted in more concentration of manure nutrients within relatively small geographic areas. Researchers in these areas have reported that manure production is contributing more phosphorus (P) than available cropland can assimilate. Overapplication of manure nutrients combined with low P removal rates by many crops is frequently cited as a reason for the accumulation of excess soil P. We propose that higher amounts of soil P can be removed from soil using vegetative management. Soil P concentration can be reduced in fields with excess levels by using P-hyperaccumulator plants or growing plants that have been modified to increase their P-uptake characteristics through traditional breeding and transgenic techniques. In this context, we identify plant properties (root architecture, secretion of organic acids, etc.) that may be improved using these two techniques.
 
The initial event in plant floral organogenesis is bract specification, followed by floral meristem (FM) initiation in bract axils, but initiation signals and the interplay between both lateral organs remain unelucidated. Floral organs are initiated on the flanks of the outgrowing FM and the enormous diversity in floral morphology throughout the plant kingdom reflects variations in organ position, meristy and ontogeny. Classical models of floral development have focused on Arabidopsis, which has mostly actinomorphic flowers, and Antirrhinum, which exhibits zygomorphy, although neither species is typical or representative of angiosperm flower diversity. Although the ABCE model defines a centripetal model of organ identity establishment in different whorls, the characterization of floral organ initiation in many species has relied on their morphological appearance, due to a lack of founder cell-specific markers. Recent progress in early Arabidopsis floral development using histology, molecular markers and mutants has led to refinements of existing floral organ initiation paradigms. In Arabidopsis, sepals initiate unidirectionally, in a temporal window characterized by the absence of CLAVATA3 and WUSCHEL stem cell markers and are partly dependent on PRESSED FLOWER function, whereas initiation of inner-whorl organs occurs centripetally. Arabidopsis mutants reveal that the FM is highly polarized along an ab-/adaxial axis and a comparison of floral development in Arabidopsis and Antirrhinum suggests that heterochrony of conserved gene functions has been evolutionarily adaptive.
 
Sunburn is a physiological disorder of apples and other fruit species caused by excess solar radiation. Damage occurs in practically all growing regions of the world, causing severe crop loss every year. Direct factors required for induction of the three currently-known types of sunburn (i.e., sunburn necrosis, sunburn browning, and photooxidative sunburn) include excess radiant heating and/or exposure to excess sunlight. Several other factors (e.g., relative humidity, wind velocity, acclimation of fruit, and cultural management practices), which alone cannot induce sunburn damage, indirectly influence the induction of sunburn by interacting with the direct factors to influence the appearance and severity of the symptoms. Sunburn affects apple fruit at many levels; it causes structural and morphological changes, alters pigment composition, influences adaptive mechanisms, impairs photosynthesis, and consequently decreases fruit quality. Fruits employ multiple physiological and biochemical mechanisms as complex defense systems to minimize damage. Photoprotective pigments, antioxidant enzymes and metabolites, heat-shock proteins, and the xanthophyll cycle help mitigate damage, but are often inadequate under field conditions to fully protect from sunburn. Quality loss significantly affects postharvest behavior, marketing and consumer acceptance of fruit. Internal fruit quality (e.g., firmness, soluble solids concentration, and titratable acidity) is affected by sunburn, and changes in these traits continue during cold storage. Sunburn-related disorders (e.g., sunburn scald in ‘Granny Smith’ and ‘Fuji’ stain) can appear in cold storage. There are several methods with various modes of action (e.g., climate ameliorating techniques, and sunburn suppressants) available to growers to decrease sunburn under field conditions. At the end of this review, the potential impact of a changing climate on sunburn incidence is considered, as both UV-B radiation and temperature are projected to change. Finally, several topics that need further research are discussed.
 
Cryopreservation is the storage of viable cells, tissues, organs and organisms at ultra-low temperatures, usually in liquid nitrogen to a minimum temperature of -196°C. The term, phytodiversity describes an assemblage of plants, algae and cyanobacteria; it is used to encourage a more holistic approach to cryopreserving the photosynthetic primary producers. In anticipation that encouraging exchange of knowledge across the different phytodiversity sectors sharing many common goals will facilitate their overall cryobanking activities. The main objective of the review is to explore the boundary between cryobiology theory and cryobanking practice. Natural adaptations will be considered with respect to cryopreservation protocol development and this theme includes a brief examination of 'cold' omics research. In addressing the problem of cryostorage recalcitrance, the review compares and contrasts phytodiversity from the perspective of environmental adaptation. A substantial part of the content is dedicated to appraising risk and safety issues and the microbial and pathological aspects of cryobanking. The importance of best practices for safeguarding the security of phytodiversity held in cryobanks is also considered. The review concludes by prospecting the use of the medical translational research paradigm in cryobanking.
 
Brassinosteroids (BRs) are steroid hormones that affect virtually every physiological process of plants throughout their life cycle. In contrast to the rapid progress in our understanding of BR signaling pathways, little is known about the regulatory mechanisms underlying BR homeostasis, particularly the upstream signals that regulate BR biosynthesis and inactivation. BR biosynthesis occurs through network pathways and basically is regulated at the transcriptional level of BR biosynthetic genes. When the BR signal is activated, BR-specific transcription factor, BZR1, inhibits transcription of BR biosynthetic genes through feedback downregulation mechanisms. Moreover, BR biosynthesis is also affected by other hormones such as auxin. This review focuses on recent progress in our understanding of the regulation of BR biosynthesis, with an emphasis on the transcriptional mechanisms that regulate this process, the effect of other hormones, exogenous signals, and inactivation of BRs.
 
Salinity is a major problem in arid and semi-arid regions, where irrigation is essential for crop production. Major sources of salinity in these regions are salt-rich irrigation water and improper irrigation management. The effects of salinity on crops include inhibition of growth and production, and ultimately, death. There are two main approaches to alleviating the adverse effects of salinity on agricultural crops: (i) development of salt-tolerant cultivars by screening, conventional breeding or genetic engineering, and (ii) the traditional approach dealing with treatments and management of the soil, plants, irrigation water, and plant environment. The success of the first approach is limited under commercial growing conditions, because salt-tolerance traits in plants are complex. The present paper reviews, analyzes, and discusses the following traditional approaches: (i) improving the plant environment, (ii) exploiting interactions between plant roots and bacteria and fungi, and (iii) treating the plant directly. With respect to improving the plant environment, we review the possibilities of decreasing salt content and concentration and improving the nutrient composition and concentration in the root zone, and controlling the plant's aerial environment. The interactions between salt-tolerant bacteria or mycorrhizal fungi and root systems, and their effects on salt-tolerance, are demonstrated and discussed. Discussed treatments aimed at alleviating salinity hazard by treating the plant directly include priming of seeds and young seedlings, using proper seed size, grafting onto tolerant rootstocks, applying non-enzymatic antioxidants, plant growth regulators or compatible solutes, and foliar application of nutrients. It can be concluded from the present review that the traditional approaches provide promising means for alleviating the adverse effects of salinity on agricultural crops.
 
Summary of hypobaric storage research on mango
Mango is one of the choicest fruits in the world and popular due to its delicate taste, pleasant aroma and nutritional value. Mango is indigenous to north-east India and north Burma, but now grown in over 90 countries. In the past two decades, mango production has increased appreciably with international trade jumping approximately four-fold valued close to US$ 950 million. Mango belongs to the category of climacteric fruits and its ripening is initiated and proceeded by a burst in ethylene production and a dramatic rise in the rate of respiration. Although there are a few hundred mango cultivars grown in the Indian subcontinent and other parts of the world, the most popular cultivars are generally highly perishable and ripen within 7 to 9 days of harvest at ambient temperature. Currently, the export potential and international trade of mango is limited due to several factors such as its perishable nature, disease and pest infestation, and susceptibility of certain premium cultivars to chilling injury when stored at low temperatures. Efforts are ongoing to develop technologies for improved storage and packaging, and overcome limitations encountered during storage and transit. Controlled atmosphere (CA) and hypobaric storage of mango are powerful means to overcome its perishable nature. The composition of CA varies among cultivars to ensure its original taste, flavor and aroma. Edible coating on the fruit skin may further cut down the rate of deterioration. Recently, significant advances have been made in understanding ripening characteristics of mango at the molecular level. Candidate genes related to ethylene biosynthesis and signalling, cell wall modification, aroma production and stress response have been cloned and characterized for future use in mango improvement. Efforts are also being made to establish a suitable transformation and plant regeneration system so that transgenic mango with added value and increased shelf life for long distance transportation could be developed.
 
With high quality petroleum running out in the next 50 years, the world governments and petrochemical industry alike are looking at biomass as a substitute refinery feedstock for liquid fuels and other bulk chemicals. New large plantations are being established in many countries, mostly in the tropics, but also in China, North America, Northern Europe, and in Russia. These industrial plantations will impact the global carbon, nitrogen, phosphorus, and water cycles in complex ways. The purpose of this paper is to use thermodynamics to quantify a few of the many global problems created by industrial forestry and agriculture. It is assumed that a typical tree biomass-for-energy plantation is combined with an efficient local pelleting facility to produce wood pellets for overseas export. The highest biomass-to-energy conversion efficiency is afforded by an efficient electrical power plant, followed by a combination of the FISCHER-TROPSCH diesel fuel burned in a 35%-efficient car, plus electricity. Wood pellet conversion to ethanol fuel is always the worst option. It is then shown that neither a prolific acacia stand in Indonesia nor an adjacent eucalypt stand is “sustainable.” The acacia stand can be made “sustainable” in a limited sense if the cumulative free energy consumption in wood drying and chipping is cut by a factor of two by increased reliance on sun-drying of raw wood. The average industrial sugarcane-for-ethanol plantation in Brazil could be “sustainable” if the cane ethanol powered a 60%-efficient fuel cell that, we show, does not exist. With some differences (ethanol distillation vs. pellet production), this sugarcane plantation performs very similarly to the acacia plantation, and is unsustainable in conjunction with efficient internal combustion engines.
 
Road map demonstrating the potential for integrating in vitro conservation with seed bank and environmental biobank operations that are organized within Biospecimen Science and Quality Management (QM) frameworks. Abbreviations: BRC = Biological Resource Centre; A = Authenticity; P = Purity; S = Stability; IVAG = In Vitro Active Genebank; IVBG = In Vitro Base Genebank; MMP = Modern Manufacturing Principles; SPREC = Standard Pre-analytical Code. 
Increasing the number of species conserved Ex Situ in Megadiverse countries is a major task exacerbated by many intricate factors including: biome complexity, wide range of biodiversity and an incomplete knowledge of life cycles, reproductive strategies, adaptations and species interactions. Although, establishing safe reserves is a crucial conservation measure their security and effective maintenance can be unfavourably compromised by climate change and the risks incurred by socioeconomic instability and changes in land use. Anthropogenic impacts, non-sustainable practices and habitat erosion have motivated current international efforts which focused on Brazil as host of ‘Rio+20’ the United Nation's twentieth anniversary conference on sustainable development. The revised targets of the Global Strategy for Plant Conservation (GSPC) are responses to species decline and realizing Target 8, which concerns Ex Situ conservation, places the heaviest burdens on countries that are custodians of the highest levels of global biodiversity. At the scientific level, Ex Situ conservation of endemic species in genebanks is often hindered by a lack of information about molecular genetics and problematic (recalcitrant) storage behaviors that restrict the preservation of flora native to Megadiverse countries. The potential for applying the ‘Biospecimen Science’ paradigm in expediting conservation in biodiversity-rich biomes is considered using Brazil as an exemplar of a Megadiverse country. The impacts of process chains on the quality of preserved plant germplasm and using evidence-based research to improve conservation outcomes, risk and quality management systems are appraised. The Biospecimen Science approach is not intended to displace conventional conservation practices but rather, to enhance their effectiveness in terms of the scale and efficiency of their scientific and technical operations.
 
Transmission electron micrograph of mature oil bodies of Lophozia ventricosa . c. chloroplast; er. endoplasmic reticulum; m. mitochondrion; ob. oil body with lipophilic globules enclosed. 11,000 x (reproduced from Pihakaski 1966) (color figure available online). 
Oil bodies of liverworts are intracellular organelles bounded by a single unit membrane containing lipophilic globules suspended in a proteinaceous matrix. They are a prominent and highly distinctive organelle uniquely found in liverworts. Although they have been widely used in taxonomy and chemosystematics, and many of their secondary metabolites are known to be bioactive and are considered as potential sources of medicines, their origin, development and function still remain poorly understood. Recently, biochemical studies have indicated that the isoprenoid biosynthetic pathways in liverworts are similar to those of the seed plants and that oil bodies of Marchantia polymorpha contain a protein complex immunologically related to plastid and cytosolic enzymes of isoprenoid synthesis. Cytoplasmic lipid droplets lacking a bounding membrane have recently been recognized as important dynamic organelles playing active roles in cell physiology. Structural proteins, covering the surface of the lipid droplets and preventing them coalescing during desiccation, have been found in seed plants and also in the moss Physcomitrella patens. However, whether liverwort oil bodies play a dynamic role in cell metabolism, in addition to their role as sites of essential oil accumulation and sequestration, has not been formally tested. In this review, we present current knowledge on the oil bodies of liverworts on their origin and development, their role in taxonomy, chemosystematics and potential pharmaceutical applications leading to their functional significance, and we also identify avenues for future studies on this important but long-overlooked organelle.
 
Improvement in salt tolerance of cereal crops using transgenic/genetic engineering approach
Cereals are grown in almost every region of the world and are exposed to a variety of environmental stresses that severely affect their growth and grain yield. Of various abiotic stresses, salinity is one of the more significant threats to cereal crops. To ensure food security, there is a need to adopt strategies to overcome this specific threat. Undoubtedly, plant scientists have been exploiting a variety of approaches to achieve enhanced crop productivity on salt affected soils. Of the various biotic approaches, conventional breeding, marker-assisted selection and genetic engineering to develop salt-tolerant lines/cultivars of cereals all seem plausible. Some success stories have been reported for improvement in salt tolerance of wheat and rice, but are scarce for other cereals. A number of barriers to the development of salt-tolerant cultivars/lines have been identified and include a lack of knowledge about the genetics of crops, their physiological and biochemical behavior, wide variation in environmental conditions, and the complex polygenic nature of the salt tolerance character. This review focuses on how improvements have been made in salt tolerance in cereals through different biotic means, such as conventional breeding, marker assisted selection and genetic engineering.
 
Referee: Dr. C. Neal Stewart, Jr., Department of Plant Science and Landscape Systems, The University of Tennessee, 2431 Center Drive, Knoxville, TN 37996-4561 There is major international concern over the widescale contamination of soil and associated groundwater by persistant explosives residues. The development of methods to remediate these contaminants has been a significant research interest for several decades. In the last 10 years, phytoremediation has emerged as a focus for explosives remediation because of its low cost, low energy requirements, and promising research observing explosives removal from contaminated groundwater and soil. More recent work has focused on the modes of transformation and metabolism of energetic compounds by plants. These biochemical studies and the experimental conditions enabling the degradation and uptake of explosives by different plant species are discussed.
 
Engineered minichromosomes provide the ability to target transgenes to a defined insertion position for predictable expression on an independent chromosome. This technology promises to provide a means to add many genes to a synthetic chromosome in sequential manner. An additional advantage is that the multiple transgenes will not be inserted into the normal chromosomes and thus will not exhibit linkage drag when converging the transgenes to different germplasm nor will they be mutagenic. Telomere truncation coupled with the introduction of site-specific recombination cassettes has proven to be an easy method to produce minichromosomes. Telomere truncation results from the transformation of plasmids carrying a block of telomere repeats at one end. Minichromosomes consisting of little more than a centromere have been produced for B chromosomes of maize. Such small chromosomes have been studied for their meiotic behavior, which differs from normal sized chromosomes in that homologue pairing is rare or nonexistent and sister chromatid cohesion fails at meiosis I. Potential modifications of the minichromosomes that can address these issues are discussed. Minichromosomes can be recovered from transformed plants that are polyploid or that carry an additional chromosome as the preferred target for truncation. Site-specific recombination has been demonstrated to operate on these terminally located sites. By introducing normal B chromosomes into lines with engineered mini-B chromosomes, the latter can be increased in copy number, which provides the potential to augment the expression of the introduced genes. Because the vast majority of plant species have the same telomere sequence, the truncating transgenes should be effective in most plants to generate engineered minichromosomes. Such chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agronomic applications or to use plants as factories for the production of foreign proteins or metabolites.
 
Marker genes (MGs) are essential tools for plant research and biotechnology. Positive selectable marker genes (SMGs) are used in genetic transformation to allow only transgenic cells to grow and develop and are necessary for efficient transformation. Negative SMGs confer a selective disadvantage to the cells that express them, and have several uses in both basic and applied research. Reporter genes (RGs) make it possible to easily screen cells or tissues for their expression. Several tens of different genes from bacteria, fungi, plants, and animals have been demonstrated to function as SMGs. Here, SMGs are classified based on the mechanism of action of the gene products. To provide the readers with practically useful information, details on transformation and selection efficiency are given. RGs are the object of intense research. Refinement of existing RGs and development of new ones is constant, and has provided powerful aids for fine studies on cell biology and more efficient genetic engineering. They are classified as vital and non vital, depending on the possibility to screen their expression in living cells. The effect of MG expression on the phenotype and their safety in crops is briefly discussed. The picture emerging from this literature review is that a plentiful array of powerful and versatile tools for basic and applied research is available.
 
Referee: Dr. E. Charles Brummer, Forage Breeding and Genetics, 1204 Agromonomy, Iowa State University, Ames, IA 50011 Much of the research on the genetic modification of herbaceous plant cell walls has been conducted to improve the utilization of forages by ruminant livestock. The rumen of these animals is basically an anaerobic fermentation vat in which the micro flora break down the complex polysaccharides of plant cell walls into simpler compounds that can be further digested and absorbed by the mammalian digestive system. Research on improving the forage digestibility of switchgrass, Panicum virgatum L., and other herbaceous species has demonstrated that genetic improvements can be made in forage quality that can have significant economic value. To meet future energy needs, herbaceous biomass will need to be converted into a liquid fuel, probably ethanol, via conversion technologies still under development. If feedstock quality can be genetically improved, the economics and efficiency of the conversion processes could be significantly enhanced. Improving an agricultural product for improved end product use via genetic modification requires knowledge of desired quality attributes, the relative economic value of the quality parameters in relation to yield, genetic variation for the desired traits, or for molecular breeding, knowledge of genes to suppress or add, and knowledge of any associated negative consequences of genetic manipulation. Because conversion technology is still under development, desirable plant feedstock characteristics have not been completely delineated. Some traits such as cellulose and lignin concentration will undoubtably be important. Once traits that affect biomass feedstock conversion are identified, it will be highly feasible to genetically modify the feedstock quality of herbaceous plants using both conventional and molecular breeding techniques. The use of molecular markers and transformation technology will greatly enhance the capability of breeders to modify the morphologic structure and cell walls of herbaceous species. It will be necessary to monitor gene flow to remnant wild populations of biomass plants and have strategies available to curtail gene flow if it becomes a potential problem. It will also be necessary to monitor plant survival and long-term productivity as affected by these genetic changes to herbaceous species.
 
An important driving force for the floriculture industry is the development of novel plants and flowers. New varieties provide marketing opportunities for retailers and judicious selection can increase productivity for growers, as well as improving the quality of the final product in the consumer's hands. While plant exploration and conventional breeding programs have been very successful in achieving these goals, genetic modification offers additional routes for the generation of new varieties of important floricultural plants. This can be achieved by the incorporation of genes from outside of the normally available gene pool. This paper provides a summary of the potential applications of gene technology in floriculture and reviews progress to date, with a particular emphasis on the manipulation of flower color. The manipulation of the anthocyanin biosynthesis pathway in carnation to produce novel-colored flowers is so far the only commercial application of genetic modification in floriculture. This progress is in stark contrast to the widespread cultivation of genetically modified broad-acre crops. The commercial use of gene technology requires adherence to regulatory regimes specific to genetically modified plants, and compliance with intellectual property laws. These added complexities are a significant cost, which may be hampering the use of gene technology by breeders of floricultural crops. Another factor may be a perception that the public and retail trade may not accept genetically modified floricultural products. Experience in the real marketplace with the Florigene Moon-series™ of genetically modified carnation suggests that these concerns are unwarranted.
 
Example of a mass balance chamber.
The use of plants (directly or indirectly) to remediate contaminated soil or water is known as phytoremediation. This technology has emerged as a more cost effective, noninvasive, and publicly acceptable way to address the removal of environmental contaminants. Plants can be used to accumulate inorganic and organic contaminants, metabolize organic contaminants, and encourage microbial degradation of organic contaminants in the root zone. Widespread utilization of phytoremediation can be limited by the small habitat range or size of plants expressing remediation potential, and insufficient abilities of native plants to tolerate, detoxify, and accumulate contaminants. A better understanding and appreciation of the potential mechanisms for removing contaminants from the root zone and the interaction between plants, microorganisms, and contaminants will be useful in extending the application of phytoremediation to additional contaminated sites.
 
Top-cited authors
Kadambot H M Siddique
  • University of Western Australia
Muhammad Farooq
  • Sultan Qaboos University
Maurizio G Paoletti
  • University of Padova
Kristina Schierenbeck
  • California State University, Chico
Jairo A. Palta
  • CSIRO and The University of Western Australia