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  • The Impact of Environmental Stress on Bt Crop Performance
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-24
    Patricia S. Girón-Calva; Richard M. Twyman; Ramon Albajes; Angharad M.R. Gatehouse; Paul Christou

    Bt crops have been grown commercially for more than two decades. They have proven remarkably effective in the control of target insect pests. However, Bt crops can become less effective under various forms of environmental stress. Most studies in this area have considered the effect of environmental stress on Bt insecticidal protein levels or target pest mortality, but not both, resulting in a lack of mechanistic analysis. In this review, we critically examine previous research addressing the impact of environmental stress on the effectiveness of Bt crops. We find that the body of research data is not sufficiently robust to allow the reliable prediction of the performance of Bt crops under extreme climatic conditions.

  • Genetic Control of Glandular Trichome Development
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-23
    Camille Chalvin; Stéphanie Drevensek; Michel Dron; Abdelhafid Bendahmane; Adnane Boualem

    Plant glandular trichomes are epidermal secretory structures producing various specialized metabolites. These metabolites are involved in plant adaptation to its environment and many of them have remarkable properties exploited by fragrance, flavor, and pharmaceutical industries. The identification of genes controlling glandular trichome development is of high interest to understand how plants produce specialized metabolites. Our knowledge about this developmental process is still limited, but genes controlling glandular trichome initiation and morphogenesis have recently been identified. In particular, R2R3-MYB and HD-ZIP IV transcription factors appear to play essential roles in glandular trichome initiation in Artemisia annua and tomato. In this review, we focus on the results obtained in these two species and we propose genetic regulation models integrating these data.

  • Woody Plant Declines. What’s Wrong with the Microbiome?
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-23
    Pauline Bettenfeld; Florence Fontaine; Sophie Trouvelot; Olivier Fernandez; Pierre-Emmanuel Courty

    Woody plant (WP) declines have multifactorial determinants as well as a biological and economic reality. The vascular system of WPs involved in the transport of carbon, nitrogen, and water from sources to sinks has a seasonal activity, which places it at a central position for mediating plant–environment interactions from nutrient cycling to community assembly and for regulating a variety of processes. To limit effects and to fight against declines, we propose: (i) to consider the WP and its associated microbiota as an holobiont and as a set of functions; (ii) to consider simultaneously, without looking at what comes first, the physiological or pathogenic disorders; and (iii) to define pragmatic strategies, including preventive and curative agronomical practices based on microbiota engineering.

  • Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-21
    Zuoren Yang; Ghulam Qanmber; Zhi Wang; Zhaoen Yang; Fuguang Li

    Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.

  • Digging Deeper for Agricultural Resources, the Value of Deep Rooting
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-18
    Kristian Thorup-Kristensen; Niels Halberg; Mette Nicolaisen; Jørgen Eivind Olesen; Timothy E. Crews; Philippe Hinsinger; John Kirkegaard; Alain Pierret; Dorte Bodin Dresbøll

    In the quest for sustainable intensification of crop production, we discuss the option of extending the root depth of crops to increase the volume of soil exploited by their root systems. We discuss the evidence that deeper rooting can be obtained by appropriate choice of crop species, by plant breeding, or crop management and its potential contributions to production and sustainable development goals. Many studies highlight the potentials of deeper rooting, but we evaluate its contributions to sustainable intensification of crop production, the causes of the limited research into deep rooting of crops, and the research priorities to fill the knowledge gaps.

  • Flowering Plants in the Anthropocene: A Political Agenda
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-18
    Ioan Negrutiu; Michael W. Frohlich; Olivier Hamant

    Flowering plants are the foundation of human civilization, providing biomass for food, fuel, and materials to satisfy human needs, dependent on fertile soil, adequate water, and favorable weather. Conversely, failure of any of these inputs has caused catastrophes. Today, human appropriation of biomass is threatening planetary boundaries, inducing social and political unrest worldwide. Human societies are bound to rethink agriculture and forestry to restore and safeguard natural resources while improving the overall quality of life. Here, we explore why and how. Through an evolutionary and quantitative analysis of agriculture, and bridging plant and Earth sciences, we anticipate the advent of a research and policy framework, integrating plant science in all sectors: the economy, local and global governance, and geopolitics.

  • GORK Channel: A Master Switch of Plant Metabolism?
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-18
    Getnet D. Adem; Guang Chen; Lana Shabala; Zhong-Hua Chen; Sergey Shabala

    Potassium regulates a plethora of metabolic and developmental response in plants, and upon exposure to biotic and abiotic stresses a substantial K+ loss occurs from plant cells. The outward-rectifying potassium efflux GORK channels are central to this stress-induced K+ loss from the cytosol. In the mammalian systems, signaling molecules such as gamma-aminobutyric acid, G-proteins, ATP, inositol, and protein phosphatases were shown to operate as ligands controlling many K+ efflux channels. Here we present the evidence that the same molecules may also regulate GORK channels in plants. This mechanism enables operation of the GORK channels as a master switch of the cell metabolism, thus adjusting intracellular K+ homeostasis to altered environmental conditions, to maximize plant adaptive potential.

  • Counting on Crossovers: Controlled Recombination for Plant Breeding
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-17
    Ella Taagen; Adam J. Bogdanove; Mark E. Sorrells

    Crossovers (COs), that drive genetic exchange between homologous chromosomes, are strongly biased toward subtelomeric regions in plant species. Manipulating the rate and positions of COs to increase the genetic variation accessible to breeders is a longstanding goal. Use of genome editing reagents that induce double-stranded breaks (DSBs) or modify the epigenome at desired sites of recombination, and manipulation of CO factors, are increasingly applicable approaches for achieving this goal. These strategies for ‘controlled recombination’ have potential to reduce the time and expense associated with traditional breeding, reveal currently inaccessible genetic diversity, and increase control over the inheritance of preferred haplotypes. Considerable challenges to address include translating knowledge from models to crop species and determining the best stages of the breeding cycle at which to control recombination.

  • The Modular Control of Cereal Endosperm Development
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-16
    Odd-Arne Olsen

    Expansion of the human population demands a significant increase in cereal production. The main component of cereal grains is endosperm, a body of starchy endosperm (SE) cells surrounded by aleurone (AL) cells with transfer cells (TC) at the base and embryo surrounding (ESR) cells adjacent to the embryo. The data reviewed here emphasize the modular nature of endosperm by first suggesting that sucrose promotes development of the fertilized triploid endosperm cell. Next, that the basal syncytial endosperm responds to glucose by turning on TC development. The default endosperm cell fate is SE and ESR differentiation is likely activated by signaling from the embryo. Cells on the exterior surface of the endosperm are specified as AL cells.

  • Prospects for Carotenoid Biofortification Targeting Retention and Catabolism
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-16
    Jacinta L. Watkins; Barry J. Pogson

    Due to the ongoing prevalence of vitamin A deficiency (VAD) in developing countries there has been a large effort towards increasing the carotenoid content of staple foods via biofortification. Common strategies used for carotenoid biofortification include altering flux through the biosynthesis pathway to direct synthesis to a specific product, generally β-carotene, or via increasing the expression of genes early in the carotenoid biosynthesis pathway. Recently, carotenoid biofortification strategies are turning towards increasing the retention of carotenoids in plant tissues either via altering sequestration within the cell or via downregulating enzymes known to cause degradation of carotenoids. To date, little attention has focused on increasing the stability of carotenoids, which may be a promising method of increasing carotenoid content in staple foods.

  • A Model for Nitrogen Fixation in Cereal Crops
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-15
    Alan B. Bennett; Vânia C.S. Pankievicz; Jean-Michel Ané

    Nitrogen-fixing microbial associations with cereals have been of intense interest for more than a century (Roesch et al., Plant Soil 2008;302:91–104; Triplett, Plant Soil 1996;186:29–38; Mus et al., Appl. Environ. Microbiol. 2016;82:3698–3710; Beatty and Good, Science 2011;333:416–417). A recent report demonstrated that an indigenous Sierra Mixe maize landrace, characterized by an extensive development of aerial roots that secrete large amounts of mucilage, can acquire 28–82% of its nitrogen from atmospheric dinitrogen (Van Deynze et al., PLoS Biol. 2018;16:e2006352). Although the Sierra Mixe maize landrace is unique in the large quantity of mucilage produced, other cereal crops secrete mucilage from underground and aerial roots and we hypothesize that this may represent a general mechanism for cereals to support associations with microbial diazotrophs. We propose a model for the association of nitrogen-fixing microbes with maize mucilage and identify the four main functionalities for such a productive diazotrophic association.

  • Linking Plant Functional Ecology to Island Biogeography
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-14
    Gianluigi Ottaviani; Gunnar Keppel; Lars Götzenberger; Susan Harrison; Øystein H. Opedal; Luisa Conti; Pierre Liancourt; Jitka Klimešová; Fernando A.O. Silveira; Borja Jiménez-Alfaro; Luka Negoita; Jiří Doležal; Michal Hájek; Thomas Ibanez; Francisco E. Méndez-Castro; Milan Chytrý

    The study of insular systems has a long history in ecology and biogeography. Island plants often differ remarkably from their noninsular counterparts, constituting excellent models for exploring eco-evolutionary processes. Trait-based approaches can help to answer important questions in island biogeography, yet plant trait patterns on islands remain understudied. We discuss three key hypotheses linking functional ecology to island biogeography: (i) plants in insular systems are characterized by distinct functional trait syndromes (compared with noninsular environments); (ii) these syndromes differ between true islands and terrestrial habitat islands; and (iii) island characteristics influence trait syndromes in a predictable manner. We are convinced that implementing trait-based comparative approaches would considerably further our understanding of plant ecology and evolution in insular systems.

  • The Many Models of Strigolactone Signaling
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-13
    Marco Bürger; Joanne Chory

    Strigolactones (SLs) are a class of plant hormones involved in several biological processes that are of great agricultural concern. While initiating plant–fungal symbiosis, SLs also trigger germination of parasitic plants that pose a major threat to farming. In vascular plants, SLs control shoot branching, which is linked to crop yield. SL research has been a fascinating field that has produced a variety of different signaling models, reflecting a complex picture of hormone perception. Here, we review recent developments in the SL field and the crystal structures that gave rise to various models of receptor activation. We also highlight the increasing number of discovered SL molecules, reflecting the existence of cross-kingdom SL communication.

  • Real-Time Volatilomics: A Novel Approach for Analyzing Biological Samples
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-13
    Tomasz Majchrzak; Wojciech Wojnowski; Małgorzata Rutkowska; Andrzej Wasik

    The use of the ‘omics techniques in environmental research has become common-place. The most widely implemented of these include metabolomics, proteomics, genomics, and transcriptomics. In recent years, a similar approach has also been taken with the analysis of volatiles from biological samples, giving rise to the so-called ‘volatilomics’ in plant analysis. Developments in direct infusion mass spectrometry (DI-MS) techniques have made it possible to monitor the changes in the composition of volatile flux from parts of plants, single specimens, and entire ecosystems in real-time. The application of these techniques enables a unique insight into the dynamic metabolic processes that occur in plants. Here, we provide an overview of the use of DI-MS in real-time volatilomics research involving plants.

  • Promoting Model Systems of Microbiota–Medicinal Plant Interactions
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-13
    Valentina Maggini; Alessio Mengoni; Patrizia Bogani; Fabio Firenzuoli; Renato Fani

    The role of the interaction(s) between medicinal plants (MPs) and their endophytes (bacterial microbiome) in the production of bioactive compounds (BCs) with therapeutic properties is emerging. Here, we propose Echinacea purpurea (L.) Moench as a new model to reveal the intimate crosstalk between MPs and bacterial endophytes, aiming to discover (new) BCs.

  • Eating Away at ROS to Regulate Stomatal Opening
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-10
    David B. Medeiros; Jessica A.S. Barros; Alisdair R. Fernie; Wagner L. Araújo

    Although reactive oxygen species (ROS) function in guard cell signaling has been demonstrated, the control of ROS homeostasis remains elusive. Recent findings point to multiple mechanisms controlling ROS levels in guard cells. These mechanisms require secondary metabolism and autophagy, providing the guard cells with a degree of plasticity during stomatal movements.

  • Revisiting the Role of Master Regulators in Tomato Ripening
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-08
    Rufang Wang; Gerco C. Angenent; Graham Seymour; Ruud A. de Maagd

    The study of transcriptional regulation of tomato ripening has been led by spontaneous mutations in transcription factor (TF) genes that completely inhibit normal ripening, suggesting that they are ‘master regulators’. Studies using CRISPR/Cas9 mutagenesis to produce knockouts of the underlying genes indicate a different picture, suggesting that the regulation is more robust than previously thought. This requires us to revisit our model of the regulation of ripening and replace it with one involving a network of partially redundant components. At the same time, the fast rise of CRISPR/Cas mutagenesis, resulting in unexpectedly weak phenotypes, compared with knockdown technology, suggests that compensatory mechanisms may obscure protein functions. This emphasises the need for assessment of these mechanisms in plants and for the careful design of mutagenesis experiments.

  • Fatty Acid Amide Hydrolases: An Expanded Capacity for Chemical Communication?
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-07
    Mina Aziz; Kent D. Chapman

    Fatty acid amide hydrolase (FAAH) is an enzyme that belongs to the amidase signature (AS) superfamily and is widely distributed in multicellular eukaryotes. FAAH hydrolyzes lipid signaling molecules – namely, N-acylethanolamines (NAEs) – which terminates their actions. Recently, the crystal structure of Arabidopsis thaliana FAAH was solved and key residues were identified for substrate-specific interactions. Here, focusing on residues surrounding the substrate-binding pocket, a comprehensive analysis of FAAH sequences from angiosperms reveals a distinctly different family of FAAH-like enzymes. We hypothesize that FAAH, in addition to its role in seedling development, also acts in an N-acyl amide communication axis to facilitate plant–microbe interactions and that structural diversity provides for the flexible use of a wide range of small lipophilic signaling molecules.

  • Alternative Biome States in Terrestrial Ecosystems
    Trends Plant Sci. (IF 14.006) Pub Date : 2020-01-06
    Juli G. Pausas; William J. Bond

    There is growing interest in the application of alternative stable state (ASS) theory to explain major vegetation patterns of the world. Here, we introduce the theory as applied to the puzzle of nonforested (open) biomes growing in climates that are warm and wet enough to support forests (alternative biome states, ABSs). Long thought to be the product of deforestation, diverse lines of evidence indicate that many open ecosystems are ancient. They have also been characterized as ‘early successional’ even where they persist for millennia. ABS is an alternative framework to that of climate determinism and succession for exploring forest/nonforest mosaics. This framework explains not only tropical forest–savanna landscapes, but also other landscape mosaics across the globe.

  • CRISPR-TSKO: A Tool for Tissue-Specific Genome Editing in Plants
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-16
    Zahir Ali; Magdy M. Mahfouz; Shahid Mansoor

    Functional genomics is at the core of studying the exact function of genes. However, homozygous knockouts of essential and pleiotropic effectors (almost 10% of the genome) are not always possible, thus, functions of these genes remain obscured. The tissue-specific genome editing tool (CRISPR-TSKO) recently described by Decaestecker et al., can characterize these indispensable genes and has wide applications in plants.

  • MAPK Signaling: Emerging Roles in Lateral Root Formation
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-14
    Yunxia He; Xiangzong Meng

    Lateral root (LR) formation is a multistep developmental process in which auxin and peptide hormones play essential roles. Recent studies in arabidopsis by Huang et al. and Zhu et al. have revealed that the mitogen-activated protein kinase (MAPK) cascade MKK4/MKK5–MPK3/MPK6 functions in both a noncanonical auxin signaling pathway and the IDA peptide signaling pathway to regulate LR morphogenesis and emergence, respectively.

  • Light Emission in Betalains: From Fluorescent Flowers to Biotechnological Applications
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-13
    M. Alejandra Guerrero-Rubio; Josefa Escribano; Francisco García-Carmona; Fernando Gandía-Herrero

    The discovery of visible fluorescence in the plant pigments betalains revealed the existence of fluorescent patterns in flowers of plants of the order Caryophyllales, where betalains substitute anthocyanins. The serendipitous initial discovery led to a systemized characterization of the role of different substructures on the photophysical phenomenon. Strong fluorescence is general to all members of the family of betaxanthins linked to the structural property that the betalamic acid moiety is connected to an amine group. This property has led to bioinspired tailor-made probes and to the development of novel biotechnological applications in screening techniques or microscopy labeling. Here, we comprehensively review the photophysics, photochemistry, and photobiology of betalain fluorescence and describe all current applications.

  • Adaptive Growth: Shaping Auxin-Mediated Root System Architecture
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-13
    Guanghui Xiao; Yuzhou Zhang

    Root system architecture (RSA), governed by the phytohormone auxin, endows plants with an adaptive advantage in particular environments. Using geographically representative arabidopsis (Arabidopsis thaliana) accessions as a resource for GWA mapping, Waidmann et al. and Ogura et al. recently identified two novel components involved in modulating auxin-mediated RSA and conferring plant fitness in particular habitats.

  • Allelopathic Plants: Models for Studying Plant–Interkingdom Interactions
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-11
    Niklas Schandry, Claude Becker

    Allelopathy is a biochemical interaction between plants in which a donor plant releases secondary metabolites, allelochemicals, that are detrimental to the growth of its neighbours. Traditionally considered as bilateral interactions between two plants, allelopathy has recently emerged as a cross-kingdom process that can influence and be modulated by the other organisms in the plant’s environment. Here, we review the current knowledge on plant–interkingdom interactions, with a particular focus on benzoxazinoids. We highlight how allelochemical-producing plants influence not only their plant neighbours but also insects, fungi, and bacteria that live on or around them. We discuss challenges that need to be overcome to study chemical plant–interkingdom interactions, and we propose experimental approaches to address how biotic and chemical processes impact plant health.

  • 3D Bioprinting in Plant Science: An Interdisciplinary Approach
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-05
    Shakti Mehrotra, Smita Kumar, Vikas Srivastava, Taijshee Mishra, Bhartendu Nath Mishra

    Here we highlight advances and opportunities for using 3D bioprinting in plant biology research that could lead to low-cost solutions for biomedical and other applications. For example, the development of plant cell-based and plant-inspired 3D-printed constructs could provide information about single-cell, tissue, and whole-plant interactions with the surrounding environment.

  • Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-12-02
    Saoirse R. Tracy, Kerstin A. Nagel, Johannes A. Postma, Heike Fassbender, Anton Wasson, Michelle Watt

    Root systems determine the water and nutrients for photosynthesis and harvested products, underpinning agricultural productivity. We highlight 11 programs that integrated root traits into germplasm for breeding, relying on phenotyping. Progress was successful but slow. Today’s phenotyping technologies will speed up root trait improvement. They combine multiple new alleles in germplasm for target environments, in parallel. Roots and shoots are detected simultaneously and nondestructively, seed to seed measures are automated, and field and laboratory technologies are increasingly linked. Available simulation models can aid all phenotyping decisions. This century will see a shift from single root traits to rhizosphere selections that can be managed dynamically on farms and a shift to phenotype-based improvement to accommodate the dynamic complexity of whole crop systems.

  • Unraveling the Linkage between Retrograde Signaling and RNA Metabolism in Plants
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-30
    Xiaobo Zhao, Jianyan Huang, Joanne Chory

    Retrograde signals are signals that originate in organelles to regulate nuclear gene expression. In plant cells, retrograde signaling from both chloroplasts and mitochondria is essential for plant development and growth. Over the past few years, substantial progress has been made in unraveling the linkages between chloroplast retrograde signaling and nuclear RNA metabolism processes or plastidial RNA editing. These findings add to the complexity of the regulation of organelle-to-nucleus communication. Chloroplast development and function rely on the coordinated regulation of chloroplast and nuclear gene expression, especially under stress conditions. A better understanding of retrograde signaling and RNA metabolism, as well as their connection, is essential for breeding stress-tolerant plants to cope with the dynamic and rapidly changing environment.

  • Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-29
    Aamir W. Khan, Vanika Garg, Manish Roorkiwal, Agnieszka A. Golicz, David Edwards, Rajeev K. Varshney

    The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop’s gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.

  • Nanovehicles for Plant Modifications towards Pest- and Disease-Resistance Traits
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-25
    Sandeep Kumar, Monika Nehra, Neeraj Dilbaghi, Giovanna Marrazza, Satish K. Tuteja, Ki-Hyun Kim

    In agriculture, plant transformation is a versatile platform for crop improvement with the aim of increased pest resistance and an improved nutrient profile. Nanotechnology can overcome several challenges that face conventional methods of gene delivery. Specifically, nanomaterials offer an optimal platform for biomolecule delivery with unique physiochemical properties as well as the ability to traverse the challenging barrier of the plant cell wall. We review the potential of diverse nanovehicles for biomolecule delivery in plant systems to obtain desired genetic traits. The efficacy of nanoparticles against pests or pathogens is also explored, as well as the interaction of nanovehicles with plant organelles, with due consideration of the effects and toxic profile of nanoparticles.

  • Similar and Yet Different: Oxygen Sensing in Animals and Plants
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-25
    Francesco Licausi, Beatrice Giuntoli, Pierdomenico Perata

    The ability to perceive oxygen levels and adapt metabolism on the basis of its availability is vital for most eukaryotic cells. Here, we retrace the key steps that led to the identification of oxygen-sensing mechanisms in animals and plants and compare the essential features of the two strategies.

  • Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-25
    Charlotte Rich-Griffin, Annika Stechemesser, Jessica Finch, Emma Lucas, Sascha Ott, Patrick Schäfer

    Plant function is the result of the concerted action of single cells in different tissues. Advances in RNA-seq technologies and tissue processing allow us now to capture transcriptional changes at single-cell resolution. The incredible potential of single-cell RNA-seq lies in the novel ability to study and exploit regulatory processes in complex tissues based on the behaviour of single cells. Importantly, the independence from reporter lines allows the analysis of any given tissue in any plant. While there are challenges associated with the handling and analysis of complex datasets, the opportunities are unique to generate knowledge of tissue functions in unprecedented detail and to facilitate the application of such information by mapping cellular functions and interactions in a plant cell atlas.

  • The Long-Standing Paradox of Seed Dormancy Unfolded?
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-07-18
    Hiroyuki Nonogaki

    There has been a long-standing question in seed research, why cyanide, a respiration inhibitor, breaks seed dormancy. While the alternative respiratory pathway and reactive oxygen species have been suggested to be part of the mechanism, the cell biological and mechanistic significance of this paradox remains unclear. The outcomes of recent research on mitochondrial RNA processing for the subunits of the electron transport chain complexes seem to offer a logical explanation. This opinion article attempts to integrate the accumulating evidence of mitochondrial involvement in ABA signaling with the frontier of seed research on DELAY OF GERMINATION1, a master regulator of dormancy, to present a coherent model for ABA signaling in seeds, which could also address the old paradox in seed research.

  • Evolution of Photochemical Reaction Centres: More Twists?
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-07-24
    Tanai Cardona, A. William Rutherford

    One of the earliest events in the molecular evolution of photosynthesis is the structural and functional specialisation of type I (ferredoxin-reducing) and type II (quinone-reducing) reaction centres. In this opinion article we point out that the homodimeric type I reaction centre of heliobacteria has a calcium-binding site with striking structural similarities to the Mn4CaO5 cluster of photosystem II. These similarities indicate that most of the structural elements required to evolve water oxidation chemistry were present in the earliest reaction centres. We suggest that the divergence of type I and type II reaction centres was made possible by a drastic structural shift linked to a change in redox properties that coincided with or facilitated the origin of photosynthetic water oxidation.

  • A Molecular Blueprint of Lignin Repression
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-07-29
    Marc Behr, Gea Guerriero, Jacqueline Grima-Pettenati, Marie Baucher

    Although lignin is essential to ensure the correct growth and development of land plants, it may be an obstacle to the production of lignocellulosics-based biofuels, and reduces the nutritional quality of crops used for human consumption or livestock feed. The need to tailor the lignocellulosic biomass for more efficient biofuel production or for improved plant digestibility has fostered considerable advances in our understanding of the lignin biosynthetic pathway and its regulation. Most of the described regulators are transcriptional activators of lignin biosynthesis, but considerably less attention has been devoted to the repressors of this pathway. We provide a comprehensive overview of the molecular factors that negatively impact on the lignification process at both the transcriptional and post-transcriptional levels.

  • Challenges of Translating Gene Regulatory Information into Agronomic Improvements
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-07-31
    Nathan Springer, Natalia de León, Erich Grotewold

    Improvement of agricultural species has exploited the genetic variation responsible for complex quantitative traits. Much of the functional variation is regulatory, in cis-regulatory elements and trans-acting factors that ultimately contribute to gene expression differences. However, the identification of gene regulatory network components that, when modulated, will increase plant productivity or resilience, is challenging, yet essential to provide increased predictive power for genome engineering approaches that are likely to benefit useful traits. Here, we discuss the opportunities and limitations of using data obtained from gene coexpression, transcription factor binding, and genome-wide association mapping analyses to predict regulatory interactions that impact crop improvement. It is apparent that a combination of information from these data types is necessary for the reliable identification and utilization of important regulatory interactions that underlie complex agronomic traits.

  • Ethylene Signaling Controls Fast Oxygen Sensing in Plants
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-13
    Pierdomenico Perata

    When plants are submerged by water they suffer from hypoxia. Although it has long been known that ethylene accumulates in submerged plants, its role in plant tolerance to hypoxia remained elusive. Recently, Hartman et al. described a mechanism that explains the role of ethylene in oxygen sensing and signaling.

  • CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-11
    Hakim Manghwar, Keith Lindsey, Xianlong Zhang, Shuangxia Jin

    Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its high efficiency, ease of use, and accuracy. It can be used to add desirable and remove undesirable alleles simultaneously in a single event. Here, we discuss various applications of CRISPR/Cas9 in a range of important crops, compare it with other GE tools, and review its mechanism, limitations, and future possibilities. Various newly emerging CRISPR/Cas systems, including base editing (BE), xCas9, and Cas12a (Cpf1), are also considered.

  • DNA-Damaging Effectors: New Players in the Effector Arena
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-05
    Laurent Camborde, Cécile Raynaud, Bernard Dumas, Elodie Gaulin

    In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is activated to ensure lesion repair. Accumulation of DNA breaks is also detected in plants during microbial infection. In this opinion article we propose that phytopathogens can produce DNA-damaging effectors. The recent identification of a functional genotoxin in devastating eukaryotic plant pathogens, such as oomycetes, supports the concept that DNA-damaging effectors may contribute to pathogenicity. Additionally, this raises the question of how plants can perceive these damages and whether this perception can be connected to the plant immune system.

  • Applying the Solanaceae Strategies to Strawberry Crop Improvement
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-04
    Amelia Gaston, Sonia Osorio, Béatrice Denoyes, Christophe Rothan

    Strawberry is a fruit crop species of major horticultural importance, for which fruit quality and the control of flowering (for fruit yield), runnering (for vegetative propagation), and the trade-off between the two are main breeding targets. The octoploid cultivated strawberry has a limited genetic basis. This raises the question of how to identify important gene targets and successfully exploit them for strawberry improvement. In this Opinion article we propose to apply to woodland strawberry, a wild diploid species displaying wide diversity, the strategies successfully employed in recent years for the identification of genetic variations underlying fruit quality and fruit yield traits in solanaceous crops (tomato, potato). Next we propose to use gene editing technologies to translate the findings to cultivated strawberry.

  • Structural Basis of Design and Engineering for Advanced Plant Optogenetics
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-04
    Sudakshina Banerjee, Devrani Mitra

    In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.

  • Changing Color for Photoprotection: The Orange Carotenoid Protein
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-11-01
    Fernando Muzzopappa, Diana Kirilovsky

    Under high irradiance, light becomes dangerous for photosynthetic organisms and they must protect themselves. Cyanobacteria have developed a simple mechanism, involving a photoactive soluble carotenoid protein, the orange carotenoid protein (OCP), which increases thermal dissipation of excess energy by interacting with the cyanobacterial antenna, the phycobilisome. Here, we summarize our knowledge of the OCP-related photoprotective mechanism, including the remarkable progress that has been achieved in recent years on OCP photoactivation and interaction with phycobilisomes, as well as with the fluorescence recovery protein, which is necessary to end photoprotection. A recently discovered unique mechanism of carotenoid transfer between soluble proteins related to OCP is also described.

  • Plant and Animal Innate Immunity Complexes: Fighting Different Enemies with Similar Weapons
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-10-31
    Glykeria Mermigka, Maria Amprazi, Adriani Mentzelopoulou, Argyro Amartolou, Panagiotis F. Sarris

    Both animals and plants express intracellular innate immunity receptors known as NLR (NOD-like receptors or nucleotide-binding domain and leucine-rich repeat receptors, respectively). For various mammalian systems, the specific formation of macromolecular structures, such as inflammasomes by activated NLR receptors, has been extensively reported. However, for plant organisms, the formation of such structures was an open scientific question for many years. This year, the first plant ‘resistosome’ structure was reported, revealing significant structural similarities to mammalian apoptosome and inflammasome structures. In this review, we summarize the key components comprising the mammalian apoptosome/inflammasome structures and the newly discovered plant resistosome, highlighting their commonalities and differences.

  • Plant Phenylalanine/Tyrosine Ammonia-lyases
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-10-31
    Jaime Barros, Richard A. Dixon

    Aromatic amino acid deaminases are key enzymes mediating carbon flux from primary to secondary metabolism in plants. Recent studies have uncovered a tyrosine ammonia-lyase that contributes to the typical characteristics of grass cell walls and contributes to about 50% of the total lignin synthesized by the plant. Grasses are currently preferred bioenergy feedstocks and lignin is the most important limiting factor in the conversion of plant biomass to liquid biofuels, as well as being an abundant renewable carbon source that can be industrially exploited. Further research on the structure, evolution, regulation, and biological function of functionally distinct ammonia-lyases has multiple implications for improving the economics of the agri-food and biofuel industries.

  • Harnessing Wheat Fhb1 for Fusarium Resistance
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-10-31
    Yuanfeng Hao, Awais Rasheed, Zhanwang Zhu, Brande B.H. Wulff, Zhonghu He

    Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, is an economically devastating disease of wheat worldwide. Fhb1, a widely used genetic source of FHB resistance, originated in East Asia. The recent cloning of Fhb1 opens a new avenue to improve FHB resistance in wheat and potentially other crops.

  • Beyond Digging: Noninvasive Root and Rhizosphere Phenotyping.
    Trends Plant Sci. (IF 14.006) Pub Date : null
    Anton P Wasson,Kerstin A Nagel,Saoirse Tracy,Michelle Watt

  • Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement.
    Trends Plant Sci. (IF 14.006) Pub Date : 2019-10-19
    Gwen Swinnen,Alain Goossens,Laurens Pauwels

  • The shifting paradigms of auxin biosynthesis.
    Trends Plant Sci. (IF 14.006) Pub Date : 2014-02-14
    Nathan D Tivendale,John J Ross,Jerry D Cohen

    Auxins are an important group of hormones found in all land plants and several soil-dwelling microbes. Although auxin was the first phytohormone identified, its biosynthesis remained unclear until recently. In the past few years, our understanding of auxin biosynthesis has im-proved dramatically, to the stage where many believe there is a single predominant pathway in Arabidopsis (Arabidopsis thaliana L.). However, there is still uncertainty over the applicability of these findings to other plant species. Indeed, it appears that in certain organs of some species, other pathways can operate. Here we review the key advances that have led to our current understanding of auxin biosynthesis and its many pro-posed pathways.

  • An interview with Jen Sheen.
    Trends Plant Sci. (IF 14.006) Pub Date : 2012-08-04
    Jen Sheen

  • Interview with Martin Heil.
    Trends Plant Sci. (IF 14.006) Pub Date : 2012-06-26
    Martin Heil

  • Flavonoids and auxin transport: modulators or regulators?
    Trends Plant Sci. (IF 14.006) Pub Date : 2008-01-18
    Wendy Ann Peer,Angus S Murphy

    Flavonoids are polyphenolic compounds found in all vascular and non-vascular plants. Although nonessential for plant growth and development, flavonoids have species-specific roles in nodulation, fertility, defense and UV protection. Flavonoids have been shown to modulate transport of the phytohormone auxin in addition to auxin-dependent tropic responses. However, flavonoids are not essential regulators of these processes because transport and tropic responses occur in their absence. Flavonoids modulate the activity of auxin-transporting P-glycoproteins and seem to modulate the activity of regulatory proteins such as phosphatases and kinases. Phylogenetic analysis suggests that auxin transport mechanisms evolved in the presence of flavonoid compounds produced for the scavenging of reactive oxygen species and defense from herbivores and pathogens.

  • Real Time QTL of complex phenotypes in tomato interspecific introgression lines.
    Trends Plant Sci. (IF 14.006) Pub Date : 2004-04-03
    Amit Gur,Yaniv Semel,Avigdor Cahaner,Dani Zamit

  • A molecular view of plant centromeres.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-12-09
    Jiming Jiang,James A Birchler,Wayne A Parrott,R Kelly Dawe

    Although plants were the organisms of choice in several classical centromere studies, molecular and biochemical studies of plant centromeres have lagged behind those in model animal species. However, in the past several years, several centromeric repetitive DNA elements have been isolated in plant species and their roles in centromere function have been demonstrated. Most significantly, a Ty3/gypsy class of centromere-specific retrotransposons, the CR family, was discovered in the grass species. The CR elements are highly enriched in chromatin domains associated with CENH3, the centromere-specific histone H3 variant. CR elements as well as their flanking centromeric satellite DNA are actively transcribed in maize. These data suggest that the deposition of centromeric histones might be a transcription-coupled event.

  • Zea mays ontology--a database of international terms.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-11-11
    P Leszek D Vincent,Edward H Coe,Mary L Polacco

    Data retrieval, comprehension and sharing within and between plant-based databases are essential to exploit comparative genomic information to elucidate functional aspects of plant biology and to conduct studies of synteny and homology. However, the functionality is often hampered by the variability of terms used to describe comparable objects. The Zea mays Plant Structure Ontology database is designed to overcome this problem via the provision of a controlled vocabulary that facilitates knowledge sharing. It comprises international botanical terms, references, synonyms, and phylogenetic information and is open-source.

  • Carbon cycling by arbuscular mycorrhizal fungi in soil-plant systems.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-09-19
    Yong-Guan Zhu,R Michael Miller

  • Planning for remodelling: nuclear architecture, chromatin and chromosomes.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-05-22
    J S Heslop-Harrison

    DNA sequences occupy three-dimensional positions and their architecture is related to gene expression, gene-protein interactions and epigenetic processes. The recent analysis of chromosome 4 in Arabidopsis interphase nuclei reveals that gene-rich, undermethylated DNA is composed of active loops of 200 to 2000 kb associated with acetylated histones, providing a well-defined model system to study chromatin in its nuclear context.

  • Plant snoRNAs: functional evolution and new modes of gene expression.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-01-14
    John W S Brown,Manuel Echeverria,Liang Hu Qu

    Small nucleolar RNAs (snoRNAs) are a well-characterized family of non-coding RNAs whose main function is rRNA modification. The diversity and complexity of this gene family continues to expand with the discovery of snoRNAs with non-rRNA or unknown targets. Plants contain more snoRNAs than other eukaryotes and have developed novel expression and processing strategies. The increased number of modifications, which will influence ribosome function, and the novel modes of expression might reflect the environmental conditions to which plants are exposed. Polyploidy and chromosomal rearrangements have generated multiple copies of snoRNA genes, allowing the generation of new snoRNAs for selection. The large snoRNA family in plants is an ideal model for investigation of mechanisms of evolution of gene families in plants.

  • Chloroplast redox signals: how photosynthesis controls its own genes.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-01-14
    Thomas Pfannschmidt

    The photosynthetic apparatus of higher plants and algae is composed of plastid- and nuclear-encoded components, therefore the expression of photosynthesis genes needs to be highly coordinated. Expression is regulated by various factors, one of the most important of which is light. Photosynthesis functions as a sensor for such light signals, and the redox state of photosynthetic electron transport components and redox-active soluble molecules act as regulating parameters. This provides a feedback response loop in which the expression of photosynthesis genes is coupled to the function of the photosynthetic process, and highlights the dual role of photosynthesis in energy fixation and the reception of environmental information.

  • Balancing the central roles of the thylakoid proton gradient.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-01-14
    David M Kramer,Jeffrey A Cruz,Atsuko Kanazawa

    The photosynthetic electron transfer chain generates proton motive force (pmf), composed of both electric field (Deltapsi) and concentration (DeltapH) gradients. Both components can drive ATP synthesis, whereas the DeltapH component alone can trigger feedback regulation of the antenna. It has often been suggested that a relatively large pmf is needed to sustain the energetic contributions of the ATP synthase reaction (DeltaG(ATP)), and that the Deltapsi component is dissipated during illumination, leading to an acidic lumen in the light. We suggest that this is incompatible with the stabilities of lumenal components and the observed activation of downregulation. Recent work on the chloroplast ATP synthase suggests that a more moderate pmf can sustain DeltaG(ATP). In addition, in vivo probes suggest that a substantial fraction of pmf can be stored as Deltapsi. Together, these factors should allow sufficient DeltaG(ATP) to maintain lumen pH in a range where lumenal enzyme activities are nearly optimal, and where the level of NPQ is regulated.

  • Abscisic acid, nitric oxide and stomatal closure - is nitrate reductase one of the missing links?
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-01-14
    Carlos García-Mata,Lorenzo Lamattina

    Once plant endogenous nitric oxide (NO) production had been proved, NO research was directed toward both the source and the targets of this extremely bioactive molecule. As in mammals, plant NO was first thought to be generated mainly by a NO synthase-like enzymatic activity. However, nitrate reductase (NR)-dependent NO production is now receiving much of the attention because of the ubiquity of this enzyme in higher plant tissues and the precise regulation of its NO-production activity. NO has been reported to be a signal in many and diverse physiological processes, such as growth and biotic and abiotic stresses. Recently, NO has been shown to affect stomatal closure and interact with abscisic acid signaling pathways. We propose NR as a putative component in the signaling cascade of ABA-induced stomatal closure.

  • Cyclic, pseudocyclic and noncyclic photophosphorylation: new links in the chain.
    Trends Plant Sci. (IF 14.006) Pub Date : 2003-01-14
    John F Allen

    Photosynthetic electron transport is coupled to ATP synthesis. This process - photosynthetic phosphorylation - proceeds by several alternative electron-transport pathways in isolated chloroplasts. The question: 'Which of these works in real life?' has long occupied students of photosynthesis. Recent results from structural biology and genomics suggest that the answer is 'All of them'. The interplay between the pathways might explain the flexibility of photosynthesis in meeting different metabolic demands for ATP.

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上海纽约大学William Glover