Soil Biodiversity Effects from Field to Fork Trends Plant. Sci. (IF 11.911) Pub Date : 2017-11-13 Matthias C. Rillig, Anika Lehmann, Johannes Lehmann, Tessa Camenzind, Cornelia Rauh
Our knowledge of soil biodiversity in agriculture in general is currently increasing rapidly. However, almost all studies have stopped with the quantification of soil biodiversity effects on crops at harvest time, ignoring subsequent processes along the agrifood chain until food arrives on our plates. Here we develop a conceptual framework for the study of such postharvest effects. We present the main mechanisms (direct and indirect) via which soil biodiversity can influence crop quality aspects and give examples of how effects at harvest time may become attenuated through postharvest operations and how biodiversity may also affect some of these operations (i.e., storage) themselves. Future research with a broader focus has the potential to unveil how soil biodiversity may benefit from what ends up on our forks.
Database Taxonomics as Key to Modern Plant Biology Trends Plant. Sci. (IF 11.911) Pub Date : 2017-11-13 Marcus A. Koch, Dmitry A. German, Markus Kiefer, Andreas Franzke
The advent of omic technologies opened new and multiple avenues to access higher levels of complexity. Taxonomy – discovering and naming biodiversity – has also entered a taxonomics epoch and serves as a tool not only to name biological diversity, but also to fully explore biological knowledge and to build bridges between disciplines.
Translational Research: Exploring and Creating Genetic Diversity Trends Plant. Sci. (IF 11.911) Pub Date : 2017-11-07 Pierre Jacob, Adi Avni, Abdelhafid Bendahmane
The crop selection process has created a genetic bottleneck ultimately restricting breeding output. Wild relatives of major crops as well as the so-called ‘neglected plant’ species represent a reservoir of genetic diversity that remains underutilized. These species could be used as a tool to discover new alleles of agronomic interest or could be the target of breeding programs. Targeted induced local lesions in the genome (TILLING) can be used to translate in neglected crops what has been discovered in major crops and reciprocally. However, random mutagenesis, used in TILLING approaches, provides only a limited density of mutational events at a defined target locus. Alternatively, clustered regularly interspaced short palindromic repeats (CRISPR) associated 9 (Cas9) fused to a cytidine deaminase could serve as a localized mutagenic agent to produce high-density mutant populations. Artificial evolution is at hand.
Molecular Control of Male Fertility for Crop Hybrid Breeding Trends Plant. Sci. (IF 11.911) Pub Date : 2017-11-07 Yu-Jin Kim, Dabing Zhang
In many plant species, male-sterile female lines with cytoplasmic male sterility (CMS) or nuclear-controlled environment-sensitive genic male sterility (EGMS) have long been used to efficiently produce hybrids that harness hybrid vigor or heterosis. However, the underlying molecular mechanisms for these applications have only recently been uncovered in a few species. We provide here an update on the understanding of cytoplasmic–nuclear communication based on the discovery of mitochondrial CMS genes and their corresponding nuclear fertility determinants. Recent findings that uncover diverse mechanisms such as epigenetic, transcriptional, and post-transcriptional controls of EGMS by temperature and photoperiod signals are also reviewed. Furthermore, translational research that applies basic knowledge of plant male fertility control to hybrid seed production practice is highlighted.
Can Peroxisomes Inform Cellular Response to Drought? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-11-05 Andrei Smertenko
Although plant germplasm contains numerous unknown traits for drought-tolerance, the ability to phenotype this material remains challenging. I propose that peroxisome abundance may be a viable parameter for the evaluation of drought response at the cellular level, and hence could be useful to improve phenotyping efforts.
Dimensionless Numbers for Plant Biology Trends Plant. Sci. (IF 11.911) Pub Date : 2017-11-05 Joseph K.E. Ortega
Dimensionless numbers are ubiquitous in the physical sciences because they provide insight into physical processes, organize large quantities of data, facilitate ‘scale analysis’ and establish ‘similarity’. Here I explore the use of dimensionless numbers in plant biology, focusing on the expansive growth rate of plant, fungal, and algal cells.
Class VIIIb APETALA2 Ethylene Response Factors in Plant Development Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-23 John W. Chandler
The APETALA2 (AP2) transcription factor superfamily in many plant species is extremely large. In addition to well-documented roles in stress responses, some AP2 members in arabidopsis, such as those of subgroup VIIIb, which includes DORNRÖSCHEN, DORNRÖSCHEN-LIKE, PUCHI, and LEAFY PETIOLE, are also important developmental regulators throughout the plant life cycle. Information is accumulating from orthologs of these proteins in important crop species that they influence key agronomic traits, such as the release of bud-burst in woody perennials and floral meristem identity and branching in cereals, and thereby represent potential for agronomic improvement. Given the increasing recognition of their developmental significance, this review highlights the function of these proteins and addresses their phylogenetic and evolutionary relationships.
Alternative Splicing Control of Abiotic Stress Responses Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-23 Tom Laloum, Guiomar Martín, Paula Duque
Alternative splicing, which generates multiple transcripts from the same gene, is an important modulator of gene expression that can increase proteome diversity and regulate mRNA levels. In plants, this post-transcriptional mechanism is markedly induced in response to environmental stress, and recent studies have identified alternative splicing events that allow rapid adjustment of the abundance and function of key stress-response components. In agreement, plant mutants defective in splicing factors are severely impaired in their response to abiotic stress. Notably, mounting evidence indicates that alternative splicing regulates stress responses largely by targeting the abscisic acid (ABA) pathway. We review here current understanding of post-transcriptional control of plant stress tolerance via alternative splicing and discuss research challenges for the near future.
MTPSLs: New Terpene Synthases in Nonseed Plants Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-20 Qidong Jia, Tobias G. Köllner, Jonathan Gershenzon, Feng Chen
Terpenes constitute a large class of plant secondary metabolites. It was once presumed that these compounds are biosynthesized by typical plant terpene synthases in all land plants. This view has changed with the identification of a new group of terpene synthase genes called MTPSLs for microbial terpene synthase-like genes. MTPSLs are structurally and phylogenetically more related to bacterial and fungal terpene synthases than to typical plant terpene synthases. They are widely distributed in nonseed plants but absent in seed plants and green algae. Much of the terpene diversity in nonseed plants is presumed to be determined by MTPSLs. Phylogenetic analysis suggests that ancestral MTPSL genes were acquired by early land plants from bacteria and fungi through horizontal gene transfer.
New Molecular Mechanisms to Reduce Arsenic in Crops Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-19 Emma R. Lindsay, Frans J.M. Maathuis
Arsenic is toxic to all life forms and is a potent carcinogen. Its accumulation in crop plants and subsequent consumption poses a serious threat to public health worldwide. Recent developments have enhanced our understanding of the molecular mechanisms governing arsenic uptake, detoxification, and accumulation in plants. In particular, the identification of plant arsenate reductase enzymes and emerging details of the processes underlying arsenic distribution and deposition in the seed will prove invaluable in the development of new strategies to mitigate this threat. Here we provide an outline of these recent developments and suggest new molecular mechanisms that could be employed to reduce arsenic in crops.
Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-19 Carla P. Coelho, Pu Huang, Dong-Yeon Lee, Thomas P. Brutnell
The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C4 kranz anatomy, with implications for the engineering of C4 traits into C3 crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C4 photosynthesis and other developmental processes.
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-17 Joelle Sasse, Enrico Martinoia, Trent Northen
Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant–microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly.
Mixed-Ploidy Species: Progress and Opportunities in Polyploid Research Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-17 Filip Kolář, Martin Čertner, Jan Suda, Peter Schönswetter, Brian C. Husband
Mixed-ploidy species harbor a unique form of genomic and phenotypic variation that influences ecological interactions, facilitates genetic divergence, and offers insights into the mechanisms of polyploid evolution. However, there have been few attempts to synthesize this literature. We review here research on the cytotype distribution, diversity, and dynamics of intensively studied mixed-ploidy species and consider the implications for understanding mechanisms of polyploidization such as cytotype formation, establishment, coexistence, and post-polyploid divergence. In general, mixed-ploidy species are unevenly represented among families: they exhibit high cytotype diversity, often within populations, and frequently comprise rare and odd-numbered ploidies. Odd-ploidies often occur in association with asexuality. We highlight research hypotheses and opportunities that take advantage of the unique properties of ploidy variation.
Balancing Immunity and Yield in Crop Plants Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-14 Yuese Ning, Wende Liu, Guo-Liang Wang
Crop diseases cause enormous yield losses and threaten global food[ED1] security. The use of highly resistant cultivars can effectively control plant diseases, but in crops, genetic immunity to disease often comes with an unintended reduction in growth and yield. Here, we review recent advances in understanding how nucleotide-binding domain, leucine-rich repeat (NLR) receptors and cell wall-associated kinase (WAK) proteins function in balancing immunity and yield. We also discuss the role of plant hormones and transcription factors in regulating the trade-offs between plant growth and immunity. Finally, we describe how a novel mechanism of translational control of defense proteins can enhance immunity without the reduction in fitness.
Small RNAs: Big Impact on Plant Development Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-12 Marco D’Ario, Sam Griffiths-Jones, Minsung Kim
While the role of proteins in determining cell identity has been extensively studied, the contribution of small noncoding RNA molecules such as miRNAs and siRNAs has been also recognised. miRNAs bind to complementary sites in target mRNA molecules to trigger the degradation or translational inhibition of those targets. Recent studies have revealed that miRNAs play pivotal roles in key developmental processes such as patterning of the embryo, meristem, leaf, and flower. Furthermore, these miRNAs have been recruited throughout plant evolution into pathways that create diverse plant organ forms and shapes. This review focuses on the roles of miRNAs in establishing plant cell identity during key plant development processes and creating morphological diversity during plant evolution.
Bridging Scales in Plant Biology Using Network Science Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-10 Salva Duran-Nebreda, George W. Bassel
Three recent studies have captured the organizational properties of plants at each the cellular, organ, and whole organism level. Data abstraction into networks enabled topological analyses to be performed, identifying optimizations within each scale. Multiscale network analysis provides the opportunity to integrate these levels, and quantitatively link genotype to phenotype.
Oxygen, Energy, and Light Signalling Direct Meristem Fate Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-10 Michael J. Considine
Light, nutrition, and oxygen are each important cues for developmental transitions in plants. A small number of recent studies have converged to give the first indication of how these environmental cues act together and independently via auxin, cytokinin, and ethylene to regulate cell proliferation in the root and shoot meristems.
Plant Phospholipid Diversity: Emerging Functions in Metabolism and Protein–Lipid Interactions Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-06 Yuki Nakamura
Phospholipids are essential components of biological membranes and signal transduction cascades in plants. In recent years, plant phospholipid research was greatly advanced by the characterization of numerous mutants affected in phospholipid biosynthesis and the discovery of a number of functionally important phospholipid-binding proteins. It is now accepted that most phospholipids to some extent have regulatory functions, including those that serve as constituents of biological membranes. Phospholipids are more than an inert end product of lipid biosynthesis. This review article summarizes recent advances on phospholipid biosynthesis with a particular focus on polar head group synthesis, followed by a short overview on protein–phospholipid interactions as an emerging regulatory mechanism of phospholipid function in arabidopsis (Arabidopsis thaliana).
Stabilizing the Transcription Factors by E3 Ligase COP1 Trends Plant. Sci. (IF 11.911) Pub Date : 2017-10-04 Ying Pan, Hui Shi
Photomorphogenesis is oppositely regulated by two groups of transcription factors. CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) degrades the positive factors but stabilizes the negative ones to predominantly repress photomorphogenesis. It is known that COP1 degrades substrates as an E3 ligase. Two recent studies unraveled the long-sought mechanisms of how COP1 stabilizes the negative transcription factors.
Novel Stress in Plants by Altering the Photoperiod Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-29 Silvia Nitschke, Anne Cortleven, Thomas Schmülling
Recent work has shown that changing the photoperiod induces stress in Arabidopsis thaliana. It has particularly dramatic consequences in cytokinin-deficient plants and clock mutants. Here, we argue that studying the impact of an altered photoperiod will provide novel insights into the circadian clock, factors regulating it, and pathways under its control.
Plant Systems Biology at the Single-Cell Level Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-29 Marc Libault, Lise Pingault, Prince Zogli, John Schiefelbein
Our understanding of plant biology is increasingly being built upon studies using ‘omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system.
Are GM Crops for Yield and Resilience Possible? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-29 Matthew J. Paul, Michael L. Nuccio, Shib Sankar Basu
Crop yield improvements need to accelerate to avoid future food insecurity. Outside Europe, genetically modified (GM) crops for herbicide- and insect-resistance have been transformative in agriculture; other traits have also come to market. However, GM of yield potential and stress resilience has yet to impact on food security. Genes have been identified for yield such as grain number, size, leaf growth, resource allocation, and signaling for drought tolerance, but there is only one commercialized drought-tolerant GM variety. For GM and genome editing to impact on yield and resilience there is a need to understand yield-determining processes in a cell and developmental context combined with evaluation in the grower environment. We highlight a sugar signaling mechanism as a paradigm for this approach.
Genomic Selection in Plant Breeding: Methods, Models, and Perspectives Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-28 José Crossa, Paulino Pérez-Rodríguez, Jaime Cuevas, Osval Montesinos-López, Diego Jarquín, Gustavo de los Campos, Juan Burgueño, Juan M. Camacho-González, Sergio Pérez-Elizalde, Yoseph Beyene, Susanne Dreisigacker, Ravi Singh, Xuecai Zhang, Manje Gowda, Manish Roorkiwal, Jessica Rutkoski, Rajeev K. Varshney
Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype × environment (G × E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding.
Plant Volatiles: Going ‘In’ but not ‘Out’ of Trichome Cavities Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-25 Alain Tissier, John A. Morgan, Natalia Dudareva
Plant glandular trichomes are able to secrete and store large amounts of volatile organic compounds (VOCs). VOCs typically accumulate in dedicated extracellular spaces, which can be either subcuticular, as in the Lamiaceae or Asteraceae, or intercellular, as in the Solanaceae. Volatiles are retained at high concentrations in these storage cavities with limited release into the atmosphere and without re-entering the secretory cells, where they would be toxic. This implies the existence of mechanisms allowing transport of VOCs to the cavity but preventing their diffusion out once they have been delivered. The cuticle and cell wall lining the cavity are likely to have key roles in retaining volatiles, but their exact composition and the potential molecular players involved are largely unknown.
Phytochrome Responses: Think Globally, Act Locally Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-21 Carlos L. Ballaré
Localized responses to changes in the red to far-red ratio (R:FR) allow plants to efficiently forage for light in patchy canopies, and to fine-tune physiological activities to the local light environment. Recent studies are elucidating the molecular mechanisms that mediate localized responses to R:FR and the functional implications of these responses.
Pearl Millet Genome: Lessons from a Tough Crop Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-19 Marilyne Debieu, Ghislain Kanfany, Laurent Laplaze
Pearl millet is an important cereal for food security in the arid regions of Africa and India. The recently published genome of this tough cereal crop has shed new light on its history and adaptation to dry, hot climates and paves the way for much-needed genomic-based breeding efforts.
Epicormic Resprouting in Fire-Prone Ecosystems Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-17 Juli G. Pausas, Jon E. Keeley
Many plants resprout from basal buds after disturbance, and this is common in shrublands subjected to high-intensity fires. However, resprouting after fire from epicormic (stem) buds is globally far less common. Unlike basal resprouting, post-fire epicormic resprouting is a key plant adaptation for retention of the arborescent skeleton after fire, allowing rapid recovery of the forest or woodland and leading to greater ecosystem resilience under recurrent high-intensity fires. Here we review the biogeography of epicormic resprouting, the mechanisms of protection, the fire regimes where it occurs, and the evolutionary drivers that shaped this trait. We propose that epicormic resprouting is adaptive in ecosystems with high fire frequency and relatively high productivity, at moderate–high fire intensities.
Non-26S Proteasome Endomembrane Trafficking Pathways in ABA Signaling Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-14 Feifei Yu, Qi Xie
The phytohormone abscisic acid (ABA) is a vital endogenous messenger that regulates diverse physiological processes in plants. The regulation of ABA signaling has been well studied at both the transcriptional and translational levels. Post-translational modification of key regulators in ABA signaling by the 26S ubiquitin proteasome pathway is well known. Recently, increasing evidence demonstrates that atypical turnover of key regulators by the endocytic trafficking pathway and autophagy also play vital roles in ABA perception, signaling, and action. We summarize and synthesize here recent findings in the field of ABA signaling.
Epichloë Fungal Endophytes and Plant Defenses: Not Just Alkaloids Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-08 Daniel A. Bastias, M. Alejandra Martínez-Ghersa, Carlos L. Ballaré, Pedro E. Gundel
Although the role of fungal alkaloids in protecting grasses associated with Epichloë fungal endophytes has been extensively documented, the effects of the symbiont on the host plant’s immune responses have received little attention. We propose that, in addition to producing protective alkaloids, endophytes enhance plant immunity against chewing insects by promoting endogenous defense responses mediated by the jasmonic acid (JA) pathway. We advance a model that integrates this dual effect of endophytes on plant defenses and test its predictions by means of a standard meta-analysis. This analysis supports a role of Epichloë endophytes in boosting JA-mediated plant defenses. We discuss the ecological scenarios where this effect of endophytes on plant defenses would be most beneficial for increasing plant fitness.
Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-05 Fei Zhang, Alan May, Vivian F. Irish
The WUSCHEL (WUS) gene is necessary for the maintenance of stem cells in the shoot apical meristem. Four recent reports show that cytokinin responsive type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) directly activate WUS expression, providing a long-awaited explanation for how cytokinin influences the maintenance of the stem cell niche.
Divergence in How Genetic Pathways Respond to Environments Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-05 Kathleen Donohue
An upstream gene in the pathway that induces flowering in response to cold has been identified. The gene, RVR1, occurs in several plant lineages and operates in a pathway that exhibits functional divergence across development and across taxa. Such divergence can provide insight into how genetic pathways evolve.
Challenges towards Revitalizing Hemp: A Multifaceted Crop Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-05 Craig Schluttenhofer, Ling Yuan
Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop.
Determining Cellular Responses: Phytoglobins May Direct the Traffic Trends Plant. Sci. (IF 11.911) Pub Date : 2017-09-04 Claudio Stasolla, Robert D. Hill
How stem cells retain their undifferentiated state or how differentiated cells are capable of having dissimilar responses to perturbations are major open questions in plant biology. Cell-specific phytoglobin expression may be one mechanism determining cell fate by the modulation of nitric oxide (NO), affecting cellular hormonal responses and processes such as cell differentiation.
Plant–Pathogen Maneuvering over Apoplastic Sugars Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-02 Muhammad Naseem, Meik Kunz, Thomas Dandekar
The nutrient-rich extracellular plant compartment, the apoplast, is an attractive niche for attacks by microbial pathogens. Here, we highlight recent trends in plant–pathogen competition for apoplastic sugars in the context of innate immune responses in various plant–pathogen interaction systems.
Plant-derived Secondary Organic Material in the Air and Ecosystems Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-05 J.K. Holopainen, M. Kivimäenpää, S.A. Nizkorodov
Biogenic secondary organic aerosol (SOA) and deposited secondary organic material (SOM) are formed by oxidation of volatile organic compounds (VOCs) emitted by plants. Many SOA compounds have much longer chemical lifetimes than the original VOC, and may accumulate on plant surfaces and in soil as SOM because of their low volatility. This suggests that they may have important and presently unrecognized roles in plant adaptation. Using reactive plant terpenoids as a model we propose a three-tier (atmosphere–vegetation–soil) framework to better understand the ecological and evolutionary functions of SOM. In this framework, SOA in the atmosphere is known to affect solar radiation, SOM on the plant surfaces influences the interactive organisms, and wet and dry deposition of SOM on soil affects soil organisms.
Plant Hormones: Key Players in Gut Microbiota and Human Diseases? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-22 Emilie Chanclud, Benoît Lacombe
It is well established that plant hormones such as auxins, cytokinins (CKs), and abscisic acid (ABA) not only govern important plant physiological traits but are key players in plant–microbe interactions. A poorly appreciated fact, however, is that both microbes and animals produce and perceive plant hormones and their mimics. Moreover, dietary plant hormones impact on human physiological process such as glucose assimilation, inflammation, and cell division. This leads us to wonder whether plant hormones could ensure functions in microbes per se as well as in animal–microbe interactions. We propose here and explore the hypothesis that plant hormones play roles in animal–microbiota relationships, with consequences for human health.
A Conceptual Framework for Integrated Pest Management Trends Plant. Sci. (IF 11.911) Pub Date : 2017-07-04 Johan A. Stenberg
The concept of integrated pest management (IPM) has been accepted and incorporated in public policies and regulations in the European Union and elsewhere, but a holistic science of IPM has not yet been developed. Hence, current IPM programs may often be considerably less efficient than the sum of separately applied individual crop protection actions. Thus, there is a clear need to formulate general principles for synergistically combining traditional and novel IPM actions to improve efforts to optimize plant protection solutions. This paper addresses this need by presenting a conceptual framework for a modern science of IPM. The framework may assist attempts to realize the full potential of IPM and reduce risks of deficiencies in the implementation of new policies and regulations.
Steering Soil Microbiomes to Suppress Aboveground Insect Pests Trends Plant. Sci. (IF 11.911) Pub Date : 2017-07-27 Ana Pineda, Ian Kaplan, T. Martijn Bezemer
Soil-borne microbes affect aboveground herbivorous insects through a cascade of molecular and chemical changes in the plant, but knowledge of these microbe–plant–insect interactions is mostly limited to one or a few microbial strains. Yet, the soil microbial community comprises thousands of unique taxa interacting in complex networks, the so-called ‘microbiome’, which provides plants with multiple beneficial functions. There has been little exploration of the role and management of whole microbiomes in plant–insect interactions, calling for the integration of this complexity in aboveground–belowground research. Here, we propose holistic approaches to select soil microbiomes that can be used to protect plants from aboveground attackers.
Sensing Danger: Key to Activating Plant Immunity Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-02 Andrea A. Gust, Rory Pruitt, Thorsten Nürnberger
In both plants and animals, defense against pathogens relies on a complex surveillance system for signs of danger. Danger signals may originate from the infectious agent or from the host itself. Immunogenic plant host factors can be roughly divided into two categories: molecules which are passively released upon cell damage (‘classical’ damage-associated molecular patterns, DAMPs), and peptides which are processed and/or secreted upon infection to modulate the immune response (phytocytokines). We highlight the ongoing challenge to understand how plants sense various danger signals and integrate this information to produce an appropriate immune response to diverse challenges.
Cytokinins in Symbiotic Nodulation: When, Where, What For? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-07-21 Pascal Gamas, Mathias Brault, Marie-Françoise Jardinaud, Florian Frugier
Substantial progress has been made in the understanding of early stages of the symbiotic interaction between legume plants and rhizobium bacteria. Those include the specific recognition of symbiotic partners, the initiation of bacterial infection in root hair cells, and the inception of a specific organ in the root cortex, the nodule. Increasingly complex regulatory networks have been uncovered in which cytokinin (CK) phytohormones play essential roles in different aspects of early symbiotic stages. Intriguingly, these roles can be either positive or negative, cell autonomous or non-cell autonomous, and vary, depending on time, root tissues, and possibly legume species. Recent developments on CK symbiotic functions and interconnections with other signaling pathways during nodule initiation are the focus of this review.
Multiple Routes of Light Signaling during Root Photomorphogenesis Trends Plant. Sci. (IF 11.911) Pub Date : 2017-07-10 Hyo-Jun Lee, Young-Joon Park, Jun-Ho Ha, Ian T. Baldwin, Chung-Mo Park
Plants dynamically adjust their architecture to optimize growth and performance under fluctuating light environments, a process termed photomorphogenesis. A variety of photomorphogenic responses have been studied extensively in the shoots, where diverse photoreceptors and signaling molecules have been functionally characterized. Notably, accumulating evidence demonstrates that the underground roots also undergo photomorphogenesis, raising the question of how roots perceive and respond to aboveground light. Recent findings indicate that root photomorphogenesis is mediated by multiple signaling routes, including shoot-to-root transmission of mobile signaling molecules, direct sensing of light by the roots, and light channeling through the plant body. In this review we discuss recent advances in how light signals are transmitted to the roots to trigger photomorphogenic responses.
Plant ESCRT Complexes: Moving Beyond Endosomal Sorting Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-31 Caiji Gao, Xiaohong Zhuang, Jinbo Shen, Liwen Jiang
The endosomal sorting complex required for transport (ESCRT) machinery is an ancient system that deforms membrane and severs membrane necks from the inside. Extensive evidence has accumulated to demonstrate the conserved functions of plant ESCRTs in multivesicular body (MVB) biogenesis and MVB-mediated membrane protein sorting. In addition, recent exciting findings have uncovered unique plant ESCRT components and point to emerging roles for plant ESCRTs in non-endosomal sorting events such as autophagy, cytokinesis, and viral replication. Plant-specific processes, such as abscisic acid (ABA) signaling and chloroplast turnover, provide further evidence for divergences in the functions of plant ESCRTs during evolution. We summarize the multiple roles and current working models for plant ESCRT machinery and speculate on future ESCRT studies in the plant field.
Strigolactones and Gibberellins: A New Couple in the Phytohormone World? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-24 Marek Marzec
Strigolactones (SLs) and gibberellins (GAs) are plant hormones that share some unique aspects of their perception and signalling pathways. Recent discoveries indicate that these two phytohormones may act together in processes of plant development and that SL biosynthesis is regulated by GAs.
Exploiting DELLA Signaling in Cereals Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-24 Karel Van De Velde, Philip Ruelens, Koen Geuten, Antje Rohde, Dominique Van Der Straeten
The spectacular yield increases in rice and wheat during the green revolution were partly realized by reduced gibberellin (GA) synthesis or sensitivity, both causing the accumulation of DELLA proteins. Although insights into the regulation of plant growth and development by DELLA proteins advanced rapidly in arabidopsis (Arabidopsis thaliana), DELLA-mediated regulation of downstream responses in cereals has received little attention to date. Furthermore, translating this research from arabidopsis to cereals is challenging given their different growth patterns and our phylogenetic analysis which reveals that DELLA-related DGLLA proteins exist in cereals but not in arabidopsis. Therefore, understanding the molecular basis of DELLA function in cereals holds great potential to improve yield. In this review, we propose to extend the focus of DELLA functional research to cereals, and highlight the appropriate tools that are now available to achieve this.
To Stimulate or Inhibit? That Is the Question for the Function of Abscisic Acid Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-23 Jan F. Humplík, Véronique Bergougnoux, Elizabeth Van Volkenburgh
Physiologically, abscisic acid (ABA) is believed to be a general inhibitor of plant growth, including during the crucial early development of seedlings. However, this view contradicts many reports of stimulatory effects of ABA that, so far, have not been considered in the debate concerning ABA’s function in plant development. To address this apparent contradiction, we propose a hypothetical mechanism to explain how ABA might contribute to the promotion of cell expansion. We wish to overturn conventional views on ABA’s role during juvenile plant development and put forward the idea that, as for other phytohormones, the role of ABA is determined by dose and sensitivity and ranges from stimulatory to inhibitory effects.
Landscaping Crossover Interference Across a Genome Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-16 Lidan Sun, Jing Wang, Mengmeng Sang, Libo Jiang, Bingyu Zhao, Tangran Cheng, Qixiang Zhang, Rongling Wu
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations. We further discuss the crucial role of CO interference in amplifying and maintaining genetic diversity through sex-, stress-, and age-induced differentiation.
Climate Change, CO2, and Defense: The Metabolic, Redox, and Signaling Perspectives Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-12 Graham Noctor, Amna Mhamdi
Ongoing human-induced changes in the composition of the atmosphere continue to stimulate interest in the effects of high CO2 on plants, but its potential impact on inducible plant defense pathways remains poorly defined. Recently, several studies have reported that growth at elevated CO2 is sufficient to induce defenses such as the salicylic acid pathway, thereby increasing plant resistance to pathogens. These reports contrast with evidence that defense pathways can be promoted by photorespiration, which is inhibited at high CO2. Here, we review signaling, metabolic, and redox processes modulated by CO2 levels and discuss issues to be resolved in elucidating the relationships between primary metabolism, inducible defense, and biotic stress resistance.
Shaping an Optimal Soil by Root–Soil Interaction Trends Plant. Sci. (IF 11.911) Pub Date : 2017-08-10 Kemo Jin, Philip J. White, William R. Whalley, Jianbo Shen, Lei Shi
Crop production depends on the availability of water and mineral nutrients, and increased yields might be facilitated by a greater focus on roots–soil interactions. Soil properties affecting plant growth include drought, compaction, nutrient deficiency, mineral toxicity, salinity, and submergence. Plant roots respond to the soil environment both spatially and temporally by avoiding stressful soil environments and proliferating in more favorable environments. We observe that crops can be bred for specific root architectural and biochemical traits that facilitate soil exploration and resource acquisition, enabling greater crop yields. These root traits affect soil physical and chemical properties and might be utilized to improve the soil for subsequent crops. We argue that optimizing root–soil interactions is a prerequisite for future food security.
New Beginnings: Mitochondrial Renewal by Massive Mitochondrial Fusion Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-13 Ray J. Rose, David W. McCurdy
Massive mitochondrial fusion (MMF) in germinating arabidopsis seeds, together with earlier studies, suggests a significant role for MMF in the life cycle of flowering plants. MMF is likely to facilitate nucleoid transmission, mitochondrial DNA (mtDNA) recombination, and the homogenization of mitochondrial components, thus providing a type of quality control for mitochondrial populations in new generations.
Boosting Rice Yield by Fine-Tuning SPL Gene Expression Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-21 Lei Wang, Qifa Zhang
Plant architecture is an important determinant of crop yield. Recent studies showed that SPL family genes regulate the architecture of rice plants. SPLs inhibit tillering in general, but promote panicle branching at optimal expression levels to increase grain number. Fine-tuning the expression of SPL genes may provide useful strategies for crop improvement.
Autophagy: A Double-Edged Sword to Fight Plant Viruses Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-17 Marion Clavel, Simon Michaeli, Pascal Genschik
In metazoans, autophagy is an essential component of host defense against viruses, orchestrating their degradation. Such antiviral functions for autophagy have also been long suspected in the green lineage. Two recent reports provide molecular insights on how plants selectively send viral proteins and even particles to the vacuole.
On Plant Modularity Traits: Functions and Challenges Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-16 Gianluigi Ottaviani, Jana Martínková, Tomáš Herben, Juli G. Pausas, Jitka Klimešová
On-spot persistence, space occupancy, and recovery after damage are key plant functions largely understudied. Traits relevant to these functions are difficult to assess because of their relationships to plant modularity. We suggest that developing collection protocols for these traits is feasible and could facilitate their inclusion in global syntheses.
Diet of Arbuscular Mycorrhizal Fungi: Bread and Butter? Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-13 Mélanie K. Rich, Eva Nouri, Pierre-Emmanuel Courty, Didier Reinhardt
Most plants entertain mutualistic interactions known as arbuscular mycorrhiza (AM) with soil fungi (Glomeromycota) which provide them with mineral nutrients in exchange for reduced carbon from the plant. Mycorrhizal roots represent strong carbon sinks in which hexoses are transferred from the plant host to the fungus. However, most of the carbon in AM fungi is stored in the form of lipids. The absence of the type I fatty acid synthase (FAS-I) complex from the AM fungal model species Rhizophagus irregularis suggests that lipids may also have a role in nutrition of the fungal partner. This hypothesis is supported by the concerted induction of host genes involved in lipid metabolism. We explore the possible roles of lipids in the light of recent literature on AM symbiosis.
How Plant Root Exudates Shape the Nitrogen Cycle Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-07 Devrim Coskun, Dev T. Britto, Weiming Shi, Herbert J. Kronzucker
Although the global nitrogen (N) cycle is largely driven by soil microbes, plant root exudates can profoundly modify soil microbial communities and influence their N transformations. A detailed understanding is now beginning to emerge regarding the control that root exudates exert over two major soil N processes – nitrification and N2 fixation. We discuss recent breakthroughs in this area, including the identification of root exudates as nitrification inhibitors and as signaling compounds facilitating N-acquisition symbioses. We indicate gaps in current knowledge, including questions of how root exudates affect newly discovered microbial players and N-cycle components. A better understanding of these processes is urgent given the widespread inefficiencies in agricultural N use and their links to N pollution and climate change.
Revisiting Pivotal-Differential Genome Evolution in Wheat Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-22 Ghader Mirzaghaderi, Annaliese S. Mason
An interesting and possibly unique pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D, or A) together with one or two modified (differential) subgenomes, a status that has been referred to as ‘pivotal-differential’ genome evolution. In this review we discuss various mechanisms that could be responsible for this evolutionary pattern, as well as evidence for and against the putative evolutionary mechanisms involved. We suggest that, in light of recent advances in genome sequencing and related technologies in the wheat group, the time has come to reopen the investigation into pivotal-differential genome evolution.
Quantitatively Understanding Plant Signaling: Novel Theoretical–Experimental Approaches Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-28 Sophia L. Samodelov, Matias D. Zurbriggen
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical–experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
Angiosperm Plant Desiccation Tolerance: Hints from Transcriptomics and Genome Sequencing Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-13 Valentino Giarola, Quancan Hou, Dorothea Bartels
Desiccation tolerance (DT) in angiosperms is present in the small group of resurrection plants and in seeds. DT requires the presence of protective proteins, specific carbohydrates, restructuring of membrane lipids, and regulatory mechanisms directing a dedicated gene expression program. Many components are common to resurrection plants and seeds; however, some are specific for resurrection plants. Understanding how each component contributes to DT is challenging. Recent transcriptome analyses and genome sequencing indicate that increased expression is essential of genes encoding protective components, recently evolved, species-specific genes and non-protein-coding RNAs. Modification and reshuffling of existing cis-regulatory promoter elements seems to play a role in the rewiring of regulatory networks required for increased expression of DT-related genes in resurrection species.
Plant SAM-Domain Proteins Start to Reveal Their Roles Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-28 Grégoire Denay, Gilles Vachon, Renaud Dumas, Chloe Zubieta, François Parcy
Proteins often act in complexes assembled via protein–protein interaction domains. The sterile alpha motif (SAM) domain is one of the most prominent interaction domains in animals and is present in proteins of diverse functions. This domain allows head-to-tail closed oligomerisation or polymer formation resulting in homo- and/or heterocomplexes that have been shown to be important for proper protein localisation and function. In plants this domain is also present but has been poorly studied except for recent studies on the LEAFY floral regulator and the tRNA import component (TRIC)1/2 proteins. Here we catalogue SAM domain-containing proteins from arabidopsis (Arabidopsis thaliana), compare plant and other eukaryotic SAM domains, and perform homology modelling to probe plant SAM domain interaction capabilities.
The Algal Revolution Trends Plant. Sci. (IF 11.911) Pub Date : 2017-06-10 Juliet Brodie, Cheong Xin Chan, Olivier De Clerck, J. Mark Cock, Susana M. Coelho, Claire Gachon, Arthur R. Grossman, Thomas Mock, John A. Raven, Alison G. Smith, Hwan Su Yoon, Debashish Bhattacharya
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput ‘omic’ and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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