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Decoupling of soil nutrient cycles as a function of aridity in global drylands : Nature : Nature Publishing Group

Decoupling of soil nutrient cycles as a function of aridity in global drylands : Nature : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems.
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The biogeochemical cycles of carbon (C), nitrogen (N) and phosphorus (P) are interlinked by primary production, respiration and decomposition in terrestrial ecosystems1. It has been suggested that the C, N and P cycles could become uncoupled under rapid climate change because of the different degrees of control exerted on the supply of these elements by biological and geochemical processes1, 2, 3, 4, 5. Climatic controls on biogeochemical cycles are particularly relevant in arid, semi-arid and dry sub-humid ecosystems (drylands) because their biological activity is mainly driven by water availability6, 7, 8. The increase in aridity predicted for the twenty-first century in many drylands worldwide9, 10, 11 may therefore threaten the balance between these cycles, differentially affecting the availability of essential nutrients12, 13, 14. Here we evaluate how aridity affects the balance between C, N and P in soils collected from 224 dryland sites from all continents except Antarctica. We find a negative effect of aridity on the concentration of soil organic C and total N, but a positive effect on the concentration of inorganic P. Aridity is negatively related to plant cover, which may favour the dominance of physical processes such as rock weathering, a major source of P to ecosystems, over biological processes that provide more C and N, such as litter decomposition12, 13, 14. Our findings suggest that any predicted increase in aridity with climate change will probably reduce the concentrations of N and C in global drylands, but increase that of P. These changes would uncouple the C, N and P cycles in drylands and could negatively affect the provision of key services provided by these ecosystems.

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Light Signaling, Root Development, and Plasticity

Light Signaling, Root Development, and Plasticity | Plant Gene Seeker -PGS | Scoop.it

Light is the energy source for plants as it drives photosynthesis to produce sugars. Given the obvious fact that light mostly occurs above ground and not in the soil, most interactions of plants with light have been studied in shoot parts of the plant. Research over more than a century has yielded tremendous insights into how light not only drives photosynthesis but also acts as an environmental cue that informs plants about their environment. Light quality and duration, for example, drive major developmental changes such as photomorphogenesis, photoperiodic induction of flowering, phototropism, and shade avoidance (see, for example, the following recent reviews: Wu, 2014; Fankhauser and Christie, 2015; Xu et al., 2015; Ballaré and Pierik, 2017). The picture that has emerged is that plants have very detailed light signaling mechanisms, with photoreceptors dedicated to different wavelengths in the light spectrum and interactions between these photoreceptors themselves and their downstream signal transduction pathways. Studies have accumulated over the past 15 years, and intensified in recent years, showing pronounced effects of light on root physiology and development. Although some effects of light availability on root growth will be the simple consequence of differential sugar availability to the roots due to photosynthesis in the shoot, there is substantial evidence for more sophisticated signaling impacts of different aspects of the light environment. In this Update, we will briefly review the core light signaling mechanisms, their impact on root development and plasticity, and the functional implications of these aboveground-belowground interactions.

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Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless

Transcriptome analysis during ripening of table grape berry cv. Thompson Seedless | Plant Gene Seeker -PGS | Scoop.it
Ripening is one of the key processes associated with the development of major organoleptic characteristics of the fruit. This process has been extensively characterized in climacteric fruit, in contrast with non-climacteric fruit such as grape, where the process is less understood. With the aim of studying changes in gene expression during ripening of non-climacteric fruit, an Illumina based RNA-Seq transcriptome analysis was performed on four developmental stages, between veraison and harvest, on table grapes berries cv Thompson Seedless. Functional analysis showed a transcriptional increase in genes related with degradation processes of chlorophyll, lipids, macromolecules recycling and nucleosomes organization; accompanied by a decrease in genes related with chloroplasts integrity and amino acid synthesis pathways. It was possible to identify several processes described during leaf senescence, particularly close to harvest. Before this point, the results suggest a high transcriptional activity associated with the regulation of gene expression, cytoskeletal organization and cell wall metabolism, which can be related to growth of berries and firmness loss characteristic to this stage of development. This high metabolic activity could be associated with an increase in the transcription of genes related with glycolysis and respiration, unexpected for a non-climacteric fruit ripening.
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“La Vie en Rose”: Biosynthesis, Sources, and Applications of Betalain Pigments

Betalains are tyrosine-derived red-violet and yellow pigments found exclusively in plants of the Caryophyllales order, which have drawn both scientific and economic interest. Nevertheless, research into betalain chemistry, biochemistry, and function has been limited as comparison with other major classes of plant pigments such as anthocyanins and carotenoids. The core biosynthetic pathway of this pigment class has only been fully elucidated in the past few years, opening up the possibility for betalain pigment engineering in plants and microbes. In this review, we discuss betalain metabolism in light of recent advances in the field, with a current survey of characterized genes and enzymes that take part in betalain biosynthesis, catabolism, and transcriptional regulation, and an outlook of what is yet to be discovered. A broad view of currently used and potential new sources for betalains, including utilization of natural sources or metabolic engineering, is provided together with a summary of potential applications of betalains in research and commercial use.
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Auxin: small molecule, big impact | Journal of Experimental Botany 

Auxin: small molecule, big impact | Journal of Experimental Botany  | Plant Gene Seeker -PGS | Scoop.it

Auxin research touches on a very wide variety of processes in plant development, and correspondingly a range of systems and approaches is revealing new understanding. This special issue spans this range, from research on mosses and liverworts which is revealing evolutionary aspects to the exquisite detail of signalling processes shown in Arabidopsis and agronomic potential in crops. As well as compiling and analyzing our current knowledge on auxin action, the reviews also provide a roadmap for future research.

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Crop biotechnology: a pivotal moment for global acceptance

Crop biotechnology: a pivotal moment for global acceptance | Plant Gene Seeker -PGS | Scoop.it
The development and judicious use of agricultural biotechnology offers important contributions to food security and sustainability. Key contributions include improved yield, heightened pathogen and herbivore resistance, enhanced nutrient content, improved product quality, reduced spoilage, as well as entirely new traits. While a first wave of genetically engineered (GE) crop products has been commercialized and contributed to yield, other products – some posing significant benefits to target populations in the developing world – have become mired in controversy. Public misconception about nutritional and ecological risks, fears about multinational corporate dominance, as well as regulatory inaction have delayed the approval and use of GE crops. With new GE lines ready to pass through regulatory oversight, many of which originate from developing countries, we regard this as a pivotal moment for global acceptance of agricultural biotechnology. However, we note that some countries, international regulators, and even biotechnology companies seem willing to forego useful applications of GE crops. We conclude that educating and informing the public to combat misperception, and implementing review of regulatory guidelines based on decades of experience can help to realize the benefits of GE for food security, human well-being, and ecological sustainability.
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Crosstalk Complexities between Auxin, Cytokinin, and Ethylene in Arabidopsis Root Development: From Experiments to Systems Modeling, and Back Again

Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin, and ethylene are three important hormones that regulate many aspects of plant development. This review critically evaluates the crosstalk between the three hormones in Arabidopsis root development. We integrate a variety of experimental data into a crosstalk network, which reveals multiple layers of complexity in auxin, cytokinin, and ethylene crosstalk. In particular, data integration reveals an additional, largely overlooked link between the ethylene and cytokinin pathways, which acts through a phosphorelay mechanism. This proposed link addresses outstanding questions on whether ethylene application promotes or inhibits receptor kinase activity of the ethylene receptors. Elucidating the complexity in auxin, cytokinin, and ethylene crosstalk requires a combined experimental and systems modeling approach. We evaluate important modeling efforts for establishing how crosstalk between auxin, cytokinin, and ethylene regulates patterning in root development. We discuss how a novel methodology that iteratively combines experiments with systems modeling analysis is essential for elucidating the complexity in crosstalk of auxin, cytokinin, and ethylene in root development. Finally, we discuss the future challenges from a combined experimental and modeling perspective.

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Source and sink mechanisms of nitrogen transport and use

Source and sink mechanisms of nitrogen transport and use | Plant Gene Seeker -PGS | Scoop.it

Nitrogen is an essential nutrient for plant growth. World-wide, large quantities of nitrogenousfertilizer are applied to ensure maximum crop productivity. However, nitrogen fertilizerapplication is expensive and negatively affects the environment, and subsequently humanhealth. A strategy to address this problem is the development of crops that are efficient inacquiring and using nitrogen and that can achieve high seed yields with reduced nitrogen input.This review integrates the current knowledge regarding inorganic and organic nitrogenmanagement at the whole-plant level, spanning from nitrogen uptake to remobilization andutilization in source and sink organs. Plant partitioning and transient storage of inorganic andorganic nitrogen forms areevaluated, as is howthey affect nitrogenavailability, metabolism andmobilization. Essential functions of nitrogen transporters in source and sink organs and theirimportance in regulating nitrogen movement in support of metabolism, and vegetative andreproductive growth are assessed. Finally, we discuss recent advances in plant engineering,demonstrating that nitrogen transporters are effective targets to improve crop productivity andnitrogen use efficiency. While inorganic and organic nitrogen transporters were examinedseparately in these studies, they provide valuable clues about how to successfully combineapproaches for future crop engineering.

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Plant hormone transporters: what we know and what we would like to know

Plant hormone transporters: what we know and what we would like to know | Plant Gene Seeker -PGS | Scoop.it
Hormone transporters are crucial for plant hormone action, which is underlined by severe developmental and physiological impacts caused by their loss-of-function mutations. Here, we summarize recent knowledge on the individual roles of plant hormone transporters in local and long-distance transport. Our inventory reveals that many hormones are transported by members of distinct transporter classes, with an apparent dominance of the ATP-binding cassette (ABC) family and of the Nitrate transport1/Peptide transporter family (NPF). The current need to explore further hormone transporter regulation, their functional interaction, transport directionalities, and substrate specificities is briefly reviewed.
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Arabidopsis thaliana sucrose phosphate synthase (sps) genes are expressed differentially in organs and tissues, and their transcription is regulated by osmotic stress - ScienceDirect

Arabidopsis thaliana sucrose phosphate synthase (sps) genes are expressed differentially in organs and tissues, and their transcription is regulated by osmotic stress - ScienceDirect | Plant Gene Seeker -PGS | Scoop.it
Sucrose is synthesized from UDP-Glc and Fru-6-phosphate via the activity of sucrose-phosphate synthase (SPS) enzymes, which produce Suc-6-phosphate. Suc-6-phosphate is rapidly dephosphorylated by phosphatases to produce Suc and inorganic phosphate. Arabidopsis has four sps genes encoding SPS enzymes. Of these enzymes, AtSPS1F and AtSPS2F have been grouped with other dicotyledonous SPS enzymes, while AtSPS3F and AtSPS4F are included in groups with both dicotyledonous and monocotyledonous SPS enzymes. In this work, we generated Arabidopsis thaliana transformants containing the promoter region of each sps gene fused to gfp::uidA reporter genes. A detailed characterization of expression conferred by the sps promoters in organs and tissues was performed. We observed expression of AtSPS1F, AtSPS2F and AtSPS3F in the columella roots of the plants that support sucrose synthesis. Hence, these findings support the idea that sucrose synthesis occurs in the columella cells, and suggests that sucrose has a role in this tissue. In addition, the expression of AtSPS4F was identified in embryos and suggests its participation in this developmental stage. Quantitative transcriptional analysis of A. thaliana plants grown in media with different osmotic potential showed that AtSPS2F and AtSPS4F respond to osmotic stress.
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Root hairs enable high transpiration rates in drying soils

Root hairs enable high transpiration rates in drying soils | Plant Gene Seeker -PGS | Scoop.it

Do root hairs help roots take up water from the soil? Despite the well-documented role of root hairs in phosphate uptake, their role in water extraction is controversial. We grew barley (Hordeum vulgare cv Pallas) and its root-hairless mutant brb in a root pressure chamber, whereby the transpiration rate could be varied whilst monitoring the suction in the xylem. The method provides accurate measurements of the dynamic relationship between the transpiration rate and xylem suction. The relationship between the transpiration rate and xylem suction was linear in wet soils and did not differ between genotypes. When the soil dried, the xylem suction increased rapidly and non-linearly at high transpiration rates. This response was much greater with the brb mutant, implying a reduced capacity to take up water. We conclude that root hairs facilitate the uptake of water by substantially reducing the drop in matric potential at the interface between root and soil in rapidly transpiring plants. The experiments also reinforce earlier observations that there is a marked hysteresis in the suction in the xylem when the transpiration rate is rising compared with when it is falling, and possible reasons for this behavior are discussed.

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ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology | Plant Gene Seeker -PGS | Scoop.it
A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (<http://bar.utoronto.ca/eplant>;), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.

* ### Glossary

SNP
: single nucleotide polymorphism
ZUI
: zoomable user interface
RSVP
: rapid serial visual presentation
PPI
: protein-protein interaction
PDI
: protein-DNA interaction
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Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis 

Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis  | Plant Gene Seeker -PGS | Scoop.it
In nature and agriculture, nitrate availability is a main environmental cue for plant growth, development and stress responses. Nitrate signaling and regulation are hence at the center of communications between plant intrinsic programs and the environment. It is also well known that endogenous phytohormones play numerous critical roles in integrating extrinsic cues and intrinsic responses, regulating and refining almost all aspects of plant growth, development and stress responses. Therefore, interaction between nitrate and phytohormones, such as auxins, cytokinins, abscisic acid, gibberellins, and ethylene, is prevalent. The growing evidence indicates that biosynthesis, de-conjugation, transport, and signaling of hormones are partly controlled by nitrate signaling. Recent advances with nitrate signaling and transcriptional regulation in Arabidopsis give rise to new paradigms. Given the comprehensive nitrate transport, sensing, signaling and regulations at the level of the cell and organism, nitrate itself is a local and long-distance signal molecule, conveying N status at the whole-plant level. A direct molecular link between nitrate signaling and cell cycle progression was revealed with TEOSINTE BRANCHED1/CYCLOIDEA/ PROLIFERATING CELL FACTOR1-20 (TCP20) - NIN-LIKE PROTEIN 6/7 (NLP6/7) regulatory nexus. NLPs are key regulators of nitrogen responses in plants. TCPs function as the main regulators of plant morphology and architecture, with the emerging role as integrators of plant developmental responses to the environment. By analogy with auxin being proposed as a plant morphogen, nitrate may be an environmental morphogen. The morphogen-gradient-dependent and cell-autonomous mechanisms of nitrate signaling and regulation are an integral part of cell growth and cell identification. This is especially true in root meristem growth that is regulated by intertwined nitrate, phytohormones, and glucose-TOR signaling pathways. Furthermore, the nitrate transcriptional hierarchy is emerging. Nitrate regulators in primary nitrate signaling can individually and combinatorially control downstream transcriptional networks and hormonal pathways for signal propagation and amplification. Under the new paradigms, nitrate-induced hormone metabolism and signaling deserve fresh examination. The close interplay and convergent regulation of nitrate and hormonal signaling at morphological, physiological and molecular levels have significant effects on important agronomic traits, especially nutrient-dependent adaptive root system growth and architecture.
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BIG BROTHER Uncouples Cell Proliferation from Elongation in the Arabidopsis Primary Root | Plant and Cell Physiology | Oxford Academic

BIG BROTHER  Uncouples Cell Proliferation from Elongation in the Arabidopsis Primary Root | Plant and Cell Physiology | Oxford Academic | Plant Gene Seeker -PGS | Scoop.it
Plant organ size is sensitive to environmental conditions, but is also limited by hardwired genetic constraints. In Arabidopsis, a few organ size regulators have been identified. Among them, the BIG BROTHER (BB) gene has a prominent role in the determination of flower organ and leaf size. BB loss-of-function mutations result in a prolonged proliferation phase during leaf(‐like) organ formation, and consequently larger leaves, petals and sepals. Whether BB has a similar role in root growth is unknown. Here we describe a novel bb allele which carries a P235L point mutation in the BB RING finger domain. This allele behaves similarly to described bb loss-of-function alleles and displays increased root meristem size due to a higher number of dividing, meristematic cells. In contrast, mature cell length is unaffected. The increased meristematic activity does not, however, translate into overall enhanced root elongation, possibly because bb mutation also results in an increased number of cell files in the vascular cylinder. These extra formative divisions might offset any growth acceleration by extra meristematic divisions. Thus, although BB dampens root cell proliferation, the consequences on macroscopic root growth are minor. However, bb mutation accelerates overall root growth when introduced into sensitized backgrounds. For example, it partially rescues the short root phenotypes of the brevis radix and octopus mutants, but does not complement their phloem differentiation or transport defects. In summary, we provide evidence that BB acts conceptually similarly in leaf(‐like) organs and the primary root, and uncouples cell proliferation from elongation in the root meristem.
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Frontiers | Plant Responses to Biotic and Abiotic Stresses: Lessons from Cell Signaling

Frontiers | Plant Responses to Biotic and Abiotic Stresses: Lessons from Cell Signaling | Plant Gene Seeker -PGS | Scoop.it
Facing stressful conditions imposed by their environment and affecting their growth and their development throughout their life cycle, plants must be able to perceive, to process and to translate different stimuli into adaptive responses. Understanding the organism-coordinated responses involves a fine description of the mechanisms occurring at the cellular and molecular level. A major challenge is also to understand how the large diversity of molecules identified as signals, sensors or effectors could drive a cell to the appropriate plant response and to finally cope with various environmental cues. In this Research Topic we aim to provide an overview of various signaling mechanisms or to present new molecular signals involved in stress response and to demonstrate how basic/fundamental research on cell signaling will help to understand stress responses at the whole plant level.
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Genome Editing for Global Food Security

Global food security is increasingly challenging in light of population increase, the impact of climate change on crop production, and limited land available for agricultural expansion. Here we outline how genome editing provides excellent and timely methods to optimize crop plants, and argue the urgency for societal acceptance and support.

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Lateral root formation and the multiple roles of auxin | Journal of Experimental Botany 

Lateral root formation and the multiple roles of auxin | Journal of Experimental Botany  | Plant Gene Seeker -PGS | Scoop.it
Root systems can display variable architectures that contribute to survival strategies of plants. The model plant Arabidopsis thaliana possesses a tap root system, in which the primary root and lateral roots (LRs) are major architectural determinants. The phytohormone auxin fulfils multiple roles throughout LR development. In this review, we summarize recent advances in our understanding of four aspects of LR formation: (i) LR positioning, which determines the spatial distribution of lateral root primordia (LRP) and LRs along primary roots; (ii) LR initiation, encompassing the activation of nuclear migration in specified lateral root founder cells (LRFCs) up to the first asymmetric cell division; (iii) LR outgrowth, the ‘primordium-intrinsic’ patterning of de novo organ tissues and a meristem; and (iv) LR emergence, an interaction between LRP and overlaying tissues to allow passage through cell layers. We discuss how auxin signaling, embedded in a changing developmental context, plays important roles in all four phases. In addition, we discuss how rapid progress in gene network identification and analysis, modeling, and four-dimensional imaging techniques have led to an increasingly detailed understanding of the dynamic regulatory networks that control LR development.
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“NO way”! Says the plant to abiotic stress

“NO way”! Says the plant to abiotic stress | Plant Gene Seeker -PGS | Scoop.it
Nitric oxide (NO), a small sized, short lived, highly diffusible natured, gaseous, diatomic and bioactive molecule, has now gained an important position in plant science research, due to its multifunctional roles in physiological as well as pathological responses in plants. A detailed understanding of the molecular mechanisms of plants against various stresses revealed that production of NO and other reactive oxygen species (ROS) are known to interplay an essential role to counter those challenges. NO can directly or indirectly help in the modulation of different protein functions and the reprogramming of defense gene expression by interacting with certain targets. NO might act as a signal in activating ROS-scavenging enzyme activities under various abiotic stresses including drought, salinity, temperature, heavy metal and radiations stress. Furthermore, application of NO donor has tremendous potential to counteract damages in different segments of plants caused by various stresses. This review aims to discuss the overall role of NO in higher plants in response to abiotic stresses.
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The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress | Plant Gene Seeker -PGS | Scoop.it
Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epi-alleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.
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Frontiers | Insights into the Mechanisms Underlying Boron Homeostasis in Plants | Plant Science

Frontiers | Insights into the Mechanisms Underlying Boron Homeostasis in Plants | Plant Science | Plant Gene Seeker -PGS | Scoop.it
Boron is an essential element for plants but is toxic in excess. Therefore, plants must adapt to both limiting and excess boron conditions for normal growth. Boron transport in plants is primarily based on three transport mechanisms across the plasma membrane: passive diffusion of boric acid, facilitated diffusion of boric acid via channels, and export of borate anion via transporters. Under boron -limiting conditions, boric acid channels and borate exporters function in the uptake and translocation of boron to support growth of various plant species. In Arabidopsis thaliana, NIP5;1 and BOR1 are located in the plasma membrane and polarized toward soil and stele, respectively, in various root cells, for efficient transport of boron from the soil to the stele. Importantly, sufficient levels of boron induce downregulation of NIP5;1 and BOR1 through mRNA degradation and proteolysis through endocytosis, respectively. In addition, borate exporters, such as Arabidopsis BOR4 and barley Bot1, function in boron exclusion from tissues and cells under conditions of excess boron. Thus, plants actively regulate intracellular localization and abundance of transport proteins to maintain boron homeostasis. In this review, the physiological roles and regulatory mechanisms of intracellular localization and abundance of boron transport proteins are discussed.
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Connecting salt stress signalling pathways with salinity‐induced changes in mitochondrial metabolic processes in C3 plants

Salinity exerts a severe detrimental effect on crop yields globally. Growth of plants in saline soils results in physiological stress, which disrupts the essential biochemical processes of respiration, photosynthesis, and transpiration. Understanding the molecular responses of plants exposed to salinity stress can inform future strategies to reduce agricultural losses due to salinity; however, it is imperative that signalling and functional response processes are connected to tailor these strategies. Previous research has revealed the important role that plant mitochondria play in the salinity response of plants. Review of this literature shows that 2 biochemical processes required for respiratory function are affected under salinity stress: the tricarboxylic acid cycle and the transport of metabolites across the inner mitochondrial membrane. However, the mechanisms by which components of these processes are affected or react to salinity stress are still far from understood. Here, we examine recent findings on the signal transduction pathways that lead to adaptive responses of plants to salinity and discuss how they can be involved in and be affected by modulation of the machinery of energy metabolism with attention to the role of the tricarboxylic acid cycle enzymes and mitochondrial membrane transporters in this process.

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Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (V. vinifera cv. Shiraz)

Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (V. vinifera cv. Shiraz) | Plant Gene Seeker -PGS | Scoop.it
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant’s phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia Methylation Sensitive Amplified Polymorphisms (MSAP) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive Genotyping By Sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique GO terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
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Cold sensing in grapevine—Which signals are upstream of the microtubular “thermometer”

Cold sensing in grapevine—Which signals are upstream of the microtubular “thermometer” | Plant Gene Seeker -PGS | Scoop.it

Plants can acquire freezing tolerance in response to cold but non-freezing temperatures. To efficiently activate this cold acclimation, low temperature has to be sensed and processed swiftly, a process that is linked with a transient elimination of microtubules. Here, we address cold-induced microtubules elimination in a grapevine cell line stably expressing a green fluorescent protein fusion of Arabidopsis TuB6, which allows to follow their response in vivo and to quantify this response by quantitative image analysis. We use time-course studies with several specific pharmacological inhibitors and activators to dissect the signalling events acting upstream of microtubules elimination. We find that microtubules disappear within 30 min after the onset of cold stress. We provide evidence for roles of calcium influx, membrane rigidification, and activation of NAD(P)H oxidase as factors in signal susception and amplification. We further conclude that a G-protein in concert with a phospholipase D convey the signal towards microtubules, whereas calmodulin seems to be not involved. Moreover, activation of jasmonate pathway in response to cold is required for an efficient microtubule response. We summarize our findings in a working model on a complex signalling hub at the membrane-cytoskeleton interphase that assembles the susception, perception and early transduction of cold signals.

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Genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value

Genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value | Plant Gene Seeker -PGS | Scoop.it

Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots. The genome is highly repetitive (64.5% repeat content) and contains 54 438 protein-coding genes and 192 microRNA genes, with more than 99.3% having orthologous genes from glycophylic species. Stress tolerance in quinoa is associated with the expansion of genes involved in ion and nutrient transport, ABA homeostasis and signaling, and enhanced basal-level ABA responses. Epidermal salt bladder cells exhibit similar characteristics as trichomes, with a significantly higher expression of genes related to energy import and ABA biosynthesis compared with the leaf lamina. The quinoa genome sequence provides insights into its exceptional nutritional value and the evolution of halophytes, enabling the identification of genes involved in salinity tolerance, and providing the basis for molecular breeding in quinoa.

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Frontiers | Potassium in the Grape (Vitis vinifera L.) Berry: Transport and Function

Frontiers | Potassium in the Grape (Vitis vinifera L.) Berry: Transport and Function | Plant Gene Seeker -PGS | Scoop.it
K+ is the most abundant cation in the grape berry. Here we focus on the most recent information in the long distance transport and partitioning of K+ within the grapevine and postulate on the potential role of K+ in berry sugar accumulation, berry water relations, cellular growth, disease resistance and abiotic stress tolerance. By integrating information from several different plant systems we have been able to generate new hypotheses on the integral functions of this predominant cation and to improve our understanding of how these functions contribute to grape berry growth and ripening. Valuable contributions to the study of K+ in membrane stabilisation, turgor maintenance and phloem transport have allowed us to propose a mechanistic model for the role of this cation in grape berry development.
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Scooped by Andres Zurita
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Conservation and divergence of small RNA pathways and microRNAs in land plants

Conservation and divergence of small RNA pathways and microRNAs in land plants | Plant Gene Seeker -PGS | Scoop.it
As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants. Using 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms. Our phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants.
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