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De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

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Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.

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Plant Gene Seeker -PGS
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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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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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Novel signals in the regulation of Pi starvation responses in plants: facts and promises 

Novel signals in the regulation of Pi starvation responses in plants: facts and promises  | Plant Gene Seeker -PGS | Scoop.it
Plants have evolved numerous adaptive developmental and metabolic responses to cope with growth in conditions of limited phosphate (Pi). Regulation of these Pi starvation responses (PSR) at the organism level involves not only cellular Pi perception in different organs, but also inter-organ communication of Pi levels via systemic signaling. Here we summarize recent discoveries on Pi starvation sensing and signaling, with special emphasis on structure-function studies that showed a role for inositol polyphosphates (InsP) as intracellular Pi signals, and on genomic studies that identified a large number of mRNAs with inter-organ mobility, which provide an immense source of potential systemic signals in the control of PSR and other responses.
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Frontiers | Strigolactones Biosynthesis and Their Role in Abiotic Stress Resilience in Plants: A Critical Review | Plant Science

Frontiers | Strigolactones Biosynthesis and Their Role in Abiotic Stress Resilience in Plants: A Critical Review | Plant Science | Plant Gene Seeker -PGS | Scoop.it
Strigolactones (SLs) being new class of plant hormones, play regulatory roles against abiotic stresses in plants. There are multiple hormonal response pathways which are adapted by the plants to overcome these stressful environmental constraints to reduce the negative impact on overall crop plant productivity. Genetic modulation of the SLs could also be applied as a potential approach in this regard. However, endogenous plant hormones play central roles in adaptation to changing environmental conditions, by mediating growth, development, nutrient allocation, and source/sink transitions. In addition, the hormonal interactions can fine-tune the plant response and determine plant architecture in response to environmental stimuli such as nutrient deprivation and canopy shade. Considerable advancements and new insights into SLs biosynthesis, signalling and transport has been unleashed since the initial discovery. In this review we present basic overview of SL biosynthesis and perception with a detailed discussion on our present understanding of SLs and their critical role to tolerate environmental constraints. The SLs and ABA interplay during the abiotic stresses is particularly highlighted.
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Multiple Routes of Light Signaling during Root Photomorphogenesis

Multiple Routes of Light Signaling during Root Photomorphogenesis | Plant Gene Seeker -PGS | Scoop.it
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.
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Root Tip Shape Governs Root Elongation Rate under Increased Soil Strength

Root Tip Shape Governs Root Elongation Rate under Increased Soil Strength | Plant Gene Seeker -PGS | Scoop.it
Increased soil strength due to soil compaction or soil drying is a major limitation to root growth and crop productivity. Roots need to exert higher penetration force, resulting in increased penetration stress when elongating in soils of greater strength. This study aimed to quantify how the genotypic diversity of root tip geometry and root diameter influences root elongation under different levels of soil strength and to determine the extent to which roots adjust to increased soil strength. Fourteen wheat (Triticum aestivum) varieties were grown in soil columns packed to three bulk densities representing low, moderate, and high soil strength. Under moderate and high soil strength, smaller root tip radius-to-length ratio was correlated with higher genotypic root elongation rate, whereas root diameter was not related to genotypic root elongation. Based on cavity expansion theory, it was found that smaller root tip radius-to-length ratio reduced penetration stress, thus enabling higher root elongation rates in soils with greater strength. Furthermore, it was observed that roots could only partially adjust to increased soil strength. Root thickening was bounded by a maximum diameter, and root tips did not become more acute in response to increased soil strength. The obtained results demonstrated that root tip geometry is a pivotal trait governing root penetration stress and root elongation rate in soils of greater strength. Hence, root tip shape needs to be taken into account when selecting for crop varieties that may tolerate high soil strength.
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Leaf Hydraulic Architecture and Stomatal Conductance: A Functional Perspective

Leaf Hydraulic Architecture and Stomatal Conductance: A Functional Perspective | Plant Gene Seeker -PGS | Scoop.it
The structure of leaf vasculature viewed over a broad phylogenetic scale from lycophytes to eudicots correlates with stomatal conductance, providing the basis for the hypothesis that increasing vein density drove the evolution of high fluxes in angiosperms. Yet, the relationship between vascular
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Life behind the wall: sensing mechanical cues in plants

Life behind the wall: sensing mechanical cues in plants | Plant Gene Seeker -PGS | Scoop.it
There is increasing evidence that all cells sense mechanical forces in order to perform their functions. In animals, mechanotransduction has been studied during the establishment of cell polarity, fate, and division in single cells, and increasingly is studied in the context of a multicellular tissue. What about plant systems? Our goal in this review is to summarize what is known about the perception of mechanical cues in plants, and to provide a brief comparison with animals.
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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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Plant nitrogen nutrition: sensing and signaling

Plant nitrogen nutrition: sensing and signaling | Plant Gene Seeker -PGS | Scoop.it
In response to external fluctuations of nitrogen (N) supplies, plants can activate complex regulatory networks for optimizing N uptake and utilization. In this review, we highlight novel N-responsive sensors, transporters, and signaling molecules recently identified in the dicot Arabidopsis and the monocot rice, and discuss their potential roles in N sensing and signaling. Furthermore, over the last couple of years, N sensing has been shown to be affected by multiple external factors, which act as local signals to trigger systemic signaling coordinated by long-distance mobile signals. Understanding of this complex regulatory network provides a foundation for the development of novel strategies to increase the root N acquisition efficiency under varying N conditions for crop production.
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Root Bending Is Antagonistically Affected by Hypoxia and ERF-Mediated Transcription via Auxin Signaling

Root Bending Is Antagonistically Affected by Hypoxia and ERF-Mediated Transcription via Auxin Signaling | Plant Gene Seeker -PGS | Scoop.it
When plants encounter soil water logging or flooding, roots are the first organs to be confronted with reduced gas diffusion resulting in limited oxygen supply. Since roots do not generate photosynthetic oxygen, they are rapidly faced with oxygen shortage rendering roots particularly prone to damage. While metabolic adaptations to low oxygen conditions, which ensure basic energy supply, have been well characterized, adaptation of root growth and development have received less attention. In this study, we show that hypoxic conditions cause the primary root to grow sidewise in a low oxygen environment, possibly to escape soil patches with reduced oxygen availability. This growth behavior is reversible in that gravitropic growth resumes when seedlings are returned to normoxic conditions. Hypoxic root bending is inhibited by the group VII ethylene response factor (ERFVII) RAP2.12, as rap2.12-1 seedlings show exaggerated primary root bending. Furthermore, overexpression of the ERFVII member HRE2 inhibits root bending, suggesting that primary root growth direction at hypoxic conditions is antagonistically regulated by hypoxia and hypoxia-activated ERFVIIs. Root bending is preceded by the establishment of an auxin gradient across the root tip as quantified with DII-VENUS and is synergistically enhanced by hypoxia and the auxin transport inhibitor naphthylphthalamic acid. The protein abundance of the auxin efflux carrier PIN2 is reduced at hypoxic conditions, a response that is suppressed by RAP2.12 overexpression, suggesting antagonistic control of auxin flux by hypoxia and ERFVII. Taken together, we show that hypoxia triggers an escape response of the primary root that is controlled by ERFVII activity and mediated by auxin signaling in the root tip.

* ### Glossary

IAA
: indole-3-acetic acid
NPA
: naphthylphthalamic acid
RT-PCR
: reverse transcription-PCR
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Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives | Plant Gene Seeker -PGS | Scoop.it
There is a rapidly rising trend in the development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop molecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype–phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
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Plant Epigenomics

Plant Epigenomics | Plant Gene Seeker -PGS | Scoop.it
Epigenetic modifications contribute to phenotypic variation at multiple levels, from gene regulation, to development, stress response, and population-level phenotypic diversity and evolution. As sessile organisms, plants are particularly dependent on epigenetic mechanisms to express diverse phenotypic responses from the same genome sequence. Technological advances that allow genome-wide analysis of DNA or histone modifications coupled with new opportunities for editing the epigenome have the potential to reveal the functions of epigenetic regulation in plants. Here, Genome Biology highlights advances in our understanding of the functions of epigenetic modifications, and the application of this knowledge.
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New Phytologist - Virtual Issue - Root Traits

New Phytologist - Virtual Issue - Root Traits | Plant Gene Seeker -PGS | Scoop.it

New Phytologist has long been at the forefront of research on root biology, curating journal articles that have sought to advance our understanding and modeling of plant-mediated belowground processes, in special journal issues, and in sponsoring collaboration and discussion at symposia and workshops. This trend promises to continue for the foreseeable future; for example, the topic of plant roots will be highlighted in the upcoming 2017 Symposium, ‘Trait covariation: structural and functional relationships in plant ecology’. New Phytologist is now playing a prominent role in advancing the theme of root traits; the number of papers identified by a keyword search on ‘root traits’ in the journal has quintupled in the last 15 years. In a recently published Tansley insight, 2017 Tansley Medal winner Etienne Laliberté proposed six research frontiers for advancing belowground trait-based ecology: redefining fine roots, quantifying trait dimensionality, integrating mycorrhizas, broadening the suite of belowground traits, determining trait–environment linkages, and understanding ecosystem-level consequences. Research papers, Reviews, Letters, and Commentaries published in New Phytologist in recent years have all contributed to our understanding of these research frontiers, and we highlight this burgeoning ‘belowground movement’ in this Virtual Issue. Here, we present recent (2014–2017) papers in which root traits were the dominant focus, including papers describing the general concepts of root traits, how root traits can be harnessed by terrestrial biosphere models, and the relationships among root traits and root function, mycorrhizas, and ecosystem properties.

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