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Identification and Characterization of an Arabidopsis Mutant with Altered Localization of NIP5;1, a Plasma Membrane Boric Acid Channel, Reveals the Requirement for d-Galactose in Endomembrane Organ...

Identification and Characterization of an Arabidopsis Mutant with Altered Localization of NIP5;1, a Plasma Membrane Boric Acid Channel, Reveals the Requirement for d-Galactose in Endomembrane Organ... | Plant Gene Seeker -PGS | Scoop.it
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Endomembrane organization is important for various aspects of cell physiology, including membrane protein trafficking. To explore the molecular mechanisms regulating the trafficking of plasma membrane-localized proteins in plants, we screened for Arabidopsis mutants with defective localization of green fluorescent protein (GFP)–nodulin 26-like intrinsic protein (NIP)5;1. Fluorescence imaging-based screening led to the isolation of a mutant which accumulated abnormal intracellular aggregates labeled by GFP–NIP5;1. The aggregates appeared in epidermal cells in the root elongation zone and included the trans-Golgi network/early endosomes. Rough mapping and whole-genome sequencing identified the mutant as an allele of UDP-glucose 4-epimerase 4 (uge4)/root hair defective 1 (rhd1) /root epidermal bulgar 1 (reb 1), which was originally defined as a cell wall mutant. The responsible gene encodes UDP-glucose 4-epimerase 4 (UGE4), which functions in the biosynthesis of D-galactose, especially for the synthesis of the cell wall polysaccharide xyloglucan and arabinogalactan proteins (AGPs). The endomembrane aggregates in the mutants were absent in the presence of D-galactose, indicative of a requirement for a D-galactose-containing component in endomembrane organization. Genetic and pharmacological analyses suggested that the aggregates were not caused by the disruption of cell wall polysaccharides or the cytoskeleton. Overall, our results suggest that UGE4 activity in D-galactose synthesis is required for the structure of cell wall polysaccharides and endomembrane organization.

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Plant Hormone Homeostasis, Signaling, and Function during Adventitious Root Formation in Cuttings | Frontiers in Plant Science

Plant Hormone Homeostasis, Signaling, and Function during Adventitious Root Formation in Cuttings | Frontiers in Plant Science | Plant Gene Seeker -PGS | Scoop.it
Adventitious root (AR) formation in cuttings is a multiphase developmental process, resulting from wounding at the cutting site and isolation from the resource and signal network of the whole plant. Though, promotive effects of auxins are widely used for clonal plant propagation, the regulation and function of plant hormones and their intricate signaling networks during AR formation in cuttings are poorly understood. In this focused review, we discuss our recent publications on the involvement of polar auxin transport (PAT) and transcriptional regulation of auxin and ethylene action during AR formation in petunia cuttings in a broad context. Integrating new findings on cuttings of other plant species and general models on plant hormone networks, a model on the regulation and function of auxin, ethylene, and jasmonate in AR formation of cuttings is presented. PAT and cutting off from the basipetal auxin drain are considered as initial principles generating early accumulation of IAA in the rooting zone. This is expected to trigger a self-regulatory process of auxin canalization and maximization to responding target cells, there inducing the program of AR formation. Regulation of auxin homeostasis via auxin influx and efflux carriers, GH3 proteins and peroxidases, of flavonoid metabolism, and of auxin signaling via AUX/IAA proteins, TOPLESS, ARFs, and SAUR-like proteins are postulated as key processes determining the different phases of AR formation. NO and H2O2 mediate auxin signaling via the cGMP and MAPK cascades. Transcription factors of the GRAS-, AP2/ERF-, and WOX-families link auxin signaling to cell fate specification. Cyclin-mediated governing of the cell cycle, modifications of sugar metabolism and microtubule and cell wall remodeling are considered as important implementation processes of auxin function. Induced by the initial wounding and other abiotic stress factors, up-regulation of ethylene biosynthesis, and signaling via ERFs and early accumulation of jasmonic acid stimulate AR formation, while both pathways are linked to auxin. Future research on the function of candidate genes should consider their tissue-specific role and regulation by environmental factors. Furthermore, the whole cutting should be regarded as a system of physiological units with diverse functions specifically responding to the environment and determining the rooting response.
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Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science

Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
Predictions on the lifetime of phosphate (Pi) reserves usually take into account only the need for crop production. A recent report predicts the global need of chemical Pi fertilizer for sustaining productivity in cropland and grassland. Here we discuss the implications of these predictions for the lifetime of Pi reserves.
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The race to create super-crops

The race to create super-crops | Plant Gene Seeker -PGS | Scoop.it

Jonathan Lynch likes to look beneath the surface. In his quest to breed better crops, the plant physiologist spends a lot of time digging up roots to work out what makes some varieties extremely good at extracting nutrients from the ground. Lynch wants to use this knowledge to develop plants with extra-efficient roots — crops that grow well in the nutrient-starved soils of the developing world. These plants could also reduce the use of fertilizers in richer nations.



Last year, Lynch's forays into the dirt paid off. He and his team at Pennsylvania State University in University Park reported1 that they had produced a variety of common bean, or string bean (Phaseolus vulgaris), with a combination of root traits that allows it to take up phosphorus from the soil with improved efficiency. In experimental plots, the plants produced three times the bean yield of typical varieties.

That result has raised hopes in Africa, where common beans are one of the most important sources of protein for poor people. Researchers in Mozambique are testing how Lynch's beans perform in the country's ecological zones, and they expect to win regulatory approval to bring the crop to market by next year.

Lynch's beans are among the first successful attempts in a global race to develop crops that grow well in soils depleted of nutrients. “Low availability of nitrogen, phosphorus and water are the main limitations of plant growth on Earth. We desperately need this technology,” says Lynch.

His work stands out because he has taken an old-school approach. He is leading a renaissance in some conventional crop-breeding techniques that rely on laboriously examining plants' physical characteristics and then selecting for desirable traits, such as growth or the length of fine roots...


Via Christophe Jacquet
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Expanding the Regulatory Network for Meristem Size in Plants: Trends in Genetics

Expanding the Regulatory Network for Meristem Size in Plants: Trends in Genetics | Plant Gene Seeker -PGS | Scoop.it
The remarkable plasticity of post-embryonic plant development is due to groups of stem-cell-containing structures called meristems. In the shoot, meristems continuously produce organs such as leaves, flowers, and stems. Nearly two decades ago the WUSCHEL/CLAVATA (WUS/CLV) negative feedback loop was established as being essential for regulating the size of shoot meristems by maintaining a delicate balance between stem cell proliferation and cell recruitment for the differentiation of lateral primordia. Recent research in various model species (Arabidopsis, tomato, maize, and rice) has led to discoveries of additional components that further refine and improve the current model of meristem regulation, adding new complexity to a vital network for plant growth and productivity.
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The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato | Plant Gene Seeker -PGS | Scoop.it

Background 

Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. 


Results 

Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. 


Conclusions

This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.

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Carrot genome paints picture of domestication, could help improve crops

Carrot genome paints picture of domestication, could help improve crops | Plant Gene Seeker -PGS | Scoop.it
The crop's full genetic code was just deciphered by a team of researchers led by UW–Madison horticulture professor and geneticist Phil Simon.
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Molecular and systems approaches towards drought-tolerant canola crops - Zhu - 2016 - New Phytologist

Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
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Bt Toxin Cry1Ie Causes No Negative Effects on Survival, Pollen Consumption, or Olfactory Learning in Worker Honey Bees (Hymenoptera: Apidae)

Bt Toxin Cry1Ie Causes No Negative Effects on Survival, Pollen Consumption, or Olfactory Learning in Worker Honey Bees (Hymenoptera: Apidae) | Plant Gene Seeker -PGS | Scoop.it
The honey bee (Apis mellifera L.) is a key nontarget insect in environmental risk assessments of insect-resistant genetically modified crops. In controlled laboratory conditions, we evaluated the potential effects of Cry1Ie toxin on survival, pollen consumption, and olfactory learning of young adult honey bees. We exposed worker bees to syrup containing 20, 200, or 20,000 ng/ml Cry1Ie toxin, and also exposed some bees to 48 ng/ml imidacloprid as a positive control for exposure to a sublethal concentration of a toxic product. Results suggested that Cry1Ie toxin carries no risk to survival, pollen consumption, or learning capabilities of young adult honey bees. However, during oral exposure to the imidacloprid treatments, honey bee learning behavior was affected and bees consumed significantly less pollen than the control and Cry1Ie groups.
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Nanotechnology: A New Opportunity in Plant Sciences

Nanotechnology: A New Opportunity in Plant Sciences | Plant Gene Seeker -PGS | Scoop.it
The agronomic application of nanotechnology in plants (phytonanotechnology) has the potential to alter conventional plant production systems, allowing for the controlled release of agrochemicals (e.g., fertilizers, pesticides, and herbicides) and target-specific delivery of biomolecules (e.g., nucleotides, proteins, and activators). An improved understanding of the interactions between nanoparticles (NPs) and plant responses, including their uptake, localization, and activity, could revolutionize crop production through increased disease resistance, nutrient utilization, and crop yield. Herewith, we review potential applications of phytonanotechnology and the key processes involved in the delivery of NPs to plants. To ensure both the safe use and social acceptance of phytonanotechnology, the adverse effects, including the risks associated with the transfer of NPs through the food chain, are discussed.
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Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes: Trends in Plant Science

Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.
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ABA-mediated responses to water deficit separate grapevine genotypes by their genetic background

ABA-mediated responses to water deficit separate grapevine genotypes by their genetic background | Plant Gene Seeker -PGS | Scoop.it
Abstract 
Background: ABA-mediated processes are involved in plant responses to water deficit, especially the control of stomatal opening. However in grapevine it is not known if these processes participate in the phenotypic variation in drought adaptation existing between genotypes. To elucidate this question, the response to short-term water-deficit was analysed in roots and shoots of nine Vitis genotypes differing in their drought adaptation in the field. The transcript abundance of 12 genes involved in ABA biosynthesis, catabolism, and signalling were monitored, together with physiological and metabolic parameters related to ABA and its role in controlling plant transpiration. 

Results: Although transpiration and ABA responses were well-conserved among the genotypes, multifactorial analyses separated Vitis vinifera varieties and V. berlandieri x V. rupestris hybrids (all considered drought tolerant) from the other genotypes studied. Generally, V. vinifera varieties, followed by V. berlandieri x V. rupestris hybrids, displayed more pronounced responses to water-deficit in comparison to the other genotypes. However, changes in transcript abundance in roots were more pronounced for Vitis hybrids than V. vinifera genotypes. Changes in the expression of the cornerstone ABA biosynthetic gene VviNCED1, and the ABA transcriptional regulator VviABF1, were associated with the response of V. vinifera genotypes, while changes in VviNCED2 abundance were associated with the response of other Vitis genotypes. In contrast, the ABA RCAR receptors were not identified as key components of the genotypic variability of water-deficit responses. Interestingly, the expression of VviSnRK2.6 (an AtOST1 ortholog) was constitutively lower in roots and leaves of V. vinifera genotypes and higher in roots of V. berlandieri x V. rupestris hybrids. 

Conclusions: This study highlights that Vitis genotypes exhibiting different levels of drought adaptation differ in key steps involved in ABA metabolism and signalling; both under well-watered conditions and in response to water-deficit. In addition, it supports that adaptation may be related to various mechanisms related or not to ABA responses.
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BMC Plant Biology

BMC Plant Biology | Plant Gene Seeker -PGS | Scoop.it
Background
Being sessile organisms, plants are often exposed to a wide array of abiotic and biotic stresses. Abiotic stress conditions include drought, heat, cold and salinity, whereas biotic stress arises mainly from bacteria, fungi, viruses, nematodes and insects. To adapt to such adverse situations, plants have evolved well-developed mechanisms that help to perceive the stress signal and enable optimal growth response. Phytohormones play critical roles in helping the plants to adapt to adverse environmental conditions. The elaborate hormone signaling networks and their ability to crosstalk make them ideal candidates for mediating defense responses.

Results
Recent research findings have helped to clarify the elaborate signaling networks and the sophisticated crosstalk occurring among the different hormone signaling pathways. In this review, we summarize the roles of the major plant hormones in regulating abiotic and biotic stress responses with special focus on the significance of crosstalk between different hormones in generating a sophisticated and efficient stress response. We divided the discussion into the roles of ABA, salicylic acid, jasmonates and ethylene separately at the start of the review. Subsequently, we have discussed the crosstalk among them, followed by crosstalk with growth promoting hormones (gibberellins, auxins and cytokinins). These have been illustrated with examples drawn from selected abiotic and biotic stress responses. The discussion on seed dormancy and germination serves to illustrate the fine balance that can be enforced by the two key hormones ABA and GA in regulating plant responses to environmental signals.

Conclusions
The intricate web of crosstalk among the often redundant multitudes of signaling intermediates is just beginning to be understood. Future research employing genome-scale systems biology approaches to solve problems of such magnitude will undoubtedly lead to a better understanding of plant development. Therefore, discovering additional crosstalk mechanisms among various hormones in coordinating growth under stress will be an important theme in the field of abiotic stress research. Such efforts will help to reveal important points of genetic control that can be useful to engineer stress tolerant crops.
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Lipid signalling in plant responses to abiotic stress - Hou - 2016 - Plant, Cell & Environment - Wiley Online Library

Lipid signalling in plant responses to abiotic stress - Hou - 2016 - Plant, Cell & Environment - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Lipids are one of the major components of biological membranes including the plasma membrane, which is the interface between the cell and the environment. It has become clear that membrane lipids also serve as substrates for the generation of numerous signalling lipids such as phosphatidic acid, phosphoinositides, sphingolipids, lysophospholipids, oxylipins, N-acylethanolamines, free fatty acids and others. The enzymatic production and metabolism of these signalling molecules are tightly regulated and can rapidly be activated upon abiotic stress signals. Abiotic stress like water deficit and temperature stress triggers lipid-dependent signalling cascades, which control the expression of gene clusters and activate plant adaptation processes. Signalling lipids are able to recruit protein targets transiently to the membrane and thus affect conformation and activity of intracellular proteins and metabolites. In plants, knowledge is still scarce of lipid signalling targets and their physiological consequences. This review focuses on the generation of signalling lipids and their involvement in response to abiotic stress. We describe lipid-binding proteins in the context of changing environmental conditions and compare different approaches to determine lipid–protein interactions, crucial for deciphering the signalling cascades.
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Long-Sought Vacuolar Phosphate Transporters Identified: Trends in Plant Science

Long-Sought Vacuolar Phosphate Transporters Identified: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
The vacuole is an important subcellular compartment that serves as main phosphate storage in plants among other functions. Three recent studies shed light on the underlying molecular mechanisms for vacuolar phosphate transport that had long remained unknown.
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The bright side of microbial dark matter: lessons learned from the uncultivated majority - Current Opinion in Microbiology

The bright side of microbial dark matter: lessons learned from the uncultivated majority - Current Opinion in Microbiology | Plant Gene Seeker -PGS | Scoop.it
Microorganisms are the most diverse and abundant life forms on Earth. Yet, in many environments, only 0.1–1% of them have been cultivated greatly hindering our understanding of the microbial world. However, today cultivation is no longer a requirement for gaining access to information from the uncultivated majority. New genomic information from metagenomics and single cell genomics has provided insights into microbial metabolic cooperation and dependence, generating new avenues for cultivation efforts. Here we summarize recent advances from uncultivated phyla and discuss how this knowledge has influenced our understanding of the topology of the tree of life and metabolic diversity.

Via Max-Bernhard Ballhausen
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Max-Bernhard Ballhausen's curator insight, May 20, 3:07 AM
An update on hitherto uncultured bacteria. Good Friday morning read ;)
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Transcription co-activator Arabidopsis ANGUSTIFOLIA3 (AN3) regulates water-use efficiency and drought tolerance by modulating stomatal density and improving root architecture by the transrepression...

Transcription co-activator Arabidopsis ANGUSTIFOLIA3 (AN3) regulates water-use efficiency and drought tolerance by modulating stomatal density and improving root architecture by the transrepression... | Plant Gene Seeker -PGS | Scoop.it
One goal of modern agriculture is the improvement of plant drought tolerance and water-use efficiency (WUE). Although stomatal density has been linked to WUE, the causal molecular mechanisms and engineered alternations of this relationship are not yet fully understood. Moreover, YODA (YDA), which is a MAPKK kinase gene, negatively regulates stomatal development. BR-INSENSITIVE 2 interacts with phosphorylates and inhibits YDA. However, whether YDA is modulated in the transcriptional level is still unclear. Plants lacking ANGUSTIFOLIA3 (AN3) activity have high drought stress tolerance because of low stomatal densities and improved root architecture. Such plants also exhibit enhanced WUE through declining transpiration without a demonstrable reduction in biomass accumulation. AN3 negatively regulated YDA expression at the transcriptional level by target-gene analysis. Chromatin immunoprecipitation analysis indicated that AN3 was associated with a region of the YDA promoter in vivo. YDA mutation significantly decreased the stomatal density and root length of an3 mutant, thus proving the participation of YDA in an3 drought tolerance and WUE enhancement. These components form an AN3–YDA complex, which allows the integration of water deficit stress signalling into the production or spacing of stomata and cell proliferation, thus leading to drought tolerance and enhanced WUE.
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Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell | Plant Gene Seeker -PGS | Scoop.it

Background 

Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress.

Scope 

The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution | Plant Gene Seeker -PGS | Scoop.it
Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events.
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Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science

Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
Predictions on the lifetime of phosphate (Pi) reserves usually take into account only the need for crop production. A recent report predicts the global need of chemical Pi fertilizer for sustaining productivity in cropland and grassland. Here we discuss the implications of these predictions for the lifetime of Pi reserves.

Via Christophe Jacquet
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The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols - Martínez-García - 2016 - The Plant Journal - Wiley Online Library

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols - Martínez-García - 2016 - The Plant Journal - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
The Persian walnut (Juglans regia L.) a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar Chandler to discover target genes and additional unknown genes. The 667 Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with a N50 scaffold size of 464,955 bp (based on a 606 Mbp genome size), 221,640 contigs and 37% GC content. Annotation with MAKER-P and other genomic resources yielded 32,498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single PPO gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, ~130 genes in the large GGT superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-D-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.
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Connecting Source with Sink: The Role of Arabidopsis AAP8 in Phloem Loading of Amino Acids

Connecting Source with Sink: The Role of Arabidopsis AAP8 in Phloem Loading of Amino Acids | Plant Gene Seeker -PGS | Scoop.it
Allocation of large amounts of nitrogen to developing organs occurs in the phloem and is essential for plant growth and seed development. In Arabidopsis (Arabidopsis thaliana) and many other plant species, amino acids represent the dominant nitrogen transport forms in the phloem, and they are mainly synthesized in photosynthetically active source leaves. Following their synthesis, a broad spectrum of the amino nitrogen is actively loaded into the phloem of leaf minor veins and transported within the phloem sap to sinks such as developing leaves, fruits, or seeds. Controlled regulation of the source-to-sink transport of amino acids has long been postulated; however, the molecular mechanism of amino acid phloem loading was still unknown. In this study, Arabidopsis AMINO ACID PERMEASE8 (AAP8) was shown to be expressed in the source leaf phloem and localized to the plasma membrane, suggesting its function in phloem loading. This was further supported by transport studies with aap8 mutants fed with radiolabeled amino acids and by leaf exudate analyses. In addition, biochemical and molecular analyses revealed alterations in leaf nitrogen pools and metabolism dependent on the developmental stage of the mutants. Decreased amino acid phloem loading and partitioning to sinks led to decreased silique and seed numbers, but seed protein levels were unchanged, demonstrating the importance of AAP8 function for sink development rather than seed quality. Overall, these results show that AAP8 plays an important role in source-to-sink partitioning of nitrogen and that its function affects source leaf physiology and seed yield.
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Evolution of plant genome architecture

Evolution of plant genome architecture | Plant Gene Seeker -PGS | Scoop.it
Abstract

We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
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Crop Diversity: An Unexploited Treasure Trove for Food Security: Trends in Plant Science

Crop Diversity: An Unexploited Treasure Trove for Food Security: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
The prediction is that food supply must double by 2050 to cope with the impact of climate change and population pressure on global food systems. The diversification of staple crops and the systems in which they grow is essential to make future agriculture sustainable, resilient, and suitable for local environments and soils.
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Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana 

Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana  | Plant Gene Seeker -PGS | Scoop.it
Plants have evolved a series of tolerance mechanisms to saline stress, which perturbs physiological processes throughout the plant. To identify genetic mechanisms associated with salinity tolerance, we performed linkage analysis and genome-wide association study (GWAS) on maintenance of root growth of Arabidopsis thaliana in hydroponic culture with weak and severe NaCl toxicity. The top 200 single-nucleotide polymorphisms (SNPs) determined by GWAS could cumulatively explain approximately 70% of the variation observed at each stress level. The most significant SNPs were linked to the genes of ATP-binding cassette B10 and vacuolar proton ATPase A2. Several known salinity tolerance genes such as potassium channel KAT1 and calcium sensor SOS3 were also linked to SNPs in the top 200. In parallel, we constructed a gene co-expression network to independently verify that particular groups of genes work together to a common purpose. We identify molecular mechanisms to confer salt tolerance from both predictable and novel physiological sources and validate the utility of combined genetic and network analysis. Additionally, our study indicates that the genetic architecture of salt tolerance is responsive to the severity of stress. These gene datasets are a significant information resource for a following exploration of gene function.
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Online collaboration: Scientists and the social network

Online collaboration: Scientists and the social network | Plant Gene Seeker -PGS | Scoop.it
Giant academic social networks have taken off to a degree that no one expected even a few years ago. A Nature survey explores why.
Andres Zurita's insight:
An interesting trend! Don't stay off-line 
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