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NY Times: The Worldwide Vulnerability of Forests (2012)

NY Times: The Worldwide Vulnerability of Forests (2012) | Emerging Research in Plant Cell Biology | Scoop.it

Many trees operate with only a narrow margin of safety when it comes to their water supply, so many of the world's important forest species are vulnerable to hydraulic failure.

 

A warming climate creates summertime water stress for trees like these mountain pines in Montana, making them more vulnerable to attack by beetles. The gray trees above died several years ago.


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Emerging Research in Plant Cell Biology
A science editor's take on what's new and interesting in the plant kingdom.
Curated by Jennifer Mach
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Molecular principles of membrane microdomain targeting in plants: Trends in Plant Science

Molecular principles of membrane microdomain targeting in plants: Trends in Plant Science | Emerging Research in Plant Cell Biology | Scoop.it
•Proteins and lipids segregate into distinct and coexisting membrane microdomains in vivo.•New microscopy techniques will facilitate the visualization of membrane microdomains and protein dynamics in vivo.•Protein targeting to specific sites in the PM is dynamic and a consequence of combinatorial events.•The cell wall–PM–cytoskeleton continuum is a hallmark of membrane microdomain assembly in plants.

 

Plasma membranes (PMs) are heterogeneous lipid bilayers comprising diverse subdomains. These sites can be labeled by various proteins in vivo and may serve as hotspots for signal transduction. They are found at apical, basal, and lateral membranes of polarized cells, at cell equatorial planes, or almost isotropically distributed throughout the PM. Recent advances in imaging technologies and understanding of mechanisms that allow proteins to target specific sites in PMs have provided insights into the dynamics and complexity of their specific segregation. Here we present a comprehensive overview of the different types of membrane microdomain and describe the molecular modes that determine site-directed targeting of membrane-resident proteins at the PM.

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Molecular Plant Pathology: A new look at plant viruses and their potential beneficial roles in crops (2015)

Molecular Plant Pathology: A new look at plant viruses and their potential beneficial roles in crops (2015) | Emerging Research in Plant Cell Biology | Scoop.it

Twenty years ago most people (including many scientists) thought of bacteria solely as agents of disease, best treated with disinfectants and antibiotics. Today, most of us are aware that bacteria make up almost 90% of the cells in our bodies, and play a critical role in digestion and the immune response. In plants, bacteria also form important mutualistic relationships, providing nitrogen fixation, growth enhancement and defence against pathogens, and undoubtedly a host of other functions that have yet to be described. The stigma of bacteria has changed dramatically in recent decades, and most people are aware that we need our good microbes.

 

Although there have been recent efforts to characterize the plant microbiome with a focus on finding beneficial microbes, viruses generally have not been included in the beneficial microbe lists (Berg et al., 2014, and references cited therein). Recent work has indicated that they can also play important and beneficial roles in plants, especially in extreme environments in which they are involved in conferring tolerance to drought, cold and hot soil temperatures (Roossinck, 2011). Beneficial viruses are defined for the purposes of this discussion as viruses that provide a trait to crop plants that increases their value or growth potential, or decreases the need for the use of chemical fertilizers or pesticides.

 

See also http://www.noble.org/ag/research/microbes/


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Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana | Emerging Research in Plant Cell Biology | Scoop.it

Soil water availability represents one of the most important selective agents for plants in nature and the single greatest abiotic determinant of agricultural productivity, yet the genetic bases of drought acclimation responses remain poorly understood. Here, we developed a systems-genetic approach to characterize quantitative trait loci (QTLs), physiological traits and genes that affect responses to soil moisture deficit in the TSUxKAS mapping population of Arabidopsis thaliana. To determine the effects of candidate genes underlying QTLs, we analyzed gene expression as a covariate within the QTL model in an effort to mechanistically link markers, RNA expression, and the phenotype. This strategy produced ranked lists of candidate genes for several drought-associated traits, including water use efficiency, growth, abscisic acid concentration (ABA), and proline concentration. As a proof of concept, we recovered known causal loci for several QTLs. For other traits, including ABA, we identified novel loci not previously associated with drought. Furthermore, we documented natural variation at two key steps in proline metabolism and demonstrated that the mitochondrial genome differentially affects genomic QTLs to influence proline accumulation. These findings demonstrate that linking genome, transcriptome, and phenotype data holds great promise to extend the utility of genetic mapping, even when QTL effects are modest or complex.

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The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop

Agrobacterium rhizogenes and Agrobacterium tumefaciens are plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world’s arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences from Agrobacterium spp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 and IbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas [L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant. IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes of Agrobacterium spp. IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives. IbT-DNA2 contained at least five ORFs with significant homology to the ORF14, ORF17n, rooting locus (Rol)B/RolC, ORF13, and ORF18/ORF17n genes of A. rhizogenes. IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.

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The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives | Emerging Research in Plant Cell Biology | Scoop.it

Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersoniisubstantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.

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Nuclear processes associated with plant immunity and pathogen susceptibility

Nuclear processes associated with plant immunity and pathogen susceptibility | Emerging Research in Plant Cell Biology | Scoop.it
Plants are sessile organisms that have evolved exquisite and sophisticated mechanisms to adapt to their biotic and abiotic environment. Plants deploy receptors and vast signalling networks to detect, transmit and respond to a given biotic threat by inducing properly dosed defence responses. Genetic analyses and, more recently, next-generation -omics approaches have allowed unprecedented insights into the mechanisms that drive immunity. Similarly, functional genomics and the emergence of pathogen genomes have allowed reciprocal studies on the mechanisms governing pathogen virulence and host susceptibility, collectively allowing more comprehensive views on the processes that govern disease and resistance. Among others, the identification of secreted pathogen molecules (effectors) that modify immunity-associated processes has changed the plant–microbe interactions conceptual landscape. Effectors are now considered both important factors facilitating disease and novel probes, suited to study immunity in plants. In this review, we will describe the various mechanisms and processes that take place in the nucleus and help regulate immune responses in plants. Based on the premise that any process required for immunity could be targeted by pathogen effectors, we highlight and describe a number of functional assays that should help determine effector functions and their impact on immune-related processes. The identification of new effector functions that modify nuclear processes will help dissect nuclear signalling further and assist us in our bid to bolster immunity in crop plants.

Via Christophe Jacquet
Jennifer Mach's insight:

The abstract opens with the classic "plants are sessile organisms" gambit...

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Fatal attraction: the intuitive appeal of GMO opposition: Trends in Plant Science

•People tend to rely on intuitive reasoning to make a judgment on GMOs.•This intuitive reasoning includes folk biology, teleological and intentional intentions and disgust.•Anti-GMO activists have exploited intuitions successfully to promote their cause.•Intuitive judgments steer people away from sustainable solutions.

 

Public opposition to genetically modified organisms (GMOs) remains strong. By contrast, studies demonstrate again and again that GM crops make a valuable contribution to the development of a sustainable type of agriculture. The discrepancy between public opinion and the scientific evidence requires an explanation. We argue that intuitive expectations about the world render the human mind vulnerable to particular misrepresentations of GMOs. We explain how the involvement of particular intuitions accounts for the popularity, persistence, and typical features of GM opposition and tackle possible objections to our approach. To conclude, we discuss the implications for science education, science communication, and the environmental movement.

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Beyond the thale: comparative genomics and genetics of Arabidopsis relatives

Beyond the thale: comparative genomics and genetics of Arabidopsis relatives | Emerging Research in Plant Cell Biology | Scoop.it

For decades a small number of model species have rightly occupied a privileged position in laboratory experiments, but it is becoming increasingly clear that our knowledge of biology is greatly improved when informed by a broader diversity of species and evolutionary context.Arabidopsis thaliana has been the primary model organism for plants, benefiting from a high-quality reference genome sequence and resources for reverse genetics. However, recent studies have made a group of species also in the Brassicaceae family and closely related to A. thaliana a focal point for comparative molecular, genomic, phenotypic and evolutionary studies. In this Review, we emphasize how such studies complement continued study of the model plant itself, provide an evolutionary perspective and summarize our current understanding of genetic and phenotypic diversity in plants.

Jennifer Mach's insight:

Best #title ever.

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Rescooped by Jennifer Mach from Plant roots and rhizosphere
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A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low nitrogen stress

A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low nitrogen stress | Emerging Research in Plant Cell Biology | Scoop.it
The plasticity of root architecture is crucial for plants to acclimate to unfavourable environments including low nitrogen (LN) stress. How maize roots coordinate the growth of axile roots and lateral roots (LRs), as well as longitudinal and radial cell behaviours in response to LN stress, remains unclear. Maize plants were cultivated hydroponically under control (4 mm nitrate) and LN (40 μm) conditions. Temporal and spatial samples were taken to analyse changes in the morphology, anatomical structure and carbon/nitrogen (C/N) ratio in the axile root and LRs. LN stress increased axile root elongation, reduced the number of crown roots and decreased LR density and length. LN stress extended cell elongation zones and increased the mature cell length in the roots. LN stress reduced the cell diameter and total area of vessels and increased the amount of aerenchyma, but the number of cell layers in the crown root cortex was unchanged. The C/N ratio was higher in the axile roots than in the LRs. Maize roots acclimate to LN stress by optimizing the anatomical structure and N allocation. As a result, axile root elongation is favoured to efficiently find available N in the soil.

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Arabidopsis BREVIPEDICELLUS Interacts with the SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA to Regulate KNAT2 and KNAT6 Expression in Control of Inflorescence Architecture

Arabidopsis  BREVIPEDICELLUS Interacts with the SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA to Regulate  KNAT2  and  KNAT6  Expression in Control of Inflorescence Architecture | Emerging Research in Plant Cell Biology | Scoop.it
Author Summary BP is a class-I KNOX transcription factor that controls normal inflorescence architecture development by repressing the expression of two KNOX genes, KNAT2 and KNAT6 . In this study, we showed that Arabidopsis BP directly interacts with the SWI2/SNF2 chromatin remodeling ATPase BRM. brm and bp mutants displayed similar inflorescence architecture defects, with clustered inflorescences, horizontally orientated pedicels, and short pedicels and internodes. Furthermore, BP and BRM co-target to KNAT2 and KNAT6 genes and repress their expression. This work reveals a new regulatory mechanism that BP associates with BRM in control of inflorescence architecture development.
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Stomatal Guard Cells Co-opted an Ancient ABA-Dependent Desiccation Survival System to Regulate Stomatal Closure

During the transition from water to land, plants had to cope with the loss of water through transpiration, the inevitable result of photosynthetic CO2 fixation on land [ 1, 2 ]. Control of transpiration became possible through the development of a new cell type: guard cells, which form stomata. In vascular plants, stomatal regulation is mediated by the stress hormone ABA, which triggers the opening of the SnR kinase OST1-activated anion channel SLAC1 [ 3, 4 ]. To understand the evolution of this regulatory circuit, we cloned both ABA-signaling elements, SLAC1 and OST1, from a charophyte alga, a liverwort, and a moss, and functionally analyzed the channel-kinase interactions. We were able to show that the emergence of stomata in the last common ancestor of mosses and vascular plants coincided with the origin of SLAC1-type channels capable of using the ancient ABA drought signaling kinase OST1 for regulation of stomatal closure.


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Plants regenerated from tissue culture contain stable epigenome changes in rice

Plants regenerated from tissue culture contain stable epigenome changes in rice | Emerging Research in Plant Cell Biology | Scoop.it

Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability.

Jennifer Mach's insight:

Okay, "Plants.... in rice"? #titletrouble

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Primary transcripts of microRNAs encode regulatory peptides

Primary transcripts of microRNAs encode regulatory peptides | Emerging Research in Plant Cell Biology | Scoop.it

MicroRNAs (miRNAs) are small regulatory RNA molecules that inhibit the expression of specific target genes by binding to and cleaving their messenger RNAs or otherwise inhibiting their translation into proteins1. miRNAs are transcribed as much larger primary transcripts (pri-miRNAs), the function of which is not fully understood. Here we show that plant pri-miRNAs contain short open reading frame sequences that encode regulatory peptides. The pri-miR171b ofMedicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. The mechanism of miRNA-encoded peptide (miPEP) action involves increasing transcription of the pri-miRNA. Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications.

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A robustCRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicotplants: Molecular Plant

CRISPR/Cas9 targeting systems have been applied to a variety of species. However, most of current CRISPR/Cas9 systems for plantscan only modify one or a few target sites. Here, we report a robust CRISPR/Cas9 vector system, utilizing a plant codon-optimized Cas9 gene, for convenient and high-efficiency multiplex genome editing in monocot and dicot plants.We designed PCR-based procedures to rapidly generate multiple sgRNA expression cassettes, which can be assembled into the binary CRISPR/Cas9 vectors in one round of cloning by Golden Gate ligation or Gibson Assembly. With this system, we edited 46target sites in rice with average 85.4% of mutation rate, mostly in biallelic and homozygous statuses. We reasoned that about 16% of the homozygous mutations in rice were generated through the nonhomologous end joining mechanism followed by homologous recombination-based repairing. We also obtained uniform biallelic, heterozygous, homozygous, and chimeric mutations in ArabidopsisT1 plants. Thetargeted mutations in both rice and Arabidopsiswereheritable.We provide examples of loss-of-function gene mutations in T0 rice and T1Arabidopsis plants by simultaneous targeting of multiple (up to 8) membersof a gene family, multiple genes in a biosynthetic pathway, or multiple sites in a single gene.This systemhas provided a versatile toolbox for studying functions of multiple genes and gene families in plants for basic research and genetic improvement.

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What Do You Mean, “Epigenetic”?

Interest in the field of epigenetics has increased rapidly over the last decade, with the term becoming more identifiable in biomedical research, scientific fields outside of the molecular sciences, such as ecology and physiology, and even mainstream culture. It has become increasingly clear, however, that different investigators ascribe different definitions to the term. Some employ epigenetics to explain changes in gene expression, others use it to refer to transgenerational effects and/or inherited expression states. This disagreement on a clear definition has made communication difficult, synthesis of epigenetic research across fields nearly impossible, and has in many ways biased methodologies and interpretations. This article discusses the history behind the multitude of definitions that have been employed since the conception of epigenetics, analyzes the components of these definitions, and offers solutions for clarifying the field and mitigating the problems that have arisen due to these definitional ambiguities.

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Nitric Oxide: A Multitasked Signaling Gas in Plants: Molecular Plant

Nitric Oxide: A Multitasked Signaling Gas in Plants: Molecular Plant | Emerging Research in Plant Cell Biology | Scoop.it

Nitric oxide (NO) is a gaseous reactive oxygen species (ROS) that has evolved as a signaling hormone in many physiological processes in animals. In plants it has been demonstrated to be a crucial regulator of development, acting as a signaling molecule present at each step of the plant life cycle. NO has also been implicated as a signal in biotic and abiotic responses of plants to the environment. Remarkably, despite this plethora of effects and functional relationships, the fundamental knowledge of NO production, sensing, and transduction in plants remains largely unknown or inadequately characterized. In this review we cover the current understanding of NO production, perception, and action in different physiological scenarios. We especially address the issues of enzymatic and chemical generation of NO in plants, NO sensing and downstream signaling, namely the putative cGMP and Ca2+ pathways, ion-channel activity modulation, gene expression regulation, and the interface with other ROS, which can have a profound effect on both NO accumulation and function. We also focus on the importance of NO in cell–cell communication during developmental processes and sexual reproduction, namely in pollen tube guidance and embryo sac fertilization, pathogen defense, and responses to abiotic stress.

Jennifer Mach's insight:

#title "multitasked"? 

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A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors

A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors | Emerging Research in Plant Cell Biology | Scoop.it

The biotrophic smut fungus Ustilago maydis infects all aerial organs of maize (Zea mays) and induces tumors in the plant tissues. U. maydis deploys many effector proteins to manipulate its host. Previously, deletion analysis demonstrated that several effectors have important functions in inducing tumor expansion specifically in maize leaves. Here, we present the functional characterization of the effector See1 (Seedling efficient effector1). See1 is required for the reactivation of plant DNA synthesis, which is crucial for tumor progression in leaf cells. By contrast, See1 does not affect tumor formation in immature tassel floral tissues, where maize cell proliferation occurs independent of fungal infection. See1 interacts with a maize homolog of SGT1 (Suppressor of G2 allele of skp1), a factor acting in cell cycle progression in yeast (Saccharomyces cerevisiae) and an important component of plant and human innate immunity. See1 interferes with the MAPK-triggered phosphorylation of maize SGT1 at a monocot-specific phosphorylation site. We propose that See1 interferes with SGT1 activity, resulting in both modulation of immune responses and reactivation of DNA synthesis in leaf cells. This identifies See1 as a fungal effector that directly and specifically contributes to the formation of leaf tumors in maize.

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Vital Plant Communication with Bacteria and Fungus

Vital Plant Communication with Bacteria and Fungus | Emerging Research in Plant Cell Biology | Scoop.it
Several of the most important factors needed for plant survival are very dependent upon extremely complex back and forth, multi-layered communication – these include the use of vital plant communication with bacteria and fungus.

What is a symbiosis–two forces approaching and each learning the signaling language for the other?

Plants determine friends and foes from a wide range of microbes and fungus, and then encourage the relationships with symbionts and fight against the intrusion of pathogens. Plant communication with fungal wires is almost ubiquitous.

Via Jean-Michel Ané, Christophe Jacquet
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Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat

Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat | Emerging Research in Plant Cell Biology | Scoop.it
Host resistance is the most economical, effective and ecologically sustainable method of controlling diseases in crop plants. In bread wheat, despite the high number of resistance loci that have been cataloged to date, only few have been cloned, underlying the need for genomics-guided investigations capable of providing a prompt and acute knowledge on the identity of effective resistance genes that can be used in breeding programs. Proteins with a nucleotide-binding site (NBS) encoded by the major plant disease resistance (R) genes play an important role in the responses of plants to various pathogens. In this study, a comprehensive analysis of NBS-encoding genes within the whole wheat genome was performed, and the genome scale characterization of this gene family was established. From the recently published wheat genome sequence, we used a data mining and automatic prediction pipeline to identify 580 complete ORF candidate NBS-encoding genes and 1,099 partial-ORF ones. Among complete gene models, 464 were longer than 200 aa, among them 436 had less than 70 % of sequence identity to each other. This gene models set was deeply characterized. (1) First, we have analyzed domain architecture and identified, in addition to typical domain combinations, the presence of particular domains like signal peptides, zinc fingers, kinases, heavy-metal-associated and WRKY DNA-binding domains. (2) Functional and expression annotation via homology searches in protein and transcript databases, based on sufficient criteria, enabled identifying similar proteins for 60 % of the studied gene models and expression evidence for 13 % of them. (3) Shared orthologous groups were defined using NBS-domain proteins of rice and Brachypodium distachyon. (4) Finally, alignment of the 436 NBS-containing gene models to the full set of scaffolds from the IWGSC’s wheat chromosome survey sequence enabled high-stringence anchoring to chromosome arms. The distribution of the R genes was found balanced on the three wheat sub-genomes. In contrast, at chromosome scale, 50 % of members of this gene family were localized on 6 of the 21 wheat chromosomes and ~22 % of them were localized on homeologous group 7. The results of this study provide a detailed analysis of the largest family of plant disease resistance genes in allohexaploid wheat. Some structural traits reported had not been previously identified and the genome-derived data were confronted with those stored in databases outlining the functional specialization of members of this family. The large reservoir of NBS-type genes presented and discussed will, firstly, form an important framework for marker-assisted improvement of resistance in wheat, and, secondly, open up new perspectives for a better understanding of the evolution dynamics of this gene family in grass species and in polyploid systems.

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Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment

Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment | Emerging Research in Plant Cell Biology | Scoop.it

Gluconeogenesis is a fundamental metabolic process that allows organisms to make sugars from non-carbohydrate stores such as lipids and protein. In eukaryotes only one gluconeogenic route has been described from organic acid intermediates and this relies on the enzyme phosphoenolpyruvate carboxykinase (PCK). Here we show that two routes exist in Arabidopsis, and that the second uses pyruvate, orthophosphate dikinase (PPDK). Gluconeogenesis is critical to fuel the transition from seed to seedling. Arabidopsis pck1 and ppdk mutants are compromised in seed-storage reserve mobilization and seedling establishment. Radiolabelling studies show that PCK predominantly allows sugars to be made from dicarboxylic acids, which are products of lipid breakdown. However, PPDK also allows sugars to be made from pyruvate, which is a major product of protein breakdown. We propose that both routes have been evolutionarily conserved in plants because, while PCK expends less energy, PPDK is twice as efficient at recovering carbon from pyruvate.

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Flowering time and seed dormancy control use external coincidence to generate life history strategy

Flowering time and seed dormancy control use external coincidence to generate life history strategy | Emerging Research in Plant Cell Biology | Scoop.it

Climate change is accelerating plant developmental transitions coordinated with the seasons in temperate environments. To understand the importance of these timing advances for a stable life history strategy, we constructed a full life cycle model of Arabidopsis thaliana. Modelling and field data reveal that a cryptic function of flowering time control is to limit seed set of winter annuals to an ambient temperature window which coincides with a temperature-sensitive switch in seed dormancy state. This coincidence is predicted to be conserved independent of climate at the expense of flowering date, suggesting that temperature control of flowering time has evolved to constrain seed set environment and therefore frequency of dormant and non-dormant seed states. We show that late flowering can disrupt this bet-hedging germination strategy. Our analysis shows that life history modelling can reveal hidden fitness constraints and identify non-obvious selection pressures as emergent features.

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The future of starch bioengineering: GM microorganisms or GM plants?

Plant starches regularly require extensive modification to permit subsequent applications. Such processing is usually done by the use of chemical and/or physical treatments. The use of recombinant enzymes produced by large-scale fermentation of GM microorganisms is increasingly used in starch processing and modification, sometimes as an alternative to chemical or physical treatments.

 

However, as a means to impart the modifications as early as possible in the starch production chain, similar recombinant enzymes may also be expressed in planta in the developing starch storage organ such as in roots, tubers and cereal grains to provide a GM crop as an alternative to the use of enzymes from GM microorganisms... In planta starch bioengineering is generally challenged by yield penalties and inefficient production of the desired product. However in some situations, GM crops for starch bioengineering without deleterious effects have been achieved...

 

We have compared the use of starch modifying enzymes produced by GM microrganisms with the expression of these enzymes directly in crops. In summary we find that in planta starch bioengineering by expression of starch modifying enzymes directly in crop storage organs faces a number of challenges that need to be addressed further. In particular, starch bioengineering may sometimes be associated with significant yield loss...

 

Only a few studies have been carried through to agronomic field trials. The physiological conditions in amyloplasts of crop starch organs may not be optimal for starch modifying enzymes of non-plant origin, and in several studies only very small amounts of the desired product is formed. However, the method looks promising for situations where the transgenic enzymes remain inactive during crop development, so that the above mentioned deleterious effects are avoided.

 

For example crops expressing thermophilic hydrolytic enzymes, which are activated by heat, have been shown to reduce production costs and energy and water usage of grain processing. Other methods of “post-harvest” activation of transgenic enzymes in crops could be explored. In other situations there may not be a biotechnological alternative to transgenic enzyme expression directly in developing crop organs. For example starch kinases have been used to increase starch phosphate content in cereal grains and in potatoes, whereas there are currently no reports that a similar modification can be made during post-harvest starch processing... 

 

http://journal.frontiersin.org/article/10.3389/fpls.2015.00247/abstract

 


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Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine

Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine | Emerging Research in Plant Cell Biology | Scoop.it
Author Summary Pinot is one of the most ancient grapevine varieties made up of a large panel of clones, most of them used to produce very different wines with specific oenological characteristics in different vineyards around the world. This great diversity of clones, which is due to spontaneous somatic mutations that have occurred over time, makes Pinot a fascinating subject of study. It is the reason why we have undertaken a study focused on the color locus to identify the mutations responsible for color variation in a large panel of Pinot gris and Pinot blanc clones. The results we obtained shed light on large-scale molecular events that account for the loss of anthocyanin biosynthesis, such as chromosome replacement and deletion. These mutations first multiplied and, depending on the cell layer in which they occurred, lead to chimeras. Occasionally, cell layer rearrangements homogenize the whole plant. Clonal polymorphism of grapevine varieties results from a succession of such molecular and cellular mechanisms that are the driving forces behind the genetic drift of clones and the evolution of the grapevine genome.
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The Extent and Consequences of P-Hacking in Science

The Extent and Consequences of P-Hacking in Science | Emerging Research in Plant Cell Biology | Scoop.it
Publication bias resulting from so-called "p-hacking" is pervasive throughout the life sciences; however, its effects on general conclusions made from the literature appear to be weak.
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Endogenous Arabidopsis messenger RNAs transported to distant tissues

Endogenous Arabidopsis messenger RNAs transported to distant tissues | Emerging Research in Plant Cell Biology | Scoop.it

The concept that proteins and small RNAs can move to and function in distant body parts is well established. However, non-cell-autonomy of small RNA molecules raises the question: To what extent are protein-coding messenger RNAs (mRNAs) exchanged between tissues in plants? Here we report the comprehensive identification of 2,006 genes producing mobile RNAs in Arabidopsis thaliana. The analysis of variant ecotype transcripts that were present in heterografted plants allowed the identification of mRNAs moving between various organs under normal or nutrient-limiting conditions. Most of these mobile transcripts seem to follow the phloem-dependent allocation pathway transporting sugars from photosynthetic tissues to roots via the vasculature. Notably, a high number of transcripts also move in the opposite, root-to-shoot direction and are transported to specific tissues including flowers. Proteomic data on grafted plants indicate the presence of proteins from mobile RNAs, allowing the possibility that they may be translated at their destination site. The mobility of a high number of mRNAs suggests that a postulated tissue-specific gene expression profile might not be predictive for the actual plant body part in which a transcript exerts its function

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Guojian HU's curator insight, March 26, 4:31 AM

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