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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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Proline-rich protein-like PRPL1 controls elongation of root hairs in Arabidopsis thaliana

Proline-rich protein-like PRPL1 controls elongation of root hairs in Arabidopsis thaliana | Plant Gene Seeker -PGS | Scoop.it
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The synthesis and composition of cell walls is dynamically adapted in response to many developmental and environmental signals. In this respect, cell wall proteins involved in controlling cell elongation are critical for cell development. Transcriptome analysis identified a gene inArabidopsis thaliana, which was named proline-rich protein-like, AtPRPL1, based on sequence similarities from a phylogenetic analysis. The most resemblance was found to AtPRP1 and AtPRP3 from Arabidopsis, which are known to be involved in root hair growth and development. In A. thalianafour proline-rich cell wall protein genes, playing a role in building up the cross-connections between cell wall components, can be distinguished.AtPRPL1 is a small gene that in promoter::GUS (β-glucuronidase) analysis has high expression in trichoblast cells and in the collet. Chemical or mutational interference with root hair formation inhibited this expression. Altered expression levels in knock-out or overexpression lines interfered with normal root hair growth and etiolated hypocotyl development, but Fourier transform-infrared (FT-IR) analysis did not identify consistent changes in cell wall composition of root hairs and hypocotyl. Co-localization analysis of the AtPRPL1–green fluorescent protein (GFP) fusion protein and different red fluorescent protein (RFP)-labelled markers confirmed the presence of AtPRPL1–GFP in small vesicles moving over the endoplasmic reticulum. Together, these data indicate that the AtPRPL1 protein is involved in the cell’s elongation process. How exactly this is achieved remains unclear at present.

 
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Tandem CCCH Zinc Finger Proteins in Plant Growth, Development and Stress Response

Tandem CCCH Zinc Finger Proteins in Plant Growth, Development and Stress Response | Plant Gene Seeker -PGS | Scoop.it
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Cysteine3Histidine (CCCH)-type zinc finger proteins comprise a large family that is well conserved across eukaryotes. Among them, tandem CCCH zinc finger proteins (TZFs) play critical roles in mRNA metabolism in animals and yeast. While there are only three TZF members in humans, a much higher number of TZFs has been found in many plant species. Notably, plant TZFs are over-represented by a class of proteins containing a unique TZF domain preceded by an arginine (R)-rich (RR) motif, hereafter called RR-TZF. Recently, there have been a large number of reports indicating that RR-TZF proteins can localize to processing bodies (P-bodies) and stress granules (SG), two novel cytoplasmic aggregations of messenger ribonucleoprotein complexes (mRNPs), and play critical roles in plant growth, development and stress response, probably via RNA regulation. This review focuses on the classification and most recent development of molecular, cellular and genetic analyses of plant RR-TZF proteins.

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Molecular genetic framework for protophloem formation

Molecular genetic framework for protophloem formation | Plant Gene Seeker -PGS | Scoop.it
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The emergence of vascular tissues played a central role in the plant conquest of land. Both xylem and phloem are essential for the development of flowering plants, yet little is known about the molecular genetic control of phloem specification and differentiation. Here we show that delicate quantitative interplay between two opposing signaling pathways determines cellular commitment to protophloem sieve element fate in root meristems of the model plant Arabidopsis thaliana. Our data suggest that a recently described phloem-specific protein is a positive, quantitative master regulator of phloem fate.

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The genome of the stress-tolerant wild tomato species Solanum pennellii | Nature Genetics

The genome of the stress-tolerant wild tomato species Solanum pennellii | Nature Genetics | Plant Gene Seeker -PGS | Scoop.it
Bjorn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response.
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Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicumare replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.


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Chile needs better science governance and support

Chile needs better science governance and support | Plant Gene Seeker -PGS | Scoop.it
Its scientists have much to offer the world, but are being held back by scattered administration and changing policies, argues Pablo Astudillo Besnier.
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Yet, despite the glossy images of the telescopes promising a high-tech future, in 2012, Chile spent just 0.35% of its gross domestic product on research and development (R&D) — the least of all countries in the Organisation for Economic Co-operation and Development. Two-thirds of the academic publications come from just five universities. And, perhaps most importantly, a heavy focus on applied science threatens to stifle basic research and its potential to innovate.

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Slicing the wheat genome

Slicing the wheat genome | Plant Gene Seeker -PGS | Scoop.it
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This year celebrates the 100th anniversary of the birth of Norman Borlaug, the Nobel Prize-winning plant geneticist who, through his contribution to the “green revolution,” reminds us of the importance of applying scientific knowledge to develop crop varieties. This is even more important today as we face a rapidly expanding global population, climate change, and the need to keep agricultural efforts sustainable while minimizing environmental impacts. Accessing the fundamental information of crop genomes aids in accelerating breeding pipelines and improves our understanding of the molecular basis of agronomically important traits, such as yield and tolerance to abiotic and biotic stresses.

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Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

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Cellular signals evoke rapid and broad changes in gene regulatory networks. To uncover these network dynamics, we developed an approach able to monitor primary targets of a transcription factor (TF) based solely on gene regulation, in the absence of detectable binding. This enabled us to follow the transient propagation of a nitrogen (N) nutrient signal as a direct impact of the master TF Basic Leucine Zipper 1 (bZIP1). Unexpectedly, the largest class of primary targets that exhibit transient associations with bZIP1 is uniquely relevant to the rapid and dynamic propagation of the N signal. Our ability to uncover this transient network architecture has revealed the “dark matter” of dynamic N nutrient signaling in plants that has previously eluded detection.

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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication : Nature Biotechnology : Nature Publishing Group

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication : Nature Biotechnology : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
Genome sequences of nine species of citrus, including oranges, pummelos and mandarins, reveal pathways of domestication and provide resources for breeding.
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Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin speciesCitrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.


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An optimized procedure for plant recovery from somatic embryos significantly facilitates the genetic improvement of Vitis

An optimized procedure for plant recovery from somatic embryos significantly facilitates the genetic improvement of Vitis | Plant Gene Seeker -PGS | Scoop.it
Horticulture Research, Published online: 11 June 2014; | doi:10.1038/hortres.2014.27
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Plant regeneration from grapevine (Vitis spp.) via somatic embryogenesis typically is poor. Recovery of plants from Vitis rotundifolia Michx. (muscadine grape) is particularly problematic due to extremely low efficiency, including extended culture durations required for embryo–plant conversion. Poor plant recovery is an obstacle to the selection of improved genetically modified lines. Somatic embryos (SEs) of V. rotundifolia cultivar Delicious (Del-HS) and Vitis vinifera L cultivar Thompson Seedless (TS) were used to identify culture media and conditions that promoted embryo differentiation and plant conversion; this resulted in a two-step culture system. In comparative culture experiments, C2D medium containing 6% sucrose was the most effective, among four distinct formulae tested, for inducing precocious SE germination and cell differentiation. This medium, further supplemented with 4 µM 6-benzylaminopurine (C2D4B), was subsequently determined to enhance post-germinative growth of SE. MS medium supplemented with 0.5 µM 1-naphthaleneacetic acid (MSN) was then utilized to stimulate root and shoot growth of germinated SE. An average of 35% and 80% ‘Del-HS’ and ‘TS’ SE, respectively, developed into plants. All plants developed robust root and shoot systems and exhibited excellent survival following transfer to soil. Over 150 plants of ‘Del-HS’ were regenerated and established within 2.5 months, which is a dramatic reduction from the 6- to 12-month time period previously required. Similarly, 88 ‘TS’ plant lines were obtained within the same time period. Subsequently, seven out of eight Vitis cultivars exhibited significantly increased plant conversion percentages, demonstrating broad application of the two-step culture system to produce the large numbers of independent plant lines needed for selection of desired traits.

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PIN-driven polar auxin transport in plant developmental plasticity: a key target for environmental and endogenous signals - Habets - 2014 - New Phytologist - Wiley Online Library

PIN-driven polar auxin transport in plant developmental plasticity: a key target for environmental and endogenous signals - Habets - 2014 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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Plants master the art of coping with environmental challenges in two ways: on the one hand, through their extensive defense systems, and on the other, by their developmental plasticity. The plant hormone auxin plays an important role in a plant's adaptations to its surroundings, as it specifies organ orientation and positioning by regulating cell growth and division in response to internal and external signals. Important in auxin action is the family of PIN-FORMED (PIN) auxin transport proteins that generate auxin maxima and minima by driving polar cell-to-cell transport of auxin through their asymmetric subcellular distribution. Here, we review how regulatory proteins, the cytoskeleton, and membrane trafficking affect PIN expression and localization. Transcriptional regulation of PIN genes alters protein abundance, provides tissue-specific expression, and enables feedback based on auxin concentrations and crosstalk with other hormones. Post-transcriptional modification, for example by PIN phosphorylation or ubiquitination, provides regulation through protein trafficking and degradation, changing the direction and quantity of the auxin flow. Several plant hormones affect PIN abundance, resulting in another means of crosstalk between auxin and these hormones. In conclusion, PIN proteins are instrumental in directing plant developmental responses to environmental and endogenous signals.

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Biology of Stress Special Issue: Current Biology

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The term stress can be broadly construed, with some forms constituting an essential part of developmental processes and others representing potentially harmful changes in the environment. How an organism deals with stress is also varied and can develop on various times scales, from milliseconds, as in rapid homeostatic responses, to evolutionary time, as in the adaptation of an organism to a new environment.

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Arabidopsis ABCG14 is essential for the root-to-shoot translocation of cytokinin

Arabidopsis ABCG14 is essential for the root-to-shoot translocation of cytokinin | Plant Gene Seeker -PGS | Scoop.it
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Roots and shoots communicate with each other to synchronize and optimize plant growth and respond to environmental changes. Shoots and roots exchange signals to sense the status and respond to the needs of the other organ. Cytokinins, which are phytohormones that regulate various aspects of growth and development, are recognized as the most important signal transmitted from roots to shoots. Whereas the enzymes underlying cytokinin biosynthesis and the corresponding receptors have been identified, our knowledge of cytokinin transport is limited. In this study, we identified the Arabidopsis ATP-binding cassette transporter subfamily G14 as a major component in the transfer of cytokinins from roots to shoots and hence as a regulator of shoot development. This finding represents a major breakthrough in the field.

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Developmental Cell: A Mesoscale Abscisic Acid Hormone Interactome Reveals a Dynamic Signaling Landscape in Arabidopsis:

Developmental Cell: A Mesoscale Abscisic Acid Hormone Interactome Reveals a Dynamic Signaling Landscape in Arabidopsis: | Plant Gene Seeker -PGS | Scoop.it

Interesting study - lots of genes and pathways to ponder...


Via Mary Williams
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Licensing MLH1 sites for crossover during meiosis | Nature Communications

Licensing MLH1 sites for crossover during meiosis | Nature Communications | Plant Gene Seeker -PGS | Scoop.it
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During meiosis, homologous chromosomes synapse and recombine at sites marked by the binding of the mismatch repair protein MLH1. In hexaploid wheat, the Ph1 locus has a major effect on whether crossover occurs between homologues or between related homoeologues. Here we report that—in wheat–rye hybrids where homologues are absent—Ph1 affects neither the level of synapsis nor the number of MLH1. Thus in the case of wheat–wild relative hybrids, Ph1 must affect whether MLH1 sites are able to progress to crossover. The observed level of synapsis implies that Ph1 functions to promote homologue pairing rather than suppress homoeologue pairing in wheat. Therefore, Ph1stabilises polyploidy in wheat by both promoting homologue pairing and preventing MLH1 sites from becoming crossovers on paired homoeologues during meiosis.


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Photosynthesis in a climate change scenario | Plant Science

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PREFACE

This Special Issue takes in consideration the importance of climate change and of photosynthesis as the life process most affected by global environmental changes. The issue contains a series of papers that address some of the most important recent advances in our understanding of how plant photosynthesis is regulated by the most important drivers of climate change. Hence, several papers (e.g. Cabot et al.; Gonzalez-Meler et al., Irigoyen et al.; Morales et al.) describe revisions of the most important methodologies employed for experimentally simulating climate change scenarios, and the key conclusions that have been derived from such studies over the past decades. Other papers consider, from either theoretical or experimental approaches, several important physiological aspects to be considered when addressing studies on plant responses to climate change including mesophyll conductance to CO2 (Flexas et al., Sun et al. a), Rubisco (Galmes et al.), carbon isotope discrimination (Perez-Lopez et al.), isoprene emission (Centritto et al.), monoubiquitin expression (Tian et al. a), foliar decreases (Ogaya et al.) or water use efficiency (Gago et al.). Finally, other papers present novel data on experimental approaches for understanding species specific photosynthetic responses to components of climate change such as elevated CO2, ozone and temperature (Ayub et al., Bunce; Rosenthal et al.; Sun et al. b; Wang and Heckathorn; Zang et al. a,b).

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Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines - The Plant Journal

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines - The Plant Journal | Plant Gene Seeker -PGS | Scoop.it
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Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.


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The S-Domain Receptor Kinase Arabidopsis Receptor Kinase2 and the U Box/Armadillo Repeat-Containing E3 Ubiquitin Ligase9 Module Mediates Lateral Root Development under Phosphate Starvation in Arabi...

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When plants encounter nutrient-limiting conditions in the soil, the root architecture is redesigned to generate numerous lateral roots (LRs) that increase the surface area of roots, promoting efficient uptake of these deficient nutrients. Of the many essential nutrients, reduced availability of inorganic phosphate has a major impact on plant growth because of the requirement of inorganic phosphate for synthesis of organic molecules, such as nucleic acids, ATP, and phospholipids, that function in various crucial metabolic activities. In our screens to identify a potential role for the S-domain receptor kinase1-6 and its interacting downstream signaling partner, the Arabidopsis (Arabidopsis thaliana) plant U box/armadillo repeat-containing E3 ligase9 (AtPUB9), we identified a role for this module in regulating LR development under phosphate-starved conditions. Our results show that Arabidopsis double mutant plants lackingAtPUB9 and Arabidopsis Receptor Kinase2 (AtARK2; ark2-1/pub9-1) display severely reduced LRs when grown under phosphate-starved conditions. Under these starvation conditions, these plants accumulated very low to no auxin in their primary root and LR tips as observed through expression of the auxin reporter DR5::uidA transgene. Exogenous auxin was sufficient to rescue the LRdevelopmental defects in the ark2-1/pub9-1 lines, indicating a requirement of auxin accumulation for this process. Our subcellular localization studies with tobacco (Nicotiana tabacum) suspension-cultured cells indicate that interaction between ARK2 and AtPUB9 results in accumulation of AtPUB9 in the autophagosomes. Inhibition of autophagy in wild-type plants resulted in reduction of LR development and auxin accumulation under phosphate-starved conditions, suggesting a role for autophagy in regulating LR development. Thus, our study has uncovered a previously unknown signaling module (ARK2-PUB9) that is required for auxin-mediated LR development under phosphate-starved conditions.


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Generation of Marker-free Transgenic Plants Concurrently Resistant to a DNA Geminivirus and a RNA Tospovirus | Scientific Reports

Generation of Marker-free Transgenic Plants Concurrently Resistant to a DNA Geminivirus and a RNA Tospovirus | Scientific Reports | Plant Gene Seeker -PGS | Scoop.it
Global threats of ssDNA geminivirus and ss(-)RNA tospovirus on crops necessitate the development of transgenic resistance. Here, we constructed a two-T DNA vector carrying a hairpin of the intergenic region (IGR) of Ageratum yellow vein virus (AYVV), residing in an intron inserted in an untranslatable nucleocapsid protein (NP) fragment of Melon yellow spot virus (MYSV). Transgenic tobacco lines highly resistant to AYVV and MYSV were generated. Accumulation of 24-nt siRNA, higher methylation levels on the IGR promoters of the transgene, and suppression of IGR promoter activity of invading AYVV indicate that AYVV resistance is mediated by transcriptional gene silencing. Lack of NP transcript and accumulation of corresponding siRNAs indicate that MYSV resistance is mediated through post-transcriptional gene silencing. Marker-free progenies with concurrent resistance to both AYVV and MYSV, stably inherited as dominant nuclear traits, were obtained. Hence, we provide a novel way for concurrent control of noxious DNA and RNA viruses with less biosafety concerns.
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Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing : Nature Communications : Nature Publishing Group

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing : Nature Communications : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
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Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

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The anthocyanin reduced tomato mutant demonstrates the role of flavonols in tomato lateral root and root hair development

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This study utilized Solanum lycopersicum (tomato) mutants with altered flavonoid biosynthesis to understand the impact of these metabolites on root development. The mutant anthocyanin reduced (are) has a mutation in the gene encoding flavonoid 3-hydroxylase (F3H), the first step in flavonol synthesis, and accumulates higher concentrations of the F3H substrate, naringenin, and lower levels of the downstream products, kaempferol, quercetin, myricetin, and anthocyanins, than wild-type. Complementation of are with the p35S:F3H transgene reduced naringenin and increased flavonols to wild-type levels. The initiation of lateral roots is reduced in are and p35S:F3H complementation restores wild-type root formation. The flavonoid mutant anthocyanin without (aw) has a defect in the gene encoding dihydroflavonol reductase, resulting in elevated flavonols and the absence of anthocyanins and displays increased lateral root formation. These results are consistent with a positive role of flavonols in lateral root formation. The are mutant has increased IAA transport and greater sensitivity to the inhibitory effect of the auxin transport inhibitor naphthylphthalamic acid on lateral root formation. Expression of the auxin-induced reporter (DR5-GUS) is reduced in initiating lateral roots and increased in primary root tips of are. Levels of reactive oxygen species are elevated in are root epidermal tissues and root hairs, and are forms more root hairs, consistent with a role of flavonols as antioxidants that modulate root hair formation. Together these experiments identify positive roles of flavonols in formation of lateral roots and negative roles in formation of root hairs through modulation of auxin transport and ROS, respectively.

 

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Scaling of nitrogen and phosphorus across plant organs in shrubland biomes across Northern China : Scientific Reports : Nature Publishing Group

Scaling of nitrogen and phosphorus across plant organs in shrubland biomes across Northern China : Scientific Reports : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
Allocation of limiting resources, such as nutrients, is an important adaptation strategy for plants. Plants may allocate different nutrients within a specific organ or the same nutrient among different organs. In this study, we investigated the allocation strategies of nitrogen (N) and phosphorus (P) in leaves, stems and roots of 126 shrub species from 172 shrubland communities in Northern China using scaling analyses. Results showed that N and P have different scaling relationships among plant organs. The scaling relationships of N concentration across different plant organs tended to be allometric between leaves and non-leaf organs, and isometric between non-leaf organs. Whilst the scaling relationships of P concentration tended to be allometric between roots and non-root organs, and isometric between non-root organs. In arid environments, plant tend to have higher nutrient concentration in leaves at given root or stem nutrient concentration. Evolutionary history affected the scaling relationships of N concentration slightly, but not affected those of P concentration. Despite fairly consistent nutrients allocation strategies existed in independently evolving lineages, evolutionary history and environments still led to variations on these strategies.
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Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement

Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement | Plant Gene Seeker -PGS | Scoop.it
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
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Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability.

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Virtual Special Issue on Environmental Issues in Plant Science - Environmental and Experimental Botany

Virtual Special Issue on Environmental Issues in Plant Science - Environmental and Experimental Botany | Plant Gene Seeker -PGS | Scoop.it

Compiled by Jean-Claude Kader and Kari Taulavuori

The Journal Environmental and Experimental Botany (EEB)

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The Journal Environmental and Experimental Botany (EEB) aims to develop knowledge about the mechanisms of the adaptation of plants to environmental factors.

In addition to research papers, EEB invites the best authors to write reviews on the main priorities of the Journal.

We have compiled here some of the best reviews published in EEB these recent years.

In this Virtual Special Issue, are presented eighteen papers related to several main scientific areas such as temperature (high or low) (six reviews), salinity and water deficit (four reviews) and heavy metal stresses (five reviews). The three other reviews are devoted to the mechanisms involved in the responses of plants to environment including hormonal pathways.

We hope that this virtual special issue will encourage discussion among experts in these fields and will attract novel and exciting papers in the future issues of The Journal Environmental and Experimental Botany.

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Why asparagus makes your urine smell and onions make your cry

Why asparagus makes your urine smell and onions make your cry | Plant Gene Seeker -PGS | Scoop.it
An anonymous chemistry teacher based in the UK created the infographics to demystify the chemistry of everyday foods and show that chemicals are in everything.

Via Meristemi
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Marco Fulvio Barozzi's curator insight, May 17, 1:35 PM

La chimica è dovunque, ragazzo mio: devi fartene una ragione.

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Tempest in a Tea Pot: How did the Public Conversation on Genetically Modified Crops Drift so far from the Facts? - Goldstein (2014) - J Med Toxicol

Tempest in a Tea Pot: How did the Public Conversation on Genetically Modified Crops Drift so far from the Facts? - Goldstein (2014) - J Med Toxicol | Plant Gene Seeker -PGS | Scoop.it

The debate over genetically modified (GM) crops has raged in Europe since 1996, but had barely risen above a whisper in the USA until recent labeling debates raised public attention. This article will explain GM crops and traits discuss safety assessment provide a view on safety from authoritative organizations discuss selected issues of current debate, and provide the author’s perspective as to why the public debate has drifted so far from scientific reality.

 

The economic and environmental benefits of GM crops are beyond scope, but references are provided. GM food and feed undergo comprehensive assessments using recognized approaches to assure they are as safe as the conventional congener. Issues of food safety and nutrition, unrelated to the GM process, may arise when GM foods display novel components or composition. Unanticipated genetic effects in GM crops appear to be limited in contrast to existing variations among conventional varieties resulting from breeding, mutation, and natural mobile genetic elements.

 

Allergenic potential is assessed when selecting genes for introduction into GM crops and remains a theoretical risk to date. Emerging weed and insect resistance is not unique to GM technology and will require the use of integrated pest management/best practices for pest control. Gene flow from GM crops to wild relatives is limited by existing biological barriers but can at time be a relevant consideration in gene selection and planting practices.Insect-resistant GM crops have significantly reduced use of chemical insecticides and appear to have reduced the incidence of pesticide poisoning in areas where small scale farming and hand application are common. Changes in herbicide patterns are more complex and are evolving over time in response to weed resistance management needs. 

 

Recent public debate is driven by a combination of unfounded allegations about the technology and purveyors, pseudoscience, and attempts to apply a strict precautionary principle... Authoritative organizations such as the FDA, World Health Organization, AAAS, the Royal Society of Medicine, and the National Academy of Science have affirmed the safety of GM crops. So, how did the public conversation on GM crops become so negative? Opponents of GM have used three approaches to drive negative public opinion. The first approach has been to create negative impressions about the developers and purveyors of this technology... A second approach is to question the science underlying GM safety, often via misinterpretation of data obtained in inappropriate test systems... 

 A third approach is to invoke the “precautionary principle.” As originally proposed, the principle stated that risk assessors and policy makers should take account of uncertainties... to provide adequate margins of safety. The absolute version employed by some suggests that in the presence of any uncertainty, we should not move forward. This is of course a “black hole”—one can never prove a negative and hence one can never move forward when employing the absolute precautionary principle. The latter ignores both the risks of existing technology and the benefits of innovation and leaves decision making in the hands of anyone who chooses to raise doubts.  GM crops have a more than 20-year track record of being grown and used commercially without a single human illness known to be caused by GM food or feed. Moreover, billions of animals have been fed predominantly GM diets for consecutive generations with no evidence that animal health and productivity were affected. The safety assessment paradigm for GM crops is robust and well established, and the approach has been confirmed by authoritative regulatory agencies and scientific organizations around the globe. These are, by far, the most thoroughly assessed foods and feeds in human history, and the National Academies of Science concluded that risk or unintended effects of GM technologies falls within the range of risks for conventional breeding technologies—which include forced inter-species crosses and radiation-induced mutagenesis. We can move forward with high confidence that GM food and feed are as safe and nutritious as their conventional congeners and perhaps look forward to rationalizing food safety assessment across conventional, GM, and other new breeding technologies to achieve a more focused and resource-efficient safety assessment process.

 

http://dx.doi.org/10.1007/s13181-014-0402-7

 


Via Alexander J. Stein
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