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Indian farmer suicides: Is GM cotton to blame? - Plewis - 2014 - Significance - Wiley Online Library

Indian farmer suicides: Is GM cotton to blame? - Plewis - 2014 - Significance - Wiley Online Library | plant cell genetics | Scoop.it

“Thousands of Indian farmers are committing suicide after growing GM crops.” It is no minor claim. Genetically modified crops revolutionise agriculture – but are controversial. They will feed the world, reduce the need for pesticides and fertilisers, and add health-protecting nutrients to those who consume them, say some. They are an ecological disaster in the making, say others, and impoverish the Third World farmers who grow them. Often quoted is the example of suicides among Indian farmers who grow GM crops. Ian Plewisexamines the data and the conclusion. 

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New developments in engineering plant metabolic pathways

New developments in engineering plant metabolic pathways | plant cell genetics | Scoop.it
Plants contain countless metabolic pathways that are responsible for the biosynthesis of complex metabolites. Armed with new tools in sequencing and bioinformatics, the genes that encode these plant biosynthetic pathways have become easier to discover, putting us in an excellent position to fully harness the wealth of compounds and biocatalysts (enzymes) that plants provide. For overproduction and isolation of high-value plant-derived chemicals, plant pathways can be reconstituted in heterologous hosts. Alternatively, plant pathways can be modified in the native producer to confer new properties to the plant, such as better biofuel production or enhanced nutritional value. This perspective highlights a range of examples that demonstrate how the metabolic pathways of plants can be successfully harnessed with a variety of metabolic engineering approaches.
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Climate-smart soils : Nature : Nature Publishing Group

Climate-smart soils : Nature : Nature Publishing Group | plant cell genetics | Scoop.it
Soils are integral to the function of all terrestrial ecosystems and to food and fibre production. An overlooked aspect of soils is their potential to mitigate greenhouse gas emissions. Although proven practices exist, the implementation of soil-based greenhouse gas mitigation activities are at an early stage and accurately quantifying emissions and reductions remains a substantial challenge. Emerging research and information technology developments provide the potential for a broader inclusion of soils in greenhouse gas policies. Here we highlight ‘state of the art’ soil greenhouse gas research, summarize mitigation practices and potentials, identify gaps in data and understanding and suggest ways to close such gaps through new research, technology and collaboration.
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In vivo assembly of DNA-fragments in the moss, Physcomitrella patens

In vivo assembly of DNA-fragments in the moss, Physcomitrella patens | plant cell genetics | Scoop.it
Direct assembly of multiple linear DNA fragments via homologous recombination, a phenomenon known as in vivo assembly or transformation associated recombination, is used in biotechnology to assemble DNA constructs ranging in size from a few kilobases to full synthetic microbial genomes. It has also enabled the complete replacement of eukaryotic chromosomes with heterologous DNA. The moss Physcomitrella patens, a non-vascular and spore producing land plant (Bryophyte), has a well-established capacity for homologous recombination. Here, we demonstrate the in vivo assembly of multiple DNA fragments in P. patens with three examples of effective genome editing: we (i) efficiently deleted a genomic locus for diterpenoid metabolism yielding a biosynthetic knockout, (ii) introduced a salt inducible promoter, and (iii) re-routed endogenous metabolism into the formation of amorphadiene, a precursor of high-value therapeutics. These proof-of-principle experiments pave the way for more complex and increasingly flexible approaches for large-scale metabolic engineering in plant biotechnology.
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Production and characterization of tearless and non-pungent onion

Production and characterization of tearless and non-pungent onion | plant cell genetics | Scoop.it

The onion lachrymatory factor (LF) is produced from trans-S-1-propenyl-L-cysteine sulfoxide (PRENCSO) through successive reactions catalyzed by alliinase (EC 4.4.1.4) and lachrymatory factor synthase (LFS), and is responsible for the tear inducing-property and the pungency of fresh onions. We developed tearless, non-pungent onions non-transgenically by irradiating seeds with neon-ion at 20 Gy. The bulbs obtained from the irradiated seeds and their offspring bulbs produced by selfing were screened by organoleptic assessment of tear-inducing property or HPLC analysis of LF production. After repeated screening and seed production by selfing, two tearless, non-pungent bulbs were identified in the third generation (M3) bulbs. Twenty M4 bulbs obtained from each of them showed no tear-inducing property or pungency when evaluated by 20 sensory panelists. The LF production levels in these bulbs were approximately 7.5-fold lower than those of the normal onion. The low LF production levels were due to reduction in alliinase activity, which was a result of low alliinase mRNA expression (less than 1% of that in the normal onion) and consequent low amounts of the alliinase protein. These tearless, non-pungent onions should be welcomed by all who tear while chopping onions and those who work in facilities where fresh onions are processed.

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Convergence in the temperature response of leaf respiration across biomes and plant functional types

Convergence in the temperature response of leaf respiration across biomes and plant functional types | plant cell genetics | Scoop.it
A major concern for terrestrial biosphere models is accounting for the temperature response of leaf respiration at regional/global scales. Most biosphere models incorrectly assume that respiration increases exponentially with rising temperature, with profound effects for predicted ecosystem carbon exchange. Based on a study of 231 species in 7 biomes, we find that the rise in respiration with temperature can be generalized across biomes and plant types, with temperature sensitivity declining as leaves warm. This finding indicates universally conserved controls on the temperature sensitivity of leaf metabolism. Accounting for the temperature function markedly lowers simulated respiration rates in cold biomes, which has important consequences for estimates of carbon storage in vegetation, predicted concentrations of atmospheric carbon dioxide, and future surface temperatures.
Jean-Pierre Zryd's insight:
Higher temperature and increases CO2 fixation are not incompatible
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Cell-to-cell movement of mitochondria in plants

Cell-to-cell movement of mitochondria in plants | plant cell genetics | Scoop.it
We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer from Nicotiana sylvestris into Nicotiana tabacum cells. The alloplasmic N. tabacum line we used carries Nicotiana undulata cytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer from N. sylvestris to N. tabacum could be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility to orf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation.
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Elucidation of the first committed step in betalain biosynthesis enables the heterologous engineering of betalain pigments in plants - Polturak - 2015 - New Phytologist - Wiley Online Library

Elucidation of the first committed step in betalain biosynthesis enables the heterologous engineering of betalain pigments in plants - Polturak - 2015 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Betalains are tyrosine-derived red-violet and yellow pigments, found in plants only of the Caryophyllales order. Although much progress has been made in recent years in the understanding of the betalain biosynthetic process, many questions remain open with regards to several of the proposed steps in the pathway. Most conspicuous by its absence is the characterization of the first committed step in the pathway, namely the 3-hydroxylation of tyrosine to form l-3,4-dihydroxyphenylalanine (l-DOPA).
We used transcriptome analysis of the betalain-producing plants red beet (Beta vulgaris) and four o'clocks (Mirabilis jalapa) to identify a novel, betalain-related cytochrome P450-type gene, CYP76AD6, and carried out gene silencing and recombinant expression assays in Nicotiana benthamiana and yeast cells to examine its functionality.
l-DOPA formation in red beet was found to be redundantly catalyzed by CYP76AD6 together with a known betalain-related enzyme, CYP76AD1, which was previously thought to only catalyze a succeeding step in the pathway. While CYP76AD1 catalyzes both l-DOPA formation and its subsequent conversion to cyclo-DOPA, CYP76AD6 uniquely exhibits only tyrosine hydroxylase activity.
The new findings enabled us to metabolically engineer entirely red-pigmented tobacco plants through heterologous expression of three genes taking part in the fully decoded betalain biosynthetic pathway.
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The enhancement of tolerance to salt and cold stresses by modifying the redox state and salicylic acid content via the cytosolic malate dehydrogenase gene in transgenic apple plants -

The enhancement of tolerance to salt and cold stresses by modifying the redox state and salicylic acid content via the cytosolic malate dehydrogenase gene in transgenic apple plants - | plant cell genetics | Scoop.it
In this paper, we characterized the role of an apple cytosolic malate dehydrogenase gene (MdcyMDH) in the tolerance to salt and cold stresses and investigated its regulation mechanism in stress tolerance. The MdcyMDH transcript was induced by mild cold and salt treatments, and MdcyMDH-overexpressing apple plants possessed improved cold and salt tolerance compared to wild type (WT) plants. A digital gene expression tag profiling analysis revealed that MdcyMDH overexpression largely altered some biological processes, including hormone signal transduction, photosynthesis, citrate cycle, and oxidation-reduction. Further experiments verified that MdcyMDH overexpression modified the mitochondrial and chloroplast metabolisms and elevated the level of reducing power, primarily caused by increased ascorbate and glutathione, as well as the increased ratios of ascorbate/dehydroascorbate and glutathione/glutathione disulfide, under normal and especially stress conditions. Concurrently, the transgenic plants produced a high H2O2 content, but a low O2·- production rate was observed compared to the WT plants. On the other hand, the transgenic plants accumulated more free and total salicylic acid (SA) than the WT plants under normal and stress conditions. Taken together, MdcyMDH conferred the transgenic apple plants a higher stress tolerance by producing more reductive redox states and increasing the SA level; MdcyMDH could serve as a target gene to genetically engineer salt- and cold-tolerant trees.

Via Christophe Jacquet
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Implications of plant glycans in the development of innovative vaccines

Implications of plant glycans in the development of innovative vaccines | plant cell genetics | Scoop.it
Plant glycans play a central role in vaccinology: they can serve as adjuvants and/or delivery vehicles or backbones for the synthesis of conjugated vaccines. In addition, genetic engineering is leading to the development of platforms for the production of novel polysaccharides in plant cells, an approach with relevant implications for the design of new types of vaccines. This review contains an updated outlook on this topic and provides key perspectives including a discussion on how the molecular pharming field can be linked to the production of innovative glycan-based and conjugate vaccines.
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Tyrosine Hydroxylation in Betalain Pigment Biosynthesis Is Performed by Cytochrome P450 Enzymes in Beets ( Beta vulgaris )

Yellow and red-violet betalain plant pigments are restricted to several families in the order Caryophyllales, where betacyanins play analogous biological roles to anthocyanins. The initial step in betalain biosynthesis is the hydroxylation of tyrosine to form L-DOPA. Using gene expression experiments in beets, yeast, and Arabidopsis, along with HPLC/MS analysis, the present study shows that two novel cytochrome P450 (CYP450) enzymes, CYP76AD6 and CYP76AD5, and the previously described CYP76AD1 can perform this initial step. Co-expressing these CYP450s with DOPA 4,5-dioxygenase in yeast, and overexpression of these CYP450s in yellow beets show that CYP76AD1 efficiently uses L-DOPA leading to red betacyanins while CYP76AD6 and CYP76AD5 lack this activity. Furthermore, CYP76AD1 can complement yellow beetroots to red while CYP76AD6 and CYP76AD5 cannot. Therefore CYP76AD1 uniquely performs the beet R locus function and beets appear to be genetically redundant for tyrosine hydroxylation. These new functional data and ancestral character state reconstructions indicate that tyrosine hydroxylation alone was the most likely ancestral function of the CYP76AD alpha and beta groups and the ability to convert L-DOPA to cyclo-DOPA evolved later in the alpha group.
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Emissions reduction: Scrutinize CO2 removal methods

Emissions reduction: Scrutinize CO2 removal methods | plant cell genetics | Scoop.it

Carbon-capture plants provide one way to reduce the amount of atmospheric carbon dioxide.

In Paris last December, the 196 parties to the United Nations Framework Convention on Climate Change (UNFCCC) agreed to balance the human-driven greenhouse-gas budget some time between 2050 and 2100. This commitment is intended to limit the increase in global average temperature above pre-industrial levels to “well below 2 °C” — and preferably to 1.5 °C.

A balanced greenhouse-gas budget either requires that industry and agriculture produce zero emissions or necessitates the active removal of greenhouse gases from the atmosphere (in addition to deep and rapid emissions cuts). In most modelled scenarios that limit warming to 2 °C, several gigatonnes of carbon dioxide have to be extracted and safely stored each year1. For more ambitious targets, tens of gigatonnes per year must be removed2.

Many CO2-removal techniques have been proposed. Whether any of them could work at the scale needed to deliver the goal of the Paris agreement depends on three things: feasibility, cost and acceptability. A crucial component of all of these approaches is the non-climatic impacts that large-scale CO2-removal could have on ecosystems and biodiversity.

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Betalains, Phenols and Antioxidant Capacity in Cactus Pear [Opuntia ficus-indica (L.) Mill.] Fruits from Apulia (South Italy) Genotypes

Betalains, Phenols and Antioxidant Capacity in Cactus Pear [Opuntia ficus-indica (L.) Mill.] Fruits from Apulia  (South Italy) Genotypes | plant cell genetics | Scoop.it
Betacyanin (betanin), total phenolics, vitamin C and antioxidant capacity (by Trolox-equivalent antioxidant capacity (TEAC) and oxygen radical absorbance capacity (ORAC) assays) were investigated in two differently colored cactus pear (Opuntia ficus-indica (L.) Mill.) genotypes, one with purple fruit and the other with orange fruit, from the Salento area, in Apulia (South Italy). In order to quantitate betanin in cactus pear fruit extracts (which is difficult by HPLC because of the presence of two isomers, betanin and isobetanin, and the lack of commercial standard with high purity), betanin was purified from Amaranthus retroflexus inflorescence, characterized by the presence of a single isomer. The purple cactus pear variety showed very high betanin content, with higher levels of phenolics, vitamin C, and antioxidant capacity (TEAC) than the orange variety. These findings confirm the potential for exploiting the autochthonous biodiversity of cactus pear fruits. In particular, the purple variety could be an interesting source of colored bioactive compounds which not only have coloring potential, but are also an excellent source of dietary antioxidant components which may have beneficial effects on consumers’ health.
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Life at the boundary: photosynthesis at the soil–fluid interface. A synthesis focusing on mosses

Life at the boundary: photosynthesis at the soil–fluid interface. A synthesis focusing on mosses | plant cell genetics | Scoop.it
Mosses are among the earliest branching embryophytes and probably originated not later than the early Ordovician when atmospheric CO2 was higher and O2 was lower than today. The C3 biochemistry and physiology of their photosynthesis suggests, by analogy with tracheophytes, that growth of extant bryophytes in high CO2 approximating Ordovician values would increase the growth rate. This occurs for many mosses, including Physcomitrella patens in suspension culture, although recently published transcriptomic data on this species at high CO2 and present-day CO2 show down-regulation of the transcription of several genes related to photosynthesis. It would be useful if transcriptomic (and proteomic) data comparing growth conditions are linked to measurements of growth and physiology on the same, or parallel, cultures. Mosses (like later-originating embryophytes) have been subject to changes in bulk atmospheric CO2 and O2 throughout their existence, with evidence, albeit limited, for positive selection of moss Rubisco. Extant mosses are subject to a large range of CO2 and O2 concentrations in their immediate environments, especially aquatic mosses, and mosses are particularly influenced by CO2 generated by, and O2 consumed by, soil chemoorganotrophy from organic C produced by tracheophytes (if present) and bryophytes.
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Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR), a regulator of ABA responses unique to basal land plants and required for desiccation tolerance

Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR), a regulator of ABA responses unique to basal land plants and required for desiccation tolerance | plant cell genetics | Scoop.it
The anatomically simple plants that first colonised land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA non-responsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating population to map and identify the ABA NON-RESPONSIVE (ANR) gene encoding a modular protein kinase comprising an N-terminal PAS domain, a central EDR domain and a C-terminal MAPKKK-like domain. anr mutants fail to accumulate dehydration tolerance-associated gene products in response to drought, ABA or osmotic stress, and do not acquire ABA-dependent desiccation tolerance. The crystal structure of the PAS domain, determined to 1.7Å resolution, shows a conserved PAS-fold that dimerises through a weak dimerization interface. Targeted mutagenesis of a conserved tryptophan residue within the PAS domain generates plants with ABA non-responsive growth and strongly attenuated ABA-responsive gene expression, whereas deleting this domain retains a fully ABA-responsive phenotype. ANR orthologs are found in early-diverging land plant lineages and aquatic algae, but are absent from more recently diverged vascular plants. We propose that ANR genes represent an ancestral adaptation that enabled drought-stress survival of the first terrestrial colonisers, but were lost during land plant evolution.
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Néonicotinoïdes : pour la fin des outrances

Néonicotinoïdes : pour la fin des outrances | plant cell genetics | Scoop.it

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ForumPhyto's curator insight, May 12, 11:43 AM

Autour d'un article de Stéphane Foucart dans Le Monde.
A partir des tweets de @AEGRW et d'un article de Wackes Seppi

Sylvain Rotillon's curator insight, May 12, 4:44 PM

Comme trop souvent, forum phyto dénonce ce qu'ils pratiquent, à savoir une position de lobby. C'est dommage car les contrepoints développés pourraient enrichir le débat.

congruence-RSO's curator insight, May 12, 5:45 PM
ForumPhyto est un regroupement de professionnels du monde agricole qui travaillent ensemble à développer une protection des plantes assumée, responsable et durable sur les fruits, légumes et pommes de terre.
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Gene-edited CRISPR mushroom escapes US regulation

Gene-edited CRISPR mushroom escapes US regulation | plant cell genetics | Scoop.it
A fungus engineered with the CRISPR–Cas9 technique can be cultivated and sold without further oversight.
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Light-driven oxidation of polysaccharides by photosynthetic pigments and a metalloenzyme

Light-driven oxidation of polysaccharides by photosynthetic pigments and a metalloenzyme | plant cell genetics | Scoop.it
Oxidative processes are essential for the degradation of plant biomass. A class of powerful and widely distributed oxidative enzymes, the lytic polysaccharide monooxygenases (LPMOs), oxidize the most recalcitrant polysaccharides and require extracellular electron donors. Here we investigated the effect of using excited photosynthetic pigments as electron donors. LPMOs combined with pigments and reducing agents were exposed to light, which resulted in a never before seen 100-fold increase in catalytic activity. In addition, LPMO substrate specificity was broadened to include both cellulose and hemicellulose. LPMO enzymes and pigment derivatives common in the environment of plant-degrading organisms thus form a highly reactive and stable light-driven system increasing the turnover rate and versatility of LPMOs. This light-driven system may find applications in biotechnology and chemical processing.
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Macro-Process of Past Plant Subsistence from the Upper Paleolithic to Middle Neolithic in China: A Quantitative Analysis of Multi-Archaeobotanical Data

Macro-Process of Past Plant Subsistence from the Upper Paleolithic to Middle Neolithic in China: A Quantitative Analysis of Multi-Archaeobotanical Data | plant cell genetics | Scoop.it
Detailed studies of the long-term development of plant use strategies indicate that plant subsistence patterns have noticeably changed since the Upper Paleolithic, when humans underwent a transitional process from foraging to agriculture. This transition was best recorded in west Asia; however, information about how plant subsistence changed during this transition remains limited in China. This lack of information is mainly due to a limited availability of sufficiently large, quantified archaeobotanical datasets and a paucity of related synthetic analyses. Here, we present a compilation of extensive archaeobotanical data derived from interdisciplinary approaches, and use quantitative analysis methods to reconstruct past plant use from the Upper Paleolithic to Middle Neolithic in China. Our results show that intentional exploitation for certain targeted plants, particularly grass seeds, may be traced back to about 30,000 years ago during the Upper Paleolithic. Subsequently, the gathering of wild plants dominated the subsistence system; however, this practice gradually diminished in dominance until about 6~5 ka cal BP during the Middle Neolithic. At this point, farming based on the domestication of cereals became the major subsistence practice. Interestingly, differences in plant use strategies were detected between north and south China, with respect to (1) the proportion of certain plant taxa in assemblages, (2) the domestication rate of cereals, and (3) the type of plant subsistence practiced after the establishment of full farming. In conclusion, the transition from foraging to rice and millet agriculture in China was a slow and long-term process spanning 10s of 1000s of years, which may be analogous to the developmental paths of wheat and barley farming in west Asia.
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Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics | plant cell genetics | Scoop.it
Plants grow in dynamic environments where they can be exposed to a multitude of stressful factors, all of which affect their development, yield, and, ultimately, reproductive success. Plants are adept at rapidly acclimating to stressful conditions and are able to further fortify their defenses by retaining memories of stress to enable stronger or more rapid responses should an environmental perturbation recur. Indeed, one mechanism that is often evoked regarding environmental memories is epigenetics. Yet, there are relatively few examples of such memories; neither is there a clear understanding of their duration, considering the plethora of stresses in nature. We propose that this field would benefit from investigations into the processes and mechanisms enabling recovery from stress. An understanding of stress recovery could provide fresh insights into when, how, and why environmental memories are created and regulated. Stress memories may be maladaptive, hindering recovery and affecting development and potential yield. In some circumstances, it may be advantageous for plants to learn to forget. Accordingly, the recovery process entails a balancing act between resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting the epigenome and transcriptome and in altering memory. Exploration of this emerging area of research is becoming ever more tractable with advances in genomics, phenomics, and high-throughput sequencing methodology that will enable unprecedented profiling of high-resolution stress recovery time series experiments and sampling of large natural populations.
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EU decision process hinders use of genetically modified trees - VIB (2016)

EU decision process hinders use of genetically modified trees - VIB (2016) | plant cell genetics | Scoop.it

Just like other crops, trees can also be genetically modified in order to introduce new, useful characteristics. Although such trees offer many socio-economic and environmental benefits, complex and unpredictable EU procedures are hindering their introduction to the market. This is the conclusion reached by researchers in a joint text drawn up as part of a European Cooperation in Science and Technology (COST) project about genetically modified trees. The researchers state that Europe is lagging behind in worldwide GM developments and call for a more scientifically substantiated decision process... 

 

Genetically modified trees can be used as an efficient raw material for renewable products or bioenergy, which could in turn promote the transition to a sustainable, CO2-neutral economy. However, Europe imposes a comprehensive risk assessment and authorization procedure on the development and use of genetically modified crops... “It’s also difficult to predict exactly how detailed the risk analyses need to be. This all means that the risk-analysis process for GM trees in Europe demands a huge amount of time and money. More clarity on the data required and the use of predictive models is needed.”

The European decision process is not only complex, but also unpredictable. After the risk analysis and a scientific conclusion from EFSA, it is still by no means certain that a European approval will follow. The fact that individual EU Member States can restrict or prohibit the cultivation of GMOs on their territory for reasons having nothing to do with substantiated risks further increases this uncertainty... “This is in sharp contrast to the introduction of conventionally cultivated, non-European trees and other cultivated crops. Although these also interact differently with their environment, a prior risk analysis is not required for this.”

Genetically modified poplars are already being planted in China and it looks like the green light will also be given in North and South America... “Just like with other GM crops, the commercial developments in the field of GM trees are taking place outside Europe. The question is whether that can be scientifically substantiated. After all, more than twenty years of experiments and commercial application have shown that genetic modification poses no inherent risks. There is no reason to assume trees would be different. Europe should learn from the experience we have built up with GM technology and base its decisions more on scientific facts. Today the decision process is politicized and dogmatic and the environment itself could end up being the biggest victim of this.” 

 

http://www.vib.be/en/news/Pages/EU-regulations-impede-market-introduction-GM-forest-trees.aspx

 

Original article: http://dx.doi.org/10.1016/j.tplants.2016.01.015

 


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The dope on l-DOPA formation for betalain pigments - Schwinn - 2016 - New Phytologist - Wiley Online Library

The dope on l-DOPA formation for betalain pigments - Schwinn - 2016 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Betalains are remarkable pigments that have long intrigued both plant biologists and chemists. In plants these metabolites impart bright yellow to violet pigmentation to a variety of organs (Fig. 1). They occur only in the core Caryophyllales where in most of the families they replace anthocyanin pigments (Clement et al., 1994; Brockington et al., 2015), evolutionarily older and structurally unrelated compounds that are generally the basis for red to blue colours in plants. The final steps in betalain formation are spontaneous, and the synthesis of their core moieties involves only a few enzymatic steps centred on the production and conversion of l-3,4-dihydroxyphenylalanine (l-DOPA) (Strack et al., 2003). Despite much scientific scrutiny and the apparent relative lack of pathway complexity, progress in identifying the genes involved in the pathway has been slow, preventing the development of a depth of knowledge on betalains to match that for the anthocyanins. However, since the landmark identification of the first biosynthetic gene (Christinet et al., 2004), momentum has grown with the identification of genes for other biosynthetic steps (Hatlestad et al., 2012; Gandía-Herrero & García-Carmona, 2013) and pathway regulation (Hatlestad et al., 2015). Now, in this issue of New Phytologist, Polturak et al. (pp. 269–283) resolve a longstanding puzzle of the pathway: the formation of l-DOPA, the last of the key enzymatic steps to be elucidated. Moreover, as many plants are likely to be deficient in l-DOPA, a major block to the molecular engineering of the pathway has been overcome. The authors dramatically demonstrate this with betalain production in several species of the anthocyanin family Solanaceae. These advances broaden the scope of the questions that can be answered about betalain production and function and open up the biotechnological possibilities.
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Technological Innovations Give Rise to a New Era of Plant Evolutionary Developmental Biology

Land plants evolved from freshwater algaelike ancestors approximately 480 million years ago. Land plants developed many new morphological features during the evolution including the origin of a multicellular diploid sporophyte, a sporophytic apical meristem that produces complex body architecture, stomata and the production of lateral organs (leaves), vascular tissue, roots, seeds and flowers. Genetic changes drove the development of these morphological features and recent technological innovations in genomics and genetic modification technologies have allowed us to investigate these genetic changes. Here, I describe recent research on several transcription factors that contributed to the morphological evolution of land plants, including the homeodomain proteins KNOX, BELL and WOX, as well as transcription factors of the bHLH, NAC and FLO/LFY families. I also discuss the conservation of plant hormone signalling, which acts to coordinate the multicellular body plan.
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Generating Targeted Gene Knockout Lines in Physcomitrella patens to Study Evolution of Stress-Responsive Mechanisms - Springer

Generating Targeted Gene Knockout Lines in Physcomitrella patens to Study Evolution of Stress-Responsive Mechanisms - Springer | plant cell genetics | Scoop.it
The moss Physcomitrella patens possesses highly efficient homologous recombination allowing targeted gene manipulations and displays many features of the early land plants including high tolerance to abiotic stresses. It is therefore an invaluable model organism for studies of gene functions and comparative studies of evolution of stress responses in plants. Here, we describe a method for generating targeted gene knockout lines in P. patens using a polyethylene glycol-mediated transformation of protoplasts including basic in vitro growth, propagation, and maintenance techniques.
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Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response: Developmental Cell

Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response: Developmental Cell | plant cell genetics | Scoop.it
Highlights

•tasiRNAs have an ancestral role in tuning the auxin response via repressor ARFs
•tasiRNAs promote sensitivity and robustness of the auxin response
•tasiRNAs allow for stochastic cell fate determination and environmental plasticity
•Network properties lent to the auxin response may underlie repeated tasiRNA cooption

Summary

Novel developmental programs often evolve via cooption of existing genetic networks. To understand this process, we explored cooption of the TAS3 tasiRNA pathway in the moss Physcomitrella patens. We find an ancestral function for this repeatedly redeployed pathway in the spatial regulation of a conserved set of Auxin Response Factors. In moss, this results in stochastic patterning of the filamentous protonemal tissue. Through modeling and experimentation, we demonstrate that tasiRNA regulation confers sensitivity and robustness onto the auxin response. Increased auxin sensitivity parallels increased developmental sensitivity to nitrogen, a key environmental signal. We propose that the properties lent to the auxin response network, along with the ability to stochastically modulate development in response to environmental cues, have contributed to repeated cooption of the tasiRNA-ARF module during evolution. The signaling properties of a genetic network, and not just its developmental output, are thus critical to understanding evolution of multicellular forms.
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Frontiers | Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus | Plant Biotechnology

Frontiers | Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus | Plant Biotechnology | plant cell genetics | Scoop.it
Betalains have high nutritional value and bioactivities. Red pulp pitaya (Hylocereus polyrhizus) is the only fruit containing abundant betalains for consumer. However, no information is available about genes involved in betalain biosynthesis in H. polyrhizus. Herein, two cDNA libraries of pitaya pulps with two different coloration stages (white and red pulp stages) of Guanhuahong (H. polyrhizus) were constructed. A total of about 12 Gb raw RNA-Seq data was generated and was de novo assembled into 122,677 transcripts with an average length of 1,183 bp and an N50 value of 2008. Approximately 99.99% of all transcripts were annotated based on seven public databases. A total of 8,871 transcripts were significantly regulated. Thirty-three candidate transcripts related to betalain biosynthesis were obtained from the transcriptome data. Transcripts encoding enzymes involved in betalain biosynthesis were analyzed using RT-qPCR at the whole pulp coloration stages of H. Polyrhizus (7-1) and H. Undatus (132-4). Nine key transcripts of betalain biosynthesis were identified. They were assigned to four kinds of genes in betalain biosynthetic pathway, including tyrosinase, 4, 5-DOPA dioxygenase extradiol, cytochrome P450 and glucosyltransferase. Ultimately, a preliminary betalain biosynthetic pathway for pitaya was proposed based on betalain analyses and gene expression profiles.
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