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ScienceDirect.com - Current Opinion in Plant Biology - Making new molecules – evolution of pathways for novel metabolites in plants

ScienceDirect.com - Current Opinion in Plant Biology - Making new molecules – evolution of pathways for novel metabolites in plants | plant cell genetics | Scoop.it

Plants have adapted to their environments by diversifying in various ways. This diversification is reflected at the phytochemical level in their production of numerous specialized secondary metabolites that provide protection against biotic and abiotic stresses. Plant speciation is therefore intimately linked to metabolic diversification, yet we do not currently have a deep understanding of how new metabolic pathways evolve. Recent evidence indicates that genes for individual secondary metabolic pathways can be either distributed throughout the genome or clustered, but the relative frequencies of these two pathway organizations remain to be established. While it is possible that clustering is a feature of pathways that have evolved in recent evolutionary time, the answer to this and how dispersed and clustered pathways may be related remain to be addressed. Recent advances enabled by genomics and systems biology are beginning to yield the first insights into network evolution in plant metabolism. This review focuses on recent progress in understanding the evolution of clustered and dispersed pathways for new secondary metabolites in plants

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Green infrastructure and ecosystem services – is the devil in the detail?

Green infrastructure and ecosystem services – is the devil in the detail? | plant cell genetics | Scoop.it
Background Green infrastructure is a strategic network of green spaces designed to deliver ecosystem services to human communities. Green infrastructure is a convenient concept for urban policy makers, but the term is used too generically and with limited understanding of the relative values or benefits of different types of green space and how these complement one another. At a finer scale/more practical level, little consideration is given to the composition of the plant communities, yet this is what ultimately defines the extent of service provision. This paper calls for greater attention to be paid to urban plantings with respect to ecosystem service delivery and for plant science to engage more fully in identifying those plants that promote various services.

Scope Many urban plantings are designed based on aesthetics alone, with limited thought on how plant choice/composition provides other ecosystem services. Research is beginning to demonstrate, however, that landscape plants provide a range of important services, such as helping mitigate floods and alleviating heat islands, but that not all species are equally effective. The paper reviews a number of important services and demonstrates how genotype choice radically affects service delivery.

Conclusions Although research is in its infancy, data are being generated that relate plant traits to specific services, thereby helping identify genotypes that optimize service delivery. The urban environment, however, will become exceedingly bland if future planting is simply restricted to monocultures of a few ‘functional’ genotypes. Therefore, further information is required on how to design plant communities where the plants identified (1) provide more than a single benefit (multifunctionality), (B) complement each other in maximizing the range of benefits that can be delivered in one location, and (3) continue to maintain public acceptance through diversity. The identification/development of functional landscape plants is an exciting and potentially high-impact arena for plant science.
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Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection

Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection | plant cell genetics | Scoop.it
Aggressive fungal pathogens such as Botrytis and Verticillium spp. cause severe crop losses worldwide. We recently discovered that Botrytis cinerea delivers small RNAs (Bc–sRNAs) into plant cells to silence host immunity genes. Such sRNA effectors are mostly produced by Botrytis cinerea Dicer-like protein 1 (Bc-DCL1) and Bc-DCL2. Here we show that expressing sRNAs that target Bc-DCL1 and Bc-DCL2 in Arabidopsis and tomato silences Bc-DCL genes and attenuates fungal pathogenicity and growth, exemplifying bidirectional cross-kingdom RNAi and sRNA trafficking between plants and fungi. This strategy can be adapted to simultaneously control multiple fungal diseases. We also show that Botrytis can take up external sRNAs and double-stranded RNAs (dsRNAs). Applying sRNAs or dsRNAs that target Botrytis DCL1 and DCL2 genes on the surface of fruits, vegetables and flowers significantly inhibits grey mould disease. Such pathogen gene-targeting RNAs represent a new generation of environmentally friendly fungicides.

Via Giannis Stringlis, Jennifer Mach, Loïc Lepiniec
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The plant engineer

The plant engineer | plant cell genetics | Scoop.it
As a child, Dan Voytas developed a green thumb and business savvy running his own seedling business. Now, marrying his academic research with a company, he's poised to reshape 21st century agriculture. Over the past 20 years, he has pioneered new ways of precisely editing a crop's DNA to give it new traits or delete undesirable ones. It's an approach that is potentially more powerful than the traditional way of making genetically modified (GM) crops, and because it leaves no foreign DNA behind, it could free these products from the stigma and regulatory burden of being labeled as GM organisms. But to get to this point, he has had to overcome recalcitrant technologies, navigate intellectual property fights, and endure commercial failures.

Via Christophe Jacquet
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Editing EU legislation to fit plant genome editing

Editing EU legislation to fit plant genome editing | plant cell genetics | Scoop.it
n light of the ongoing discussion in the EU whether new plant varieties generated by genome editing are genetically modified organisms (GMOs) or not, we propose a novel approach for regulating plant breeding in general. Our proposal involves a flexible and scalable system that is capable of adapting to the rapid evolution of new technologies such as genome editing. It proposes an operational method that accounts for traditional and novel technologies, and a dynamically scalable risk assessment, which focuses on the phenotype of a novel breed instead of the method used to generate it. This approach would also resolve various dichotomies in the current debate, namely declaring new genome editing methods as highly efficient, while ignoring the impact of yet unknown risks, and proposing exemptions from regulation on the basis of the type of DNA created, whereas an older technology with fully characterized risks would still carry a heavy regulatory burden. Our proposal also takes into account that any new risk paradigm must be understood and accepted by the public, suggesting a greater role for farmers in ensuring the safe use of new breeding technologies.
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Expression of an insecticidal fern protein in cotton protects against whitefly : Nature Biotechnology : Nature Research

Expression of an insecticidal fern protein in cotton protects against whitefly : Nature Biotechnology : Nature Research | plant cell genetics | Scoop.it
Whitefly (Bemisia tabaci) damages field crops by sucking sap and transmitting viral diseases. None of the insecticidal proteins used in genetically modified (GM) crop plants to date are effective against whitefly. We report the identification of a protein (Tma12) from an edible fern, Tectaria macrodonta (Fee) C. Chr., that is insecticidal to whitefly (median lethal concentration = 1.49 μg/ml in in vitro feeding assays) and interferes with its life cycle at sublethal doses. Transgenic cotton lines that express Tma12 at ~0.01% of total soluble leaf protein were resistant to whitefly infestation in contained field trials, with no detectable yield penalty. The transgenic cotton lines were also protected from whitefly-borne cotton leaf curl viral disease. Rats fed Tma12 showed no detectable histological or biochemical changes, and this, together with the predicted absence of allergenic domains in Tma12, indicates that Tma12 might be well suited for deployment in GM crops to control whitefly and the viruses it carries.
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Frontiers: Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens (2014)

Frontiers: Historical account on gaining insights on the mechanism of crown gall tumorigenesis induced by Agrobacterium tumefaciens (2014) | plant cell genetics | Scoop.it

The plant tumor disease known as crown gall was not called by that name until more recent times. Galls on plants were described by Malpighi (1679) who believed that these extraordinary growth are spontaneously produced. Agrobacterium was first isolated from tumors in 1897 by Fridiano Cavara in Napoli, Italy. After this bacterium was recognized to be the cause of crown gall disease, questions were raised on the mechanism by which it caused tumors on a variety of plants. Numerous very detailed studies led to the identification of Agrobacterium tumefaciens as the causal bacterium that cleverly transferred a genetic principle to plant host cells and integrated it into their chromosomes. Such studies have led to a variety of sophisticated mechanisms used by this organism to aid in its survival against competing microorganisms. Knowledge gained from these fundamental discoveries has opened many avenues for researchers to examine their primary organisms of study for similar mechanisms of pathogenesis in both plants and animals. These discoveries also advanced the genetic engineering of domesticated plants for improved food and fiber.


Via Kamoun Lab @ TSL
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Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco (Nicotiana tabacum) Tnt1 retrotransposon - Vives - 2016 - New Phytologist - Wiley Online Library

Highly efficient gene tagging in the bryophyte Physcomitrella patens using the tobacco (Nicotiana tabacum) Tnt1 retrotransposon - Vives - 2016 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Because of its highly efficient homologous recombination, the moss Physcomitrella patens is a model organism particularly suited for reverse genetics, but this inherent characteristic limits forward genetic approaches.
Here, we show that the tobacco (Nicotiana tabacum) retrotransposon Tnt1 efficiently transposes in P. patens, being the first retrotransposon from a vascular plant reported to transpose in a bryophyte. Tnt1 has a remarkable preference for insertion into genic regions, which makes it particularly suited for gene mutation.
In order to stabilize Tnt1 insertions and make it easier to select for insertional mutants, we have developed a two-component system where a mini-Tnt1 with a retrotransposition selectable marker can only transpose when Tnt1 proteins are co-expressed from a separate expression unit.
We present a new tool with which to produce insertional mutants in P. patens in a rapid and straightforward manner that complements the existing molecular and genetic toolkit for this model species.
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Survey and Risk Assessment of Apis mellifera (Hymenoptera: Apidae) Exposure to Neonicotinoid Pesticides in Urban, Rural, and Agricultural Settings

Survey and Risk Assessment of Apis mellifera (Hymenoptera: Apidae) Exposure to Neonicotinoid Pesticides in Urban, Rural, and Agricultural Settings | plant cell genetics | Scoop.it
A comparative assessment of apiaries in urban, rural, and agricultural areas was undertaken in 2013 and 2014 to examine potential honey bee colony exposure to neonicotinoid insecticides from pollen foraging. Apiaries ranged in size from one to hundreds of honey bee colonies, and included those operated by commercial, sideline (semicommercial), and hobbyist beekeepers. Residues in and on wax and beebread (stored pollen in the hive) were evaluated for the nitro-substituted neonicotinoid insecticides imidacloprid and its olefin metabolite and the active ingredients clothianidin, thiamethoxam, and dinotefuran. Beebread and comb wax collected from hives in agricultural landscapes were more likely to have detectable residues of thiamethoxam and clothianidin than that collected from hives in rural or urban areas (∼50% of samples vs. <10%). The maximum neonicotinoid residue detected in either wax or beebread was 3.9 ppb imidacloprid. A probabilistic risk assessment was conducted on the residues recovered from beebread in apiaries located in commercial, urban, and rural landscapes. The calculated risk quotient based on a dietary no observable adverse effect concentration (NOAEC) suggested low potential for negative effects on bee behavior or colony health.
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Towards a multidimensional root trait framework: a tree root review - Weemstra - 2016 - New Phytologist - Wiley Online Library

Towards a multidimensional root trait framework: a tree root review - Weemstra - 2016 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
The search for a root economics spectrum (RES) has been sparked by recent interest in trait-based plant ecology. By analogy with the one-dimensional leaf economics spectrum (LES), fine-root traits are hypothesised to match leaf traits which are coordinated along one axis from resource acquisitive to conservative traits. However, our literature review and meta-level analysis reveal no consistent evidence of an RES mirroring an LES. Instead the RES appears to be multidimensional. We discuss three fundamental differences contributing to the discrepancy between these spectra. First, root traits are simultaneously constrained by various environmental drivers not necessarily related to resource uptake. Second, above- and belowground traits cannot be considered analogues, because they function differently and might not be related to resource uptake in a similar manner. Third, mycorrhizal interactions may offset selection for an RES. Understanding and explaining the belowground mechanisms and trade-offs that drive variation in root traits, resource acquisition and plant performance across species, thus requires a fundamentally different approach than applied aboveground. We therefore call for studies that can functionally incorporate the root traits involved in resource uptake, the complex soil environment and the various soil resource uptake mechanisms – particularly the mycorrhizal pathway – in a multidimensional root trait framework.
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Biofortified β-carotene rice improves vitamin A intake and reduces the prevalence of inadequacy among women and young children in a simulated analysis in Bangladesh, Indonesia, and the Philippines ...

Vitamin A deficiency continues to be a major public health problem affecting developing countries where people eat mostly rice as a staple food. In Asia, rice provides up to 80% of the total daily energy intake. 


We used existing data sets from Bangladesh, Indonesia, and the Philippines, where dietary intakes have been quantified at the individual level to 1) determine the rice and vitamin A intake in nonpregnant, nonlactating women of reproductive age and in nonbreastfed children 1-3 y old and 2) simulate the amount of change that could be achieved in the prevalence of inadequate intake of vitamin A if rice biofortified with β-carotene were consumed instead of the rice consumed at present. 


We considered a range of 4-20 parts per million (ppm) of β-carotene content and 10-70% substitution levels for the biofortified rice… the substitution of biofortified rice for white rice in the optimistic scenario (20 ppm and 70% substitution) decreased the prevalence of vitamin A inadequacy from baseline 78% in women and 71% in children in Bangladesh. In Indonesia and the Philippines, the prevalence of inadequacy fell by 55-60% in women and dropped by nearly 30% in children from baseline. 


The results of the simulation analysis were striking in that even low substitution levels and modest increases in the β-carotene of rice produced a meaningful decrease in the prevalence of inadequate intake of vitamin A. Increasing the substitution levels had a greater impact than increasing the β-carotene content by >12 ppm… 


In β-carotene rice, commonly known as golden rice because of its yellow hue, 2 genes naturally involved in carotene biosynthesis were inserted into the rice genome by using transgenics. This insertion restarts the carotenoid biosynthetic pathway that is normally inactive, leading to the production of β-carotene in the grain. The current amount of β-carotene in biofortified b-carotene rice is 35 parts per million (ppm), with an estimated bioconversion rate of 3.8:1 from β-carotene to vitamin A… 


Biofortified β-carotene rice can substantially increase vitamin A intake and consequently reduce the prevalence of inadequacy of this vitamin. Increasing vitamin A intake through biofortified rice at 8-12 ppm of β-carotene, in combination with programs that increase adoption of biofortified rice in a population, can be an effective method at reducing population prevalence of inadequate vitamin A intakes... However... increasing the β-carotene beyond 12 ppm has little added benefit; rather, public health programs will have the most impact by increasing the substitution of white rice by biofortified β-carotene rice. 


http://ajcn.nutrition.org/content/early/2016/08/10/ajcn.115.129270.abstract



Via Alexander J. Stein
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How to make a red flower: the combinatorial effect of pigments

How to make a red flower: the combinatorial effect of pigments | plant cell genetics | Scoop.it
Red flowers have evolved repeatedly across angiosperms and are frequently examined in an ecological context. However, less is known about the biochemical basis of red colouration in different taxa. In this study, we examine the spectral properties, anthocyanin composition and carotenoid expression of red flowers in the tomato family, Solanaceae, which have evolved independently multiple times across the group. Our study demonstrates that Solanaceae typically make red flowers either by the sole production of red anthocyanins or, more commonly, by the dual production of purple or blue anthocyanins and orange carotenoids. In using carotenoids to modify the effect of purple and/or blue anthocyanins, these Solanaceae species have converged on the same floral hue as those solely producing red anthocyanins, even when considering the visual system of pollinators. The use of blue anthocyanins in red flowers appears to differ from other groups, and suggests that the genetic changes underlying evolutionary shifts to red flowers may not be as predictable as previously suggested.
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Plant acoustics: in the search of a sound mechanism for sound signaling in plants

Plant acoustics: in the search of a sound mechanism for sound signaling in plants | plant cell genetics | Scoop.it
Being sessile, plants continuously deal with their dynamic and complex surroundings, identifying important cues and reacting with appropriate responses. Consequently, the sensitivity of plants has evolved to perceive a myriad of external stimuli, which ultimately ensures their successful survival. Research over past centuries has established that plants respond to environmental factors such as light, temperature, moisture, and mechanical perturbations (e.g. wind, rain, touch, etc.) by suitably modulating their growth and development. However, sound vibrations (SVs) as a stimulus have only started receiving attention relatively recently. SVs have been shown to increase the yields of several crops and strengthen plant immunity against pathogens. These vibrations can also prime the plants so as to make them more tolerant to impending drought. Plants can recognize the chewing sounds of insect larvae and the buzz of a pollinating bee, and respond accordingly. It is thus plausible that SVs may serve as a long-range stimulus that evokes ecologically relevant signaling mechanisms in plants. Studies have suggested that SVs increase the transcription of certain genes, soluble protein content, and support enhanced growth and development in plants. At the cellular level, SVs can change the secondary structure of plasma membrane proteins, affect microfilament rearrangements, produce Ca2+ signatures, cause increases in protein kinases, protective enzymes, peroxidases, antioxidant enzymes, amylase, H+-ATPase / K+ channel activities, and enhance levels of polyamines, soluble sugars and auxin. In this paper, we propose a signaling model to account for the molecular episodes that SVs induce within the cell, and in so doing we uncover a number of interesting questions that need to be addressed by future research in plant acoustics.
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Basidiomycete yeasts in the cortex of ascomycete macrolichens

Basidiomycete yeasts in the cortex of ascomycete macrolichens | plant cell genetics | Scoop.it
For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.
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Mimicry in plants

Mimicry in plants | plant cell genetics | Scoop.it


Plant mimicry is used for two major purposes that benefit the mimic.

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When is apparent mimicry by plants probably not really mimicry at all? An important caveat when interpreting potential mimicry is that the plant might benefit from a general resemblance to an archetypal ‘model’ rather than to a specific one, because of a pre-existing perceptual or cognitive bias in the selective agent. For example, it is thought that insects are attracted to the modified leaves (the pitchers) of some carnivorous pitcher plants because of a cognitive positive bias for flower-like structures.

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The next green movement: Plant biology for the environment and sustainability

The next green movement: Plant biology for the environment and sustainability | plant cell genetics | Scoop.it
From domestication and breeding to the genetic engineering of crops, plants provide food, fuel, fibers, and feedstocks for our civilization. New research and discoveries aim to reduce the inputs needed to grow crops and to develop plants for environmental and sustainability applications. Faced with population growth and changing climate, the next wave of innovation in plant biology integrates technologies and approaches that span from molecular to ecosystem scales. Recent efforts to engineer plants for better nitrogen and phosphorus use, enhanced carbon fixation, and environmental remediation and to understand plant-microbiome interactions showcase exciting future directions for translational plant biology. These advances promise new strategies for the reduction of inputs to limit environmental impacts and improve agricultural sustainability.

Via Christophe Jacquet
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Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling

Identification of line-specific strategies for improving carotenoid production in synthetic maize through data-driven mathematical modeling | plant cell genetics | Scoop.it
Plant synthetic biology is still in its infancy. However, synthetic biology approaches have been used to manipulate and improve the nutritional and health value of staple food crops such as rice, potato and maize. With current technologies, production yields of the synthetic nutrients are a result of trial and error, and systematic rational strategies to optimize those yields are still lacking. Here, we present a workflow that combines gene expression and quantitative metabolomics with mathematical modeling to identify strategies for increasing production yields of nutritionally important carotenoids in the seed endosperm synthesized through alternative biosynthetic pathways in synthetic lines of white maize, which is normally devoid of carotenoids. Quantitative metabolomics and gene expression data are used to create and fit parameters of mathematical models that are specific to four independent maize lines. Sensitivity analysis and simulation of each model is used to predict which gene activities should be further engineered in order to increase production yields for carotenoid accumulation in each line. Some of these predictions (e.g. increasing Zmlycb/Gllycb will increase accumulated β-carotenes) are valid across the four maize lines and consistent with experimental observations in other systems. Other predictions are line specific. The workflow is adaptable to any other biological system for which appropriate quantitative information is available. Furthermore, we validate some of the predictions using experimental data from additional synthetic maize lines for which no models were developed.
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Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens.

Powerful genome editing technologies are needed for efficient gene function analysis. The CRISPR-Cas9 system has been adapted as an efficient gene knock-out-technology in a variety of species. However, in a number of situations knocking out or modifying a single gene is not sufficient, this is particularly true for genes belonging to a common family or for genes showing redundant functions. Like many plants the model organism Physcomitrella patens has experienced multiple events of polyploidization during evolution that resulted in a number of families of duplicated genes. Here, we report a robust CRISPR-Cas9 system, based on the co-delivery of a CAS9 expressing cassette, multiple sgRNA vectors and a cassette for transient transformation selection for gene knock-out in multiple gene families. We demonstrate that CRISPR-Cas9 mediated targeting of five different genes allows the selection of a quintuple mutant and all possible sub-combinations of mutants in one experiment with no mutations detected in potential off target sequences. Furthermore, we confirmed the observation that the presence of repeats in the vicinity of the cutting region favors deletion due to alternative End Joining pathway for which induced frameshift mutations can be potentially predicted. Because the number of multiple gene families in Physcomitrella is substantial, this tool opens new perspectives to study the role of expanded gene families in the colonization of land by plants.

Via Pierre-Marc Delaux
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An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize

An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize | plant cell genetics | Scoop.it
CRISPR/Cas9 is a powerful genome editing tool in many organisms, including a number of monocots and dicots. Although the design and application of CRISPR/Cas9 is simpler compared to other nuclease-based genome editing tools, optimization requires the consideration of the DNA delivery and tissue regeneration methods for a particular species to achieve accuracy and efficiency. Here, we describe a public sector system, ISU Maize CRISPR, utilizing Agrobacterium-delivered CRISPR/Cas9 for high-frequency targeted mutagenesis in maize. This system consists of an Escherichia coli cloning vector and an Agrobacterium binary vector. It can be used to clone up to four guide RNAs for single or multiplex gene targeting. We evaluated this system for its mutagenesis frequency and heritability using four maize genes in two duplicated pairs: Argonaute 18 (ZmAgo18a and ZmAgo18b) and dihydroflavonol 4-reductase or anthocyaninless genes (a1 and a4). T0 transgenic events carrying mono- or diallelic mutations of one locus and various combinations of allelic mutations of two loci occurred at rates over 70% mutants per transgenic events in both Hi-II and B104 genotypes. Through genetic segregation, null segregants carrying only the desired mutant alleles without the CRISPR transgene could be generated in T1 progeny. Inheritance of an active CRISPR/Cas9 transgene leads to additional target-specific mutations in subsequent generations. Duplex infection of immature embryos by mixing two individual Agrobacterium strains harbouring different Cas9/gRNA modules can be performed for improved cost efficiency. Together, the findings demonstrate that the ISU Maize CRISPR platform is an effective and robust tool to targeted mutagenesis in maize.
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Growing monstrous organisms: the construction of anti-GMO visual rhetoric through digital media

Growing monstrous organisms: the construction of anti-GMO visual rhetoric through digital media | plant cell genetics | Scoop.it
This paper explores the international controversy over genetically modified organisms (GMOs). We argue that the uncommonly high levels of opposition to genetically modified food in both the United States and in Europe can be attributed to the overwhelming success of the online visual campaign against GMOs. By exploiting the unique characteristics of the internet to create memetic images that can travel freely across linguistic and cultural borders, opponents of the technology have been able to refute rationalist claims about the safety of GMOs. In response to the single coherent narrative of scientific certainty, a diffuse set of challenges emerges. The risk of genetic engineering holds within it the potential for catastrophe, leaving the industries that produce and manufacture the technology in a perpetual state of crisis. Instead of a unified narrative of scientific certainty, each challenge presents a multiplicity of diffuse narratives that unsettle the public’s understanding of the risk presented by GMOs. We aim to augment traditional understandings of the way that publics may interact with the “public screen” by explicating one way in which dominance of the visual in mediated political discourse may privilege non-rational political decision making.
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Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Reconciling the evolutionary origin of bread wheat (Triticum aestivum) | plant cell genetics | Scoop.it
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.

Via Pierre-Marc Delaux, Loïc Lepiniec
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Italian horticultural and culinary records of summer squash (Cucurbita pepo, Cucurbitaceae) and emergence of the zucchini in 19th-century Milan

Italian horticultural and culinary records of summer squash (Cucurbita pepo, Cucurbitaceae) and emergence of the zucchini in 19th-century Milan | plant cell genetics | Scoop.it
The results indicate that Cucurbita fruits, both young and mature, entered Italian kitchens by the mid-16th century. A half-century later, round and elongate young fruits of C. pepo were addressed as separate cookery items and the latter had largely replaced the centuries-old culinary use of young, elongate bottle gourds, Lagenaria siceraria. Allusion to a particular, extant cultivar of the longest fruited C. pepo, the Cocozelle Group, dates to 1811 and derives from the environs of Naples. The Italian diminutive word zucchini arose by the beginning of the 19th century in Tuscany and referred to small, mature, desiccated bottle gourds used as containers to store tobacco. By the 1840s, the Tuscan word zucchini was appropriated to young, primarily elongate fruits of C. pepo. The Zucchini Group traces its origins to the environs of Milan, perhaps as early as 1850. The word zucchini and the horticultural product zucchini arose contemporaneously but independently. The results confirm that the Zucchini Group is the youngest of the four cultivar-groups of C. pepo subsp. pepo but it emerged approximately a half-century earlier than previously known.
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Science: Can Apulia's olive trees be saved? (2016)

Science: Can Apulia's olive trees be saved? (2016) | plant cell genetics | Scoop.it

On 21 October 2013, the Italian phytosanitary service notified the European Commission (EC) that the plant pathogen Xylella fastidiosa had been detected in olive trees near Gallipoli, a tourist destination in Italy's southern region of Apulia (1). This xylem-limited bacterium is spread by insect vectors and causes disease in crops such as grapevines, citrus, coffee, and almond; various ornamentals; and trees such as oaks, elms, and sycamores. Because of the risks of X. fastidiosa being introduced, established, and spread throughout Europe, this species is a regulated quarantine pest. Yet, X. fastidiosa has been left unchecked and has marched northward, leaving destruction in its wake (see the photo) (2). The establishment of X. fastidiosa in Italy has been an agricultural, environmental, political, and cultural disaster.

 

The threat of X. fastidiosa to European and Mediterranean agriculture, forests, and ecosystems goes beyond specific crops such as grapevines or citrus. The current host range of this bacterium includes more than 300 plant species (3). Most of these species support some degree of pathogen multiplication without expressing symptoms. Susceptible hosts infected with X. fastidiosa often show disease symptoms only after months or years, although epidemics can spread fast and be devastating.

 

A phylogenetic study has shown that the genotype in Italy was likely introduced via contaminated plant material from Costa Rica (3). Several X. fastidiosa-infected coffee plants from Costa Rica have been intercepted at European ports since 2014, supporting this hypothesis (4). As a response, the EC in February 2014 approved European Union (EU) emergency measures aimed at preventing the introduction and spread of X. fastidiosa. Since May 2015, the import of coffee plants from Costa Rica and Honduras into the EU has been forbidden. Limiting the introduction of insect vectors is considered an easier task, but this is not possible for X. fastidiosa because any xylem-sap-sucking insect species can be a potential vector. Europe has few sharpshooter leafhopper species, the most important group of vectors in the Americas. However, various endemic spittlebug species (froghoppers) are also potential vectors of X. fastidiosa (3).

 

Trade is an important pathway in the introduction of plant pests and pathogens (5), and X. fastidiosa-infected plant material has likely been introduced via European ports on a regular basis. Given that biological and environmental conditions in Europe support X. fastidiosainfection, the question arises why the pathogen has not been reported previously. One possible explanation is that limited surveillance efforts missed previous introductions. Monitoring was one component of the EU emergency measures. After the French authorities started a systematic monitoring program for X. fastidiosa in 2014, they found 250 distinct infected areas in Corsica and several in the French Riviera. However, no disease epidemic has yet been noted in France, and the genotype of X. fastidiosa differs from that found in Italy.


Via Kamoun Lab @ TSL, Luigi Guarino
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The sticky materiality of neo-liberal neonatures: GMOs and the agrarian question - Carroll (2016) - New Political Economy

The sticky materiality of neo-liberal neonatures: GMOs and the agrarian question - Carroll (2016) - New Political Economy | plant cell genetics | Scoop.it
This article uses Marxist theories of agrarian capitalism to explore the political economy of genetically modified organisms (GMO) agriculture. It argues that the successes and failures of GMO agriculture have been partly circumscribed by the structural requirements of the capitalist system, as well as by the materiality of GMO crops themselves. Successful innovations have been able to mitigate the material barriers to accumulation found in agricultural production, and thus appeal directly to farmers as comparatively profitable capital inputs. In this way, they cohere with David Goodman’s notion of appropriationism, where manufactured capital inputs (such as pesticides, machinery and fertilisers) replace ‘natural’ inputs (such as manure or draft animals), reducing labour time and biological contingency, and thus creating a competitive advantage for those farmers who adopt the new technology (at least temporarily). Conversely, innovations that are geared at consumers rather than farmers have largely failed due to their status as value-added products (whose value is subjective and market-driven) rather than capital goods. The article uses contrasting case studies of herbicide-tolerant soybeans, beta-keratin[sic!]-enhanced rice and slow-ripening tomatoes to demonstrate how and why the structural imperatives of global capitalism have enabled the success of some, and the failure of other innovations. 

The late-twentieth-century rise of biotechnology – and GMOs (genetically modified organisms) in particular – garnered tremendous popular, activist, scholarly and corporate attention. Evaluations of GMO technologies ranged from apocalyptic to utopian, but few doubted that GMOs would significantly transform our food system… However, two decades since the commercial release of the first GMO food… GMOs have been neither a global panacea nor a pandemic. Their modest, if not underwhelming, performance may be what needs accounting. This is not to say there have been no successes, particularly early on in the late 1990s. Two transgenic events – tolerance to herbicides and resistance to pests – have been remarkably implemented, capturing substantial control over some of the world’s most significant crops… From the perspective of… corporations… these innovations have been cash cows, enabling near-monopoly control over not only transgenic seed sales, but also often other agricultural inputs, such as herbicides. But these innovations – among them Roundup Ready soybeans and canola and Bt corn and cotton – are virtually the only commercially successful GMOs. Moreover, all of these innovations were already commercially available in the late 1990s. In the meantime, no further innovations of significance have emerged, while many have faltered, such as Bt potatoes, Roundup Ready wheat and perhaps most notably, beta-keratin[sic!]-enhanced ‘Golden Rice’… 

No single factor accounts for either the early success or subsequent setbacks of the GMO food economy. To understand the contemporary context, we have to examine its juridico-political, economic, biophysical and cultural dimensions. However, this article focuses on the material, in particular the economic, considering from a Marxist perspective how the logic of capital has both enabled and constrained the development of the GMO food economy, and how the biophysicality of GMO crops has been manifested as both an opportunity and a challenge to capital. It locates GMOs within the historical context of agrarian capitalism, linking with earlier debates over the problems that agriculture poses to capital as a site of profitable accumulation, showing how both the successes and failures of GMO agriculture can be understood in the wider context of agrarian capitalism, and the problems (and opportunities) that agriculture’s unique spatial, temporal and biophysical demands pose to capital. 

I argue that technologies that can temporarily overcome or reduce these barriers to accumulation hold the potential to be highly profitable and thus successful, while those that do not directly alter the conditions of production will likely be ignored by industry. This dialectic can, therefore, help explain both the successes and failures of GMO agriculture to date, and demonstrate the extent to which corporate profitability rather than social utility has driven GMO innovation thus far. The trajectory of GMO technological innovation has been heavily structured by the logic of capital, a condition that accounts for the lack of success in innovations not targeted at reducing the temporal, spatial and biophysical constraints to capital within the production process. For example, herbicide tolerance and pest resistance are both innovations that affect production by changing the ways farmers address the problems posed by weeds and pests. Innovations geared at consumers (such as nutrient enhancement or slower ripening), which yield value-added end products but make no difference in the actual production process, have largely failed. 

The article begins with an historical overview of the agrarian question, discussing how Marxists have dealt with the problems agriculture poses to capital accumulation and how capital has sought to overcome these problems. Section II theorises the conditions under which GMO agriculture has been successful, considering how GMOs fit a wider tendency within agricultural capitalism to mitigate spatial, temporal and biophysical barriers to the reduction of labour and production time (and thus to added surplus value) through capital inputs, or what Goodman et al. (1987) have termed ‘appropriationism’. However, at stake in GMO agriculture is not simply the way biophysical inputs are replaced with synthetic industrial inputs, but how property rights are managed throughout the commodity chain with patents and technology use agreements (TUAs), ensuring the extraction of rents for patent holders, a logic of accumulation that Pechlaner (2010) has termed ‘expropriationism’. Through both of these logics, capital is able to subsume elements of the production process, extracting greater surplus value than under an unsubsumed system of production… My analysis builds on these earlier accounts by arguing and demonstrating that the logic of capital works to both enable and constrain the trajectory of GMO development. Appropriationism and expropriationism are thus significant in understanding not only how and why certain innovations have met with success, but also why so many others have failed. This demonstrates that although capitalism’s competitive logic may promote innovation, in biotechnology and elsewhere, it is only certain innovations – and by no means the most socially useful – that can ever be profitably pursued… 

Section III turns to a theorisation of the barriers to accumulation posed by both the logic of capital and the materiality of GMOs. It considers how consumption-oriented innovations have failed to provide an impetus for capital to invest and have thus been ignored, despite great potential benefits to the public. Just as the logic of capital has enabled the development of certain innovations, it has hindered the development of others. The section also considers a separate set of constraints: the ecological and biophysical barriers to accumulation that are in part a consequence of the inherent dynamism and complexity of the life sciences… Ultimately, the argument advanced here is not meant to dismiss GMOs as a failed technology. Their failures are overdetermined by the structural contours of global capitalism, among other factors. Today’s GMO food economy emerged in the context of the particular political economic configuration of neo-liberal globalisation, and its real-world manifestations cannot be detached from this context. However, a different political economic context, driven by motives other than profit and capital accumulation, would enable a different, and perhaps more hopeful, GMO food economy. The story of GMO agriculture is today only a recent iteration of the story of capitalist agriculture. The future of GMO agriculture holds the potential for a wholly different narrative… 

The story of GMOs – their successes and failures – is only the latest chapter in the story of agricultural capitalism. The path of their development has been significantly conditioned by the materiality of agricultural capitalism. GMOs have been successful because they help overcome barriers to accumulation inherent to the biophysicality of agriculture. In this way, their commercial success has paralleled earlier appropriationist technologies, including machinery and chemical inputs. As on-farm labour and production are replaced with off-farm, industrial labour and production, the barriers to accumulation posed by agriculture’s inherent materiality are diminished. However, GMOs, like hybrid seeds before them, differ from other appropriationist technologies. Their liveliness and in particular their reproducibility present both new challenges and new opportunities. There are challenges of maintaining control, not just of the reproductive capacities of the seeds, but of how ownership rights can be preserved for patent holders beyond the first generation of the plants. This challenge has necessitated a stringent IPR regime, which has substantially empowered biotechnology firms, and been termed expropriationism. 

This paper has demonstrated how the dual accumulation strategy of appropriationism and expropriationism has made certain GMOs profitable for capital and inescapable for (most) farmers. The converse of this process has been the failure of numerous innovations that do not cohere with the industrial logic inherent to successful GMOs. Biotechnology multinationals have eschewed innovations that address consumer health, nutrition or aesthetic considerations because of the uncertainty of any success in these innovations. Without any structural impetus for farmers to adopt transgenic crops that do not inherently improve the production process, there is no guarantee that such crops would even be planted, let alone sold for a premium in grocery stores. In this way, the logic of agricultural capitalism has significantly narrowed the spectrum of GMO development. 

However, if the current situation is the result of a particular set of material constraints inherent to the logic of capital, this does not render it inevitable. A categorical rejection of GMOs without consideration of the contingency of their location within capitalist political economies only serves to further entrench and naturalise the hegemony of capitalism. A critical reformulation of the global food economy must start with a decoupling of the biotech baby from the capitalist bathwater. 



Via Alexander J. Stein
Jean-Pierre Zryd's insight:
Excellent analysis of the complicity between capitalism and the anti - biotech crowd in the  (almost) killing of #GMO
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Alexander J. Stein's curator insight, August 6, 9:11 AM
“From the perspective of… corporations… these innovations have been cash cows, enabling near-monopoly control over not only transgenic seed sales, but also often other agricultural inputs, such as herbicides.” >> It’s only a monopoly if a buyer has no other option but to buy from one supplier. However, there is more than just one seed provider (and depending on the country, the global companies can be in competition with local providers, too), and farmers have the option to choose not only between different GM seeds but also to buy non-GM, for which there are even more companies and providers. Moreover, even if GM seeds from one company should dominate a market, it’s only a temporary phenomenon – which only lasts until the patent on the seed technology expires (as it in 2015 e.g. for Monsanto’s first-generation Roundup Ready soybean). Regarding agricultural inputs (herbicides), the patent on Roundup already expired in 2000… 

“corporate profitability rather than social utility has driven GMO innovation thus far” >> The reason that so far only crops that “directly alter the conditions of production” have been successful is to some extent also because social forces (activists) have blocked, hampered and opposed progress of social-utility GMOs… 

“at stake in GMO agriculture is… how property rights are managed… ensuring the extraction of rents for patent holders… termed ‘expropriationism’… Capital is able to subsume elements of the production process, extracting greater surplus value than under an unsubsumed system of production…” >> Studies showed that the gains of cultivating GM crops are shared (even if to varying degrees) by patent holders, farmers and consumers, with everybody being better off… 

“although capitalism’s competitive logic may promote innovation, in biotechnology and elsewhere, it is only certain innovations – and by no means the most socially useful – that can ever be profitably pursued” >> There’s also the (albeit smaller) public and philanthropic sectors that promote (socially useful) innovations – which (as in the case of Golden Rice) are not hampered by capital but amongst others by social forces (such as activists, incl. anti-capitalists) 

“the dual accumulation strategy of appropriationism and expropriationism has made certain GMOs profitable for capital and inescapable for (most) farmers” >> But it made GMOs not only profitable for capital but also for (most) farmers… 

“Biotechnology multinationals have eschewed innovations that address consumer health… because of the uncertainty of any success in these innovations. Without any structural impetus for farmers to adopt transgenic crops that do not inherently improve the production process, there is no guarantee that such crops would even be planted, let alone sold for a premium in grocery stores.” >> This seems far-fetched: Organic farming does not improve the production process (rather the contrary, and it does not even address consumer health etc.) and yet organic food is sold for a premium in grocery stores. Ditto for heirloom varieties or humane eggs… (And some multinationals can make some consumers pay a premium for their products, even if these do not address any issues at all, simply by slapping their logo on it…) The problem here is probably more one of lacking purchasing power (poverty) by those who could benefit from such innovations… 

“A critical reformulation of the global food economy must start with a decoupling of the biotech baby from the capitalist bathwater.” >> Indeed, biotechnology per se is not capitalist and opposing GMOs as such out of related political reasons is misguided and futile.
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Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses

Growing Out of Stress: The Role of Cell- and Organ-scale Growth Control in Plant Water-stress Responses | plant cell genetics | Scoop.it
Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses such as salinity, cold, heat and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes.
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Allowing pseudoscience into EU risk assessment processes is eroding public trust in science experts and in science as a whole: The bigger picture

Unfortunately Europe, in the application of its legislation relating to chemicals, is in danger of falling back into the medieval approach. The most recent example is the advocacy group- [1], media- and NGO- [2] driven move to have glyphosate banned, despite solid evidence and multiple expert assessments [3], [4] and [5] that this herbicide is without risk to consumers and is the herbicide with the least negative environmental and health impact. The “public” is being misled by pseudoscientists to believe that the compound is highly dangerous to humans and the environment, a claim that runs counter to the evidence and to expert (critical) assessment of that evidence. The media are rife with quotes from poorly informed and often scientifically less well-informed politicians and others who had analysed their water, urine, beer, and vegetables and reported trace amounts of glyphosate, four-thousand-fold below potentially harmful levels for humans [6]. Under this onslaught of misinformation, decision-makers may prefer to disregard evidence-based data that contradict a precautionary viewpoint.
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