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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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Copper mediates auxin signalling to control cell differentiation in the copper moss Scopelophila cataractae

Copper mediates auxin signalling to control cell differentiation in the copper moss Scopelophila cataractae | plant cell genetics | Scoop.it
The copper (Cu) moss Scopelophila cataractae (Mitt.) Broth. is often found in Cu-enriched environments, but it cannot flourish under normal conditions in nature. Excess Cu is toxic to almost all plants, and therefore how this moss species thrives in regions with high Cu concentration remains unknown. In this study, we investigated the effect of Cu on gemma germination and protonemal development in S. cataractae. A high concentration of Cu (up to 800 µM) did not affect gemma germination. In the protonemal stage, a low concentration of Cu promoted protonemal gemma formation, which is the main strategy adopted by S. cataractae to expand its habitat to new locations. Cu-rich conditions promoted auxin accumulation and induced differentiation of chloronema into caulonema cells, whereas it repressed protonemal gemma formation. Under low-Cu conditions, auxin treatment mimicked the effects of high-Cu conditions. Furthermore, Cu-induced caulonema differentiation was severely inhibited in the presence of the auxin antagonist α-(phenylethyl-2-one)-indole-3-acetic acid, or the auxin biosynthesis inhibitor l-kynurenine. These results suggest that S. cataractae flourishes in Cu-rich environments via auxin-regulated cell differentiation. The copper moss might have acquired this mechanism during the evolutionary process to benefit from its advantageous Cu-tolerance ability.

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RNAi Screening Identifies the Armadillo Repeat-Containing Kinesins Responsible for Microtubule-Dependent Nuclear Positioning in Physcomitrella patens

RNAi Screening Identifies the Armadillo Repeat-Containing Kinesins Responsible for Microtubule-Dependent Nuclear Positioning in Physcomitrella patens | plant cell genetics | Scoop.it
Proper positioning of the nucleus is critical for the functioning of various cells. Actin and myosin have been shown to be crucial for the localization of the nucleus in plant cells, whereas microtubule (MT)-based mechanisms are commonly utilized in animal and fungal cells. In this study, we combined live cell microscopy with RNA interference (RNAi) screening or drug treatment and showed that MTs and a plant-specific motor protein, armadillo repeat-containing kinesin (kinesin-ARK), are required for nuclear positioning in the moss Physcomitrella patens. In tip-growing protonemal apical cells, the nucleus was translocated to the center of the cell after cell division in an MT-dependent manner. When kinesin-ARKs were knocked down using RNAi, the initial movement of the nucleus towards the center took place normally; however, before reaching the center, the nucleus was moved back to the basal edge of the cell. In intact (control) cells, MT bundles that are associated with kinesin-ARKs were frequently observed around the moving nucleus. In contrast, such MT bundles were not identified after kinesin-ARK down-regulation. An in vitro MT gliding assay showed that kinesin-ARK is a plus-end-directed motor protein. These results indicate that MTs and the MT-based motor drive nuclear migration in the moss cells, thus showing a conservation of the mechanism underlying nuclear localization among plant, animal and fungal cells.
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DEK1; missing piece in puzzle of plant development: Trends in Plant Science

DEK1; missing piece in puzzle of plant development: Trends in Plant Science | plant cell genetics | Scoop.it
Patterning of land plant bodies is determined by positioning of cell walls. A crucial event in land plant evolution was the ability to utilize spatial information to direct cell wall deposition. Recent studies of DEK1 in Physcomitrella patens support a role for DEK1 in position dependent cell wall orientation.
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Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism

Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism | plant cell genetics | Scoop.it
Most cloned and/or characterized plant polyphenol oxidases (PPOs) have catechol oxidase activity (i.e. they oxidize o-diphenols to o-quinones) and are localized or predicted to be localized to plastids. As a class, they have broad substrate specificity and are associated with browning of produce and other plant materials. Because PPOs are often induced by wounding or pathogen attack, they are most generally believed to play important roles in plant defense responses. However, a few well-characterized PPOs appear to have very specific roles in the biosynthesis of specialized metabolites via both tyrosinase (monophenol oxidase) and catechol oxidase activities. Here we detail a few examples of these and explore the possibility that there may be many more “biosynthetic” PPOs.
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Reduced-Gliadin Wheat Bread: An Alternative to the Gluten-Free Diet for Consumers Suffering Gluten-Related Pathologies

Reduced-Gliadin Wheat Bread: An Alternative to the Gluten-Free Diet for Consumers Suffering Gluten-Related Pathologies | plant cell genetics | Scoop.it

Wheat flour cannot be tolerated by those who suffer allergies to gluten. Human pathologies associated with grain proteins have increased worldwide in recent years, and the only effective treatment available is a lifelong gluten-free diet, which is complicated to follow and detrimental to gut health. This manuscript describes the development of wheat bread potentially suitable for celiac patients and other gluten-intolerant individuals. We have made bread using wheat flour with very low content of the specific gluten proteins (near gliadin-free) that are the causal agents for pathologies such as celiac disease. Loaves were compared with normal wheat breads and rice bread. Organoleptic, nutritional, and immunotoxic properties were studied. The reduced-gliadin breads showed baking and sensory properties, and overall acceptance, similar to those of normal flour, but with up to 97% lower gliadin content. Moreover, the low-gliadin flour has improved nutritional properties since its lysine content is significantly higher than that of normal flour. Conservative estimates indicate that celiac patients could safely consume 67 grams of bread per day that is made with low-gliadin flour. However, additional studies, such as feeding trials with gluten-intolerant patients, are still needed in order to determine whether or not the product can be consumed by the general celiac population, as well as the actual tolerated amount that can be safely ingested. The results presented here offer a major opportunity to improve the quality of life for millions of sufferers of gluten intolerance throughout the world.Reduced-Gliadin Wheat Bread: An Alternative to the Gluten-Free Diet for Consumers Suffering Gluten-Related Pathologies

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Frontiers: Strategies for transferring resistance into wheat: from wide crosses to GM cassettes (2014)

Frontiers: Strategies for transferring resistance into wheat: from wide crosses to GM cassettes (2014) | plant cell genetics | Scoop.it

The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed the genetic base by introducing extreme levels of uniformity on a vast spatial and temporal scale. This reduction in genetic complexity renders the crop vulnerable to new and emerging pests and pathogens. The wild relatives of wheat represent an important source of genetic variation for disease resistance. For nearly a century farmers, breeders, and cytogeneticists have sought to access this variation for crop improvement. Several barriers restricting interspecies hybridization and introgression have been overcome, providing the opportunity to tap an extensive reservoir of genetic diversity. Resistance has been introgressed into wheat from at least 52 species from 13 genera, demonstrating the remarkable plasticity of the wheat genome and the importance of such natural variation in wheat breeding. Two main problems hinder the effective deployment of introgressed resistance genes for crop improvement: (1) the simultaneous introduction of genetically linked deleterious traits and (2) the rapid breakdown of resistance when deployed individually. In this review, we discuss how recent advances in molecular genomics are providing new opportunities to overcome these problems.


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The Sainsbury Lab's curator insight, December 8, 2014 5:30 AM

The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed the genetic base by introducing extreme levels of uniformity on a vast spatial and temporal scale. This reduction in genetic complexity renders the crop vulnerable to new and emerging pests and pathogens. The wild relatives of wheat represent an important source of genetic variation for disease resistance. For nearly a century farmers, breeders, and cytogeneticists have sought to access this variation for crop improvement. Several barriers restricting interspecies hybridization and introgression have been overcome, providing the opportunity to tap an extensive reservoir of genetic diversity. Resistance has been introgressed into wheat from at least 52 species from 13 genera, demonstrating the remarkable plasticity of the wheat genome and the importance of such natural variation in wheat breeding. Two main problems hinder the effective deployment of introgressed resistance genes for crop improvement: (1) the simultaneous introduction of genetically linked deleterious traits and (2) the rapid breakdown of resistance when deployed individually. In this review, we discuss how recent advances in molecular genomics are providing new opportunities to overcome these problems.

Bharat Employment's curator insight, January 20, 11:42 PM

www.bharatemployment.com

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Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene | plant cell genetics | Scoop.it
The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant–human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant–hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant–hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage.
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To what extent does organic farming rely on nutrient inflows from conventional farming? - IOPscience

To what extent does organic farming rely on nutrient inflows from conventional farming? - IOPscience | plant cell genetics | Scoop.it
Organic farming is increasingly recognized as a prototype for sustainable agriculture. Its guidelines ban the use of artificial fertilizers. However, organic farms may import nutrients from conventional farming through material exchanges. In this study, we aimed at estimating the magnitude of these flows through the quantification of nitrogen, phosphorus and potassium inflows from conventional farming to organic farming. Material inflows and outflows were collected for two cropping years on 63 farms. The farms were located in three French agricultural districts distributed over a gradient of farming activity defined by both the stocking rate and the ratio of the farm area under arable crops. Our results showed that on average, inflows from conventional farming were 23%, 73% and 53% for nitrogen, phosphorus and potassium, respectively. These inflows were strongly determined by the farm production systems. However, for farms similar in terms of production systems, the inflows also depended on the local context, such as the proximity of organic livestock farms: the reliance of organic farming on conventional farming was lower in mixed than in specialized districts. These results highlight the necessity to quantify the contribution of nutrient inflows from conventional farming when assessing organic farming and development scenarios.
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Recombination products suggest the frequent occurrence of aberrant gene replacement in the moss Physcomitrella patens - Wendeler - The Plant Journal - Wiley Online Library

Recombination products suggest the frequent occurrence of aberrant gene replacement in the moss Physcomitrella patens - Wendeler - The Plant Journal - Wiley Online Library | plant cell genetics | Scoop.it
In gene replacement, a variant of gene targeting, transformed DNA integrates into the genome by homologous recombination (HR) to replace resident sequences. Gene replacement in the moss Physcomitrella patens is extremely efficient, but often large amounts of additional DNA are integrated at the target locus. A detailed analysis of recombination junctions of PpCOL2 gene knockout mutants shows that the integrated DNA can be highly rearranged. Our data suggest that the replaced sequences were excised by HR and became integrated back into the genome by non-homologous end-joining (NHEJ). RAD51-mediated strand-invasion and subsequent strand-exchange is central to the two-end invasion pathway, the major gene replacement pathway in yeast. In this pathway, integration is initiated by the free ends of a single replacement vector-derived donor molecule which then integrates as an entity. Gene replacement in P. patens is entirely RAD51-dependent suggesting the existence of a pathway mechanistically similar to two-end invasion. However, invasion of the two ends does not seem to be stringently coordinated in P. patens. Actually, often only one fragment end became integrated by HR, or one-sided integration of two independent donor fragments occurred simultaneously leading to a double-strand break that is subsequently sealed by NHEJ and thus causes the observed rearrangements.
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The Inventiveness of Nature: An Interview with Werner Arber

The Inventiveness of Nature: An Interview with Werner Arber | plant cell genetics | Scoop.it

Nature is much more complex than we believe. I don′t think there is much work so far on horizontal gene transfer between higher eukaryotes and microorganisms. It is always true that you can get new insights if you develop new methodologies. This will come.

 

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RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants - Annual Review of Plant Biology, 66(1):

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants - Annual Review of Plant Biology, 66(1): | plant cell genetics | Scoop.it
RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)–related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins.Wepresent current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and PolV pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.
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Activation of Defense Mechanisms against Pathogens in Mosses and Fl... - PubMed - NCBI

Activation of Defense Mechanisms against Pathogens in Mosses and Fl... - PubMed - NCBI | plant cell genetics | Scoop.it
During evolution, plants have developed mechanisms to cope with and adapt to different types of stress, including microbial infection. Once the stress is sensed, signaling pathways are activated, leading to the induced expression of genes with different roles in defense. Mosses (Bryophytes) are non-vascular plants that diverged from flowering plants more than 450 million years ago, allowing comparative studies of the evolution of defense-related genes and defensive metabolites produced after microbial infection. The ancestral position among land plants, the sequenced genome and the feasibility of generating targeted knock-out mutants by homologous recombination has made the moss Physcomitrella patens an attractive model to perform functional studies of plant genes involved in stress responses. This paper reviews the current knowledge of inducible defense mechanisms in P. patens and compares them to those activated in flowering plants after pathogen assault, including the reinforcement of the cell wall, ROS production, programmed cell death, activation of defense genes and synthesis of secondary metabolites and defense hormones. The knowledge generated in P. patens together with comparative studies in flowering plants will help to identify key components in plant defense responses and to design novel strategies to enhance resistance to biotic stress.
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Genome Biology | Abstract | Organization and evolution of transposable elements along the bread wheat chromosome 3B

BackgroundThe 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements and two recent rounds of polyploidization. The assembly of a 774?Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of transposable elements (TEs) on the complex wheat genome structure and evolution at a resolution and scale never reached so far.ResultsWe develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation.ConclusionAccurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
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The Physcomitrella patens unique alpha-dioxygenase participates in both developmental processes and defense responses

The Physcomitrella patens unique alpha-dioxygenase participates in both developmental processes and defense responses | plant cell genetics | Scoop.it

Background

Plant α-dioxygenases catalyze the incorporation of molecular oxygen into polyunsaturated fatty acids leading to the formation of oxylipins. In flowering plants, two main groups of α-DOXs have been described. While the α-DOX1 isoforms are mainly involved in defense responses against microbial infection and herbivores, the α-DOX2 isoforms are mostly related to development. To gain insight into the roles played by these enzymes during land plant evolution, we performed biochemical, genetic and molecular analyses to examine the function of the single copy moss Physcomitrella patens α-DOX (Ppα-DOX) in development and defense against pathogens.

Results

Recombinant Ppα-DOX protein catalyzed the conversion of fatty acids into 2-hydroperoxy derivatives with a substrate preference for α-linolenic, linoleic and palmitic acids. Ppα-DOX is expressed during development in tips of young protonemal filaments with maximum expression levels in mitotically active undifferentiated apical cells. In leafy gametophores, Ppα-DOX is expressed in auxin producing tissues, including rhizoid and axillary hairs. Ppα-DOX transcript levels and Ppα-DOX activity increased in moss tissues infected with Botrytis cinerea or treated with Pectobacterium carotovorum elicitors. In B. cinerea infected leaves, Ppα-DOX-GUS proteins accumulated in cells surrounding infected cells, suggesting a protective mechanism. Targeted disruption of Ppα-DOX did not cause a visible developmental alteration and did not compromise the defense response. However, overexpressing Ppα-DOX, or incubating wild-type tissues with Ppα-DOX-derived oxylipins, principally the aldehyde heptadecatrienal, resulted in smaller moss colonies with less protonemal tissues, due to a reduction of caulonemal filament growth and a reduction of chloronemal cell size compared with normal tissues. In addition, Ppα-DOX overexpression and treatments with Ppα-DOX-derived oxylipins reduced cellular damage caused by elicitors of P. carotovorum.

Conclusions

Our study shows that the unique α-DOX of the primitive land plant P. patens, although apparently not crucial, participates both in development and in the defense response against pathogens, suggesting that α-DOXs from flowering plants could have originated by duplication and successive functional diversification after the divergence from bryophytes.


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The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development

The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development | plant cell genetics | Scoop.it

The phytohormones auxin and cytokinin interact to regulate many plant growth and developmental processes. Elements involved in the biosynthesis, inactivation, transport, perception, and signaling of these hormones have been elucidated, revealing the variety of mechanisms by which signal output from these pathways can be regulated. Recent studies shed light on how these hormones interact with each other to promote and maintain plant growth and development. In this review, we focus on the interaction of auxin and cytokinin in several developmental contexts, including its role in regulating apical meristems, the patterning of the root, the development of the gynoecium and female gametophyte, and organogenesis and phyllotaxy in the shoot.

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Why GM is the natural solution for future farming

Why GM is the natural solution for future farming | plant cell genetics | Scoop.it

Farming, by definition, is the opposite of natural. Nothing we eat could be described as “natural”, regardless of the marketing or labelling, whether it’s organic, or from Waitrose, Aldi or Abel & Cole. Breeding any organism for food, fuel, sport or for pets is effectively genetic modification – and we have been doing that for thousands of years. For example, a Granny Smith is a genetic hybrid of two other apples and even a blackberry plucked from a bramble is the product of a deeply ancient, seemingly natural but actually very human design – the hedgerow.

The crunchy flesh of an apple, or the grotesquely swollen udders – and even the black and white hide – of Holstein-Friesian cows are the result of carefully selecting genes and forcing them into subsequent generations.

Since the 1970s we’ve been ushering in the next era of breeding by physically lifting individual genes from one species and inserting them into another. The first crop was an antibiotic-resistant tobacco in 1982 and now around one 10th of the world’s planted crops are GM (a figure distorted by the vigorous embrace of the US – around 90% of corn and soy is GM, balancing the fact that EU has an outright ban). Change is afoot: the EU has slightly relaxed its laws to allow the growth of GM and we may see the first commercial crops in the UK by 2017. ...


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INRA - Mécanismes de durabilité des résistances

INRA - Mécanismes de durabilité des résistances | plant cell genetics | Scoop.it

Sommaire

Introduction

Combiner des résistances basées sur des mécanismes différents (pommier)

La dérive pour éviter le naufrage (piment)

Une avirulence chasse l’autre (colza)

Combiner variétés résistantes et techniques de culture (maraîchage)

Panoramix au pays des pyramides (vigne)

Sharka : prudence dans le déploiement des variétés résistantes


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Redefining agricultural yields: from tonnes to people nourished per hectare - Abstract - Environmental Research Letters - IOPscience

Redefining agricultural yields: from tonnes to people nourished per hectare - Abstract - Environmental Research Letters - IOPscience | plant cell genetics | Scoop.it
Worldwide demand for crops is increasing rapidly due to global population growth, increased biofuel production, and changing dietary preferences. Meeting these growing demands will be a substantial challenge that will tax the capability of our food system and prompt calls to dramatically boost global crop production. However, to increase food availability, we may also consider how the world's crops are allocated to different uses and whether it is possible to feed more people with current levels of crop production. Of particular interest are the uses of crops as animal feed and as biofuel feedstocks. Currently, 36% of the calories produced by the world's crops are being used for animal feed, and only 12% of those feed calories ultimately contribute to the human diet (as meat and other animal products). Additionally, human-edible calories used for biofuel production increased fourfold between the years 2000 and 2010, from 1% to 4%, representing a net reduction of available food globally. In this study, we re-examine agricultural productivity, going from using the standard definition of yield (in tonnes per hectare, or similar units) to using the number of people actually fed per hectare of cropland. We find that, given the current mix of crop uses, growing food exclusively for direct human consumption could, in principle, increase available food calories by as much as 70%, which could feed an additional 4 billion people (more than the projected 2–3 billion people arriving through population growth). Even small shifts in our allocation of crops to animal feed and biofuels could significantly increase global food availability, and could be an instrumental tool in meeting the challenges of ensuring global food security.
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Effects of density and sowing pattern on weed suppression and grain yield in three varieties of maize under high weed pressure

Effects of density and sowing pattern on weed suppression and grain yield in three varieties of maize under high weed pressure | plant cell genetics | Scoop.it
We tested the hypothesis that improved weed suppression by maize can be achieved through increased crop density and spatial uniformity. Field experiments on three varieties of maize sown at three densities (5, 7 and 10.5 seeds m−2) and in two spatial patterns (grid pattern and rows) under very high weed pressure from Brachiaria brizantha were performed in 2012 and 2013. We measured weed biomass 1 month after sowing and at harvest, and grain yield at harvest. Density, variety and sowing pattern all had strong and significant effects on both weed biomass and yield. On average, weed biomass was reduced (by 72% in the first year and 58% in the second year), and grain yield was increased (by 48% and 44%) at the highest density in the grid pattern compared with standard sowing practices (medium density, row pattern). There was a significant density × variety interaction, which is evidence for genetic differences in the response of the varieties to density in characteristics that influence weed suppression. The variety that suppressed weeds best at high density had the lowest variation in the angle of insertion of the oldest living leaf at harvest (leaf 6), supporting the hypothesis that reduced phenotypic plasticity may be advantageous for weed suppression under high density and spatial uniformity. Increased density and uniformity can contribute to weed management in maize in many cases, potentially reducing the need for herbicides or mechanical weed control.
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Recombination products suggest the frequent occurrence of aberrant gene replacement in the moss Physcomitrella patens

Recombination products suggest the frequent occurrence of aberrant gene replacement in the moss Physcomitrella patens | plant cell genetics | Scoop.it
In gene replacement, a variant of gene targeting, transformed DNA integrates into the genome by homologous recombination (HR) to replace resident sequences. Gene replacement in the moss Physcomitrella patens is extremely efficient, but often large amounts of additional DNA are integrated at the target locus. A detailed analysis of recombination junctions of PpCOL2 gene knockout mutants shows that the integrated DNA can be highly rearranged. Our data suggest that the replaced sequences were excised by HR and became integrated back into the genome by non-homologous end-joining (NHEJ). RAD51-mediated strand-invasion and subsequent strand-exchange is central to the two-end invasion pathway, the major gene replacement pathway in yeast. In this pathway, integration is initiated by the free ends of a single replacement vector-derived donor molecule which then integrates as an entity. Gene replacement in P. patens is entirely RAD51-dependent suggesting the existence of a pathway mechanistically similar to two-end invasion. However, invasion of the two ends does not seem to be stringently coordinated in P. patens. Actually, often only one fragment end became integrated by HR, or one-sided integration of two independent donor fragments occurred simultaneously leading to a double-strand break that is subsequently sealed by NHEJ and thus causes the observed rearrangements.
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EU Banned Pesticides to Help Bees, But Now Other Bugs Are Invading

EU Banned Pesticides to Help Bees, But Now Other Bugs Are Invading | plant cell genetics | Scoop.it

The European Union has a bug problem. 

After regulators in late 2013 banned pesticides called neonicotinoids, linked in some studies to the unintended deaths of bees, farmers across the continent applied older chemicals to which many pests had developed a resistance, allowing them to survive. Now, infestations may lead to a 15 percent drop in this year’s European harvest of rapeseed, the region’s primary source of vegetable oil used to make food ingredients and biodiesel, according to researcher Oil World. 

“When we remove a tool from the box, that puts even more pressure on the tools we’ve got left,” said farmer Martin Jenkins, who has seen flea beetles for the first time in almost a decade on his 750 acres of rapeseed outside Cambridge, England. “More pesticides are being used, and even more ridiculous is there will be massively less rapeseed.” 

At issue for the EU was protecting bees that farmers rely upon to pollinate more than 80 percent of Europe’s crops and wild plants, valued at 22 billion euros ($26 billion) annually. While research on how neonicotinoids affect beneficial insects hasn’t been conclusive, regulators said the risks were worth imposing a two-year ban that began in December 2013. The Canadian province of Ontario proposed similar restrictions last year, and new rules are under review in the U.S., the biggest oilseed producer. 

Corn, Sunflowers 

The ban left European farmers without effective alternatives, leading to widespread insect damage, Hamburg-based Oil World said in a December report. Output of rapeseed may fall to a three-year low of 20.5 million metric tons in 2015, down from a record 24 million last year, it said. The EU is the world’s largest producer of rapeseed, which is known in North America mostly as canola. 

French corn and Spanish sunflowers may also be affected, said Copa-Cogeca, the Brussels-based lobbyist for the continent’s growers. 

The EU restricted the main types of neonicotinoids, a class of chemicals similar to nicotine, while still permitting two less-toxic varieties. Bayer AG (BAYN), which markets the products as Poncho and Votivo, and Syngenta AG make the pesticide. Monsanto Co., DuPont Co. and Dow Chemical Co. (DOW) sell seeds coated in it. 

Older Chemistry 

“Farmers have had to go back to older chemistry and chemistry that is increasingly less effective,” said Nick von Westenholz, the chief executive officer of the U.K.’s Crop Protection Association, an industry lobbyist. “Companies would like to innovate and bring newer stuff, but the neonicotinoid example is not a tempting one.” 

While the EU’s approval process for new pesticides can take years, some research is under way. The U.K. last month granted over 650,000 pounds ($979,485) in funding to a project led by Arch UK Biocides Ltd. for a chemical based on spider venom that is harmless to bees. 

Some studies, including one in May from the Harvard School of Public Health, have linked neonicotinoids to Colony Collapse Disorder, a syndrome marked by bees abandoning their hives in winter and dying. Bayer scientists dubbed the research “seriously flawed,” noting that colony failures observed in the study were prompted in part because bees were fed artificially high levels of pesticides. 

Other research was less conclusive. Some versions of the insecticide were harmful in lab experiments and had little effect on healthy colonies in the field, according to a report by Wageningen University in the Netherlands. 

Question Mark 

“The risk to bee populations and the wider environment from using this chemical that has a very big question mark over it is not a risk worth taking,” said Helen Browning, the chief executive officer of the Soil Association, a U.K. charity focused on sustainable farming. “There are alternative approaches,” such as barrier crops around fields, she said. 

The number of approved crop chemicals has fallen in the EU by more than 75 percent in two decades, according to the Andersons Centre, a farm consultancy in Leicestershire, England. 

In Germany, most rapeseed farmers have sprayed crops at least twice with alternative chemicals known as pyrethroids this season, said Manuela Specht, a division head at oilseed trade group known as UFOP in Berlin. In past years, they only sprayed once or not at all, she said. Prolonged exposure to some pyrethroids can stunt bee growth, a University of London study showed last year. 

For Jenkins, the U.K. farmer, he’s balancing a fight against pests that grow stronger over time with trying to maintain food production. In addition to flea beetles in rapeseed, he’s got an infestation of black grass, a weed that chokes his wheat fields. Two of the chemicals that he used to use are now banned, and the plant is resistant to permitted treatments of Bayer’s Atlantis, he said. 

“We’re growing less tons of food on our farm than we were 10 years ago,” Jenkins said. “An attack 10 years ago we could remedy with an alternative bit of chemistry, but that is no longer the case.”

 
Via Stéphane Bisaillon
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The politics of Golden Rice

The politics of Golden Rice | plant cell genetics | Scoop.it
(2014). The politics of Golden Rice. GM Crops & Food: Vol. 5, Politics and GM crops, pp. 210-222. doi: 10.4161/21645698.2014.967570
Genetic knowledge applicable to crop improvement has erupted over the past 60 years, and the techniques of introducing genes from one organism to another have enabled new varieties of crops not achievable by previously available methodologies of crop breeding. Research and particularly development of these GMO-crops to a point where they are useful for growers and consumers in most countries is subject to complex national and international rules arising out of the UN's Cartagena Protocol on Biosafety to the Convention on Biological Diversity, with 167 country signatories. (The USA and Canada are not signatories.) The Protocol was developed based on concerns initially expressed in the 1970's that such technology presented unusual risks to man and the environment. Those ideas have comprehensively and authoritatively been proven to be wrong. The Protocol has nevertheless spawned significant regulatory obstacles to the development of GMO-crop technology at great cost to global society and in conflict with many other UN objectives. The suspicion induced by the Protocol is also widely used, overtly or covertly, for political purposes. These points are illustrated by reference to the not-for-profit Golden Rice project.
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From the Concept of Totipotency to Biofortified Cereals - Annual Review of Plant Biology, 66(1): Ingo Potrykus

From the Concept of Totipotency to Biofortified Cereals - Annual Review of Plant Biology, 66(1): Ingo Potrykus | plant cell genetics | Scoop.it
I was a college teacher when opportunity opened a path into academia. A fascination with totipotency channeled me into research on tissue culture. As I was more interested in contributions to food security than in scientific novelty, I turned my attention to the development of genetic modification technology for cereals. From my cell culture experience, I had reasons not to trust Agrobacterium for that purpose, and I developed direct gene transfer instead. In the early 1990s, I became aware of the problem of micronutrient deficiency, particularly vitamin A deficiency in rice-eating populations. Golden Rice, which contains increased amounts of provitamin A, was probably instrumental for the concept of biofortification to take off. I realized that this rice would remain an academic exercise if product development and product registration were not addressed, and this is what I focused on after my retirement. Although progress is slowly being made, had I known what this pursuit would entail, perhaps I would not have started. Hopefully Golden Rice will reach the needy during my lifetime.
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The GMO case in France: Politics, lawlessness and postmodernism

The GMO case in France: Politics, lawlessness and postmodernism | plant cell genetics | Scoop.it
The GMO debacle in France is analyzed in the light of the balance of forces around this controversy, the changes in position of governments and the opponents’ strategic use of intimidation. These factors have caused insurmountable difficulties for scientific experimentations and assessment of the technology, as well as for farmers attempting to grow GM maize in this country. The change from a “modern” to a “postmodern” framing of official public debates and scientific institutions has not appeased confrontations concerning GMOs.
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A model system for analyzing intercellular communication through plasmodesmata using moss protonemata and leaves - Online First - Springer

A model system for analyzing intercellular communication through plasmodesmata using moss protonemata and leaves - Online First - Springer | plant cell genetics | Scoop.it

Plant growth, development, and environmental responses require the proper regulation of intercellular movement of signals and nutrients. For this, plants have specialized cytoplasmic channels, the plasmodesmata (PD), which allow the symplasmic movement of micro- and macromolecules between neighboring cells. Internal and external signals spatio-temporally regulate the movement of molecules through the PD to control plant development and environmental responses. Although some aspects of targeted movement of molecules have been revealed, the mechanisms of non-targeted, diffusible flow of molecules through PD, and its regulation and function, remain poorly understood, particularly at the cellular level. Previously, we developed a system to quantitatively analyze non-targeted movement of a photoconvertible fluorescent protein, Dendra2, at the single-cell level in the filamentous protonemata tissue of the moss Physcomitrella patens. In protonemata, one-dimensional intercellular communication can be easily observed and quantitatively analyzed at the cellular level. In this review, we describe how protonemata and leaves of P. patens can be used to study symplasmic movement through PD, and discuss how this system can help improve our understanding of PD regulation and function in development and environmental responses in plants.

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