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The Archaeobotanist: Weed evolution by de-domestication: the case of rice

The Archaeobotanist: Weed evolution by de-domestication: the case of rice | plant cell genetics | Scoop.it

The study of weed origins and evolutionary history is the poor cousin of the archaeobotany of crop domestication. Archaeobotanists can potentially do much more on this, and undoubtedly should. To provide some inspiration it is worth considering some recent insights from genetics, to do with weedy rice. While it is surely the case that rice's wild progenitors may act as weeds in the crop, it now appears that much weedy rice is descended from the crop and not directly from the wild progenitor.


Via Dorian Q Fuller, Eve Emshwiller
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Barley: a translational model for adaptation to climate change - Dawson - 2015 - New Phytologist - Wiley Online Library

Barley: a translational model for adaptation to climate change - Dawson - 2015 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes – including examples that are indicative of the complexities involved in designing appropriate responses – are presented, and key developments for the future highlighted.
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GMOs of the Future: Two Recent Studies Reveal Potential of Genetic Technologies - Science Sushi

GMOs of the Future: Two Recent Studies Reveal Potential of Genetic Technologies - Science Sushi | plant cell genetics | Scoop.it
There’s no doubt that the next generation of GM crops will look very little like the oft-maligned varieties available today. The possibilities are nearly limitless, as are the rewards. And with the world’s climate changing rapidly, there’s no doubt that agriculture will need to change with it, to keep pace with an unpredictable environment. The future of agriculture may very well depend on the ingenuity of geneticists and the GMOs they create. The real question is, will these new varieties be able to do what current ones cannot: win over the hearts and minds of the people they’re designed for.

Via Mary Williams
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Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing

Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing | plant cell genetics | Scoop.it
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in non-model species that is based on homolog groups in addition to inferred ortholog groups.
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Sequencing consolidates molecular markers with plant breeding practice

Sequencing consolidates molecular markers with plant breeding practice | plant cell genetics | Scoop.it

Key message

Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding.

Abstract

The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.


Via Ali Taheri, Loïc Lepiniec
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Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids

Double-stranded RNAs (dsRNAs) targeted against essential genes can trigger a lethal RNA interference (RNAi) response in insect pests. The application of this concept in plant protection is hampered by the presence of an endogenous plant RNAi pathway that processes dsRNAs into short interfering RNAs. We found that long dsRNAs can be stably produced in chloroplasts, a cellular compartment that appears to lack an RNAi machinery. When expressed from the chloroplast genome, dsRNAs accumulated to as much as 0.4% of the total cellular RNA. Transplastomic potato plants producing dsRNAs targeted against the β-actin gene of the Colorado potato beetle, a notorious agricultural pest, were protected from herbivory and were lethal to its larvae. Thus, chloroplast expression of long dsRNAs can provide crop protection without chemical pesticides.
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Combined transcript, proteome, and metabolite analysis of transgenic maize seeds engineered for enhanced carotenoid synthesis reveals pleotropic effects in core metabolism

Combined transcript, proteome, and metabolite analysis of transgenic maize seeds engineered for enhanced carotenoid synthesis reveals pleotropic effects in core metabolism | plant cell genetics | Scoop.it
The aim of this study was to assess whether endosperm-specific carotenoid biosynthesis influenced core metabolic processes in maize embryo and endosperm and how global seed metabolism adapted to this expanded biosynthetic capacity. Although enhancement of carotenoid biosynthesis was targeted to the endosperm of maize kernels, a concurrent up-regulation of sterol and fatty acid biosynthesis in the embryo was measured. Targeted terpenoid analysis, and non-targeted metabolomic, proteomic, and transcriptomic profiling revealed changes especially in carbohydrate metabolism in the transgenic line. In-depth analysis of the data, including changes of metabolite pools and increased enzyme and transcript concentrations, gave a first insight into the metabolic variation precipitated by the higher up-stream metabolite demand by the extended biosynthesis capacities for terpenoids and fatty acids. An integrative model is put forward to explain the metabolic regulation for the increased provision of terpenoid and fatty acid precursors, particularly glyceraldehyde 3-phosphate and pyruvate or acetyl-CoA from imported fructose and glucose. The model was supported by higher activities of fructokinase, glucose 6-phosphate isomerase, and fructose 1,6-bisphosphate aldolase indicating a higher flux through the glycolytic pathway. Although pyruvate and acetyl-CoA utilization was higher in the engineered line, pyruvate kinase activity was lower. A sufficient provision of both metabolites may be supported by a by-pass in a reaction sequence involving phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme.
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Massive migration from the steppe was a source for Indo-European languages in Europe : Nature

Massive migration from the steppe was a source for Indo-European languages in Europe : Nature | plant cell genetics | Scoop.it
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, [sim]8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a [sim]24,000-year-old Siberian. By [sim]6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact [sim]4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced [sim]75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least [sim]3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.

Via Francis Martin
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Stomatal Guard Cells Co-opted an Ancient ABA-Dependent Desiccation Survival System to Regulate Stomatal Closure

Stomatal Guard Cells Co-opted an Ancient ABA-Dependent Desiccation Survival System to Regulate Stomatal Closure | plant cell genetics | Scoop.it
During the transition from water to land, plants had to cope with the loss of water through transpiration, the inevitable result of photosynthetic CO2 fixation on land [1 and 2]. Control of transpiration became possible through the development of a new cell type: guard cells, which form stomata. In vascular plants, stomatal regulation is mediated by the stress hormone ABA, which triggers the opening of the SnR kinase OST1-activated anion channel SLAC1 [3 and 4]. To understand the evolution of this regulatory circuit, we cloned both ABA-signaling elements, SLAC1 and OST1, from a charophyte alga, a liverwort, and a moss, and functionally analyzed the channel-kinase interactions. We were able to show that the emergence of stomata in the last common ancestor of mosses and vascular plants coincided with the origin of SLAC1-type channels capable of using the ancient ABA drought signaling kinase OST1 for regulation of stomatal closure.
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Plant characterization of Roundup Ready 2 Yield® soybean, MON 89788, for use in ecological risk assessment - Springer

Plant characterization of Roundup Ready 2 Yield® soybean, MON 89788, for use in ecological risk assessment - Springer | plant cell genetics | Scoop.it
During the development of a genetically modified (GM) crop product, extensive phenotypic and agronomic data are collected to characterize the plant in comparison to a conventional control with a similar genetic background. The data are evaluated for potential differences resulting from the genetic modification process or the GM trait, and the differences—if any—are subsequently considered in the context of contributing to the pest potential of the GM crop. Ultimately, these study results and those of other studies are used in an ecological risk assessment of the GM crop. In the studies reported here, seed germination, vegetative and reproductive growth, and pollen morphology of Roundup Ready 2 Yield® soybean, MON 89788, were compared to those of A3244, a conventional control soybean variety with the same genetic background. Any statistically significant differences were considered in the context of the genetic variation known to occur in soybean and were evaluated as indicators of an effect of the genetic modification process and assessed for impact on plant pest (weed) characteristics and adverse ecological impact (ecological risk). The results of these studies revealed no effects attributable to the genetic modification process or to the GM trait in the plant that would result in increased pest potential or adverse ecological impact of MON 89788 compared with A3244. These results and the associated risk assessments obtained from diverse geographic and environmental conditions in the United States and Argentina can be used by regulators in other countries to inform various assessments of ecological risk.
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Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research: Cell Reports

Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research: Cell Reports | plant cell genetics | Scoop.it

In recent years, tetracyclines, such as doxycycline, have become broadly used to control gene expression by virtue of the Tet-on/Tet-off systems. However, the wide range of direct effects of tetracycline use has not been fully appreciated. We show here that these antibiotics induce a mitonuclear protein imbalance through their effects on mitochondrial translation, an effect that likely reflects the evolutionary relationship between mitochondria and proteobacteria. Even at low concentrations, tetracyclines induce mitochondrial proteotoxic stress, leading to changes in nuclear gene expression and altered mitochondrial dynamics and function in commonly used cell types, as well as worms, flies, mice, and plants. Given that tetracyclines are so widely applied in research, scientists should be aware of their potentially confounding effects on experimental results. Furthermore, these results caution against extensive use of tetracyclines in livestock due to potential downstream impacts on the environment and human health.

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Do leftover tetracyclin affect plants in the real world of agriculture - the question remain open ?

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Farmers Weekly: Cereal disease threat may be worse than in 'horrific' 2014 (2015)

Farmers Weekly: Cereal disease threat may be worse than in 'horrific' 2014 (2015) | plant cell genetics | Scoop.it

Cereal growers could face a worse disease year this season than the “horrific” 2014 prompted by a mild autumn with plenty of inoculum in fields.

 

Wheat’s most damaging diseases – septoria and yellow rust (pictured) – are being seen earlier than normal while in barley, mildew, rhynchosporium and net blotch are worse than usual.

 

Scottish disease expert Fiona Burnett is warning that 2015 could be more serious than 2014 with lots of early-drilled and forward crops picking up disease in the autumn.

 

“We have forward, thick crops, the right weather and enough inoculum to start the fire,” she tells the Farmers Weekly.

Dr Burnett, crop protection leader at Scotland’s Rural College (SRUC), adds she is seeing more yellow rust and septoria in crops at this stage than for a long time.

 

Yellow rust crept into East Lothian winter wheat crops by early November, two months ahead of normal, while septoria is being seen in many crops.

“We have only had a little bit of cold weather, what we need is sustained cold weather to kill off disease,” she says.

 

All the signs are that disease could be worse than in 2014 which she describes as a “horrific disease year” largely due to the mild 2013-14 winter.


Via Kamoun Lab @ TSL
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Genome Biology | Full text | Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

Genome Biology | Full text | Field pathogenomics reveals the emergence of a diverse wheat yellow rust population | plant cell genetics | Scoop.it
Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious.
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Fatal attraction: the intuitive appeal of GMO opposition: Trends in Plant Science

Fatal attraction: the intuitive appeal of GMO opposition: Trends in Plant Science | plant cell genetics | Scoop.it
Highlights

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

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

Three ancient hormonal cues co-ordinate shoot branching in a moss | plant cell genetics | Scoop.it
Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.
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Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine

Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine | plant cell genetics | Scoop.it
Author Summary Pinot is one of the most ancient grapevine varieties made up of a large panel of clones, most of them used to produce very different wines with specific oenological characteristics in different vineyards around the world. This great diversity of clones, which is due to spontaneous somatic mutations that have occurred over time, makes Pinot a fascinating subject of study. It is the reason why we have undertaken a study focused on the color locus to identify the mutations respons
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Public funded field trials with transgenic plants in Europe: a comparison between Germany and Switzerland

Public funded field trials with transgenic plants in Europe: a comparison between Germany and Switzerland | plant cell genetics | Scoop.it
Field trails are indispensable for the scientific analysis of risks and potential benefits of genetically modified plants (GMP). The dramatic reduction of field trials in the European Union (EU) coincides with increasing safety demands, decreases in funding, and changes in the European directives. In parallel, opposition from non-governmental organizations (NGOs) has grown, and public acceptance has decreased. The cultivation of events approved by the EU is still allowed in principle, nevertheless, at least in Germany, there is a de facto moratorium on cultivation. In Switzerland, where development was much more hesitant compared to Germany, field trials are now possible, and a protected site has been established by the government. Public acceptance for scientific trials in Switzerland has risen, despite the continued moratorium on the cultivation based on a referendum.
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Genetic, evolutionary and plant breeding insights from the domestication of maize

Genetic, evolutionary and plant breeding insights from the domestication of maize | plant cell genetics | Scoop.it

by Sarah Hake& Jeffrey Ross-Ibarra

"The natural history of maize began nine thousand years ago when Mexican farmers started to collect the seeds of the wild grass, teosinte. Invaluable as a food source, maize permeated Mexican culture and religion. Its domestication eventually led to its adoption as a model organism, aided in large part by its large chromosomes, ease of pollination and growing agricultural importance. Genome comparisons between varieties of maize, teosinte and other grasses are beginning to identify the genes responsible for the domestication of modern maize and are also providing ideas for the breeding of more hardy varieties."


Via Mary Williams
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AckerbauHalle's curator insight, April 2, 3:08 AM

Great paper on the evolution of maize

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Increasing water-use efficiency directly through genetic manipulation of stomatal density - Franks - 2015 - New Phytologist - Wiley Online Library

Increasing water-use efficiency directly through genetic manipulation of stomatal density - Franks - 2015 - New Phytologist - Wiley Online Library | plant cell genetics | Scoop.it
Improvement in crop water-use efficiency (WUE) is a critical priority for regions facing increased drought or diminished groundwater resources. Despite new tools for the manipulation of stomatal development, the engineering of plants with high WUE remains a challenge.
We used Arabidopsis epidermal patterning factor (EPF) mutants exhibiting altered stomatal density to test whether WUE could be improved directly by manipulation of the genes controlling stomatal density. Specifically, we tested whether constitutive overexpression of EPF2 reduced stomatal density and maximum stomatal conductance (gw(max)) sufficiently to increase WUE.
We found that a reduction in gw(max) via reduced stomatal density in EPF2-overexpressing plants (EPF2OE) increased both instantaneous and long-term WUE without altering significantly the photosynthetic capacity. Conversely, plants lacking both EPF1 and EPF2 expression (epf1epf2) exhibited higher stomatal density, higher gw(max) and lower instantaneous WUE, as well as lower (but not significantly so) long-term WUE.
Targeted genetic modification of stomatal conductance, such as in EPF2OE, is a viable approach for the engineering of higher WUE in crops, particularly in future high-carbon-dioxide (CO2) atmospheres.
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Bending of Protonema Cells in a Plastid Glycolate/Glycerate Transporter Knockout Line of Physcomitrella patens

Bending of Protonema Cells in a Plastid Glycolate/Glycerate Transporter Knockout Line of  Physcomitrella patens | plant cell genetics | Scoop.it
Arabidopsis LrgB (synonym PLGG1) is a plastid glycolate/glycerate transporter associated with recycling of 2-phosphoglycolate generated via the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). We isolated two homologous genes (PpLrgB1 and B2) from the moss Physcomitrella patens. Phylogenetic tree analysis showed that PpLrgB1 was monophyletic with LrgB proteins of land plants, whereas PpLrgB2 was divergent from the green plant lineage. Experiments with PpLrgB–GFP fusion proteins suggested that both PpLrgB1 and B2 proteins were located in chloroplasts. We generated PpLrgB single (∆B1 and ∆B2) and double (∆B1/∆B2)-knockout lines using gene targeting of P. patens. The ∆B1 plants showed decreases in growth and photosynthetic activity, and their protonema cells were bent and accumulated glycolate. However, because ∆B2 and ∆B1/∆B2 plants showed no obvious phenotypic change relative to the wild-type or ∆B1 plants, respectively, the function of PpLrgB2 remains unclear. Arabidopsis LrgB could complement the ∆B1 phenotype, suggesting that the function of PpLrgB1 is the same as that of AtLrgB. When ∆B1 was grown under high-CO2 conditions, all novel phenotypes were suppressed. Moreover, protonema cells of wild-type plants exhibited a bending phenotype when cultured on media containing glycolate or glycerate, suggesting that accumulation of photorespiratory metabolites caused P. patens cells to bend.
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Nature Biotechnology: Engineering insect-free cereals (2015)

Nature Biotechnology: Engineering insect-free cereals (2015) | plant cell genetics | Scoop.it

A cluster of three rice lectin receptor kinases confers resistance to planthopper insects.

 

Insect pests reduce yields of crops worldwide through direct damage and because they spread devastating viral diseases. In Asia, the brown planthopper (BPH) decimates rice (Oryza sativa) crops, causing the loss of billions of dollars annually1. In this issue, Liu et al.2 report the cloning of a rice genetic locus that confers broad-spectrum resistance to BPH and at least one other planthopper species (white back planthopper). Introducing this locus into plant genomes is likely to provide an effective means of combating insect pests of rice and of other cereals such as maize.

 

In modern rice agriculture, BPH damage is controlled through breeding and the application of vast amounts of chemical pesticides1. Pesticides are not a sustainable approach, however, owing to high costs, harmful environmental effects and rapid development of resistant insects. Breeding programs have identified more than 20 genetic loci in cultivated or wild rice species that confer BPH resistance1. However, these Bph loci are usually only effective against specific BPH biotypes, and newly evolved BPH populations have rapidly overcome several Bph resistance loci deployed in the field..

 

Of the >20 identified Bph loci, only Bph14 and Bph26 have been cloned. Both of these loci encode coiled-coil, nucleotide-binding and leucine-rich repeat proteins3, 4, the main class of plant intracellular immune receptors5. Bph3 is a resistance locus that was first pinpointed genetically in the Sri Lankan rice indica cultivar Rathu Heenati. Notably, unlike most other Bph loci, including Bph14 and Bph26, Bph3 confers broad-spectrum resistance to many BPH biotypes as well as to the white back planthopper1, 2. The success of Bph3 as a resistance locus might be linked to the fact that it acts against BPH at an early stage of the feeding cycle, before the insect can deploy its arsenal of virulence proteins that circumvent plant defenses.

 

Despite the huge potential of Bph3 for rice agriculture, its molecular identity has been unknown. Liu et al.2 now identify Bph3 through map-based cloning in a cross between the resistant indica cultivar Rathu Heenati and the susceptible japonica cultivar 02428. Bph3 maps to a 79-kb genomic region that contains a cluster of three lectin receptor kinases, OsLecRK1–3 (ref. 2) (Fig. 1). The authors find that single-nucleotide polymorphisms in these genes are associated with BPH resistance in different cultivated rice accessions. They also show that ectopic expression of the OsLecRK1–3 gene cluster in the susceptible japonica Kitaake cultivar confers BPH resistance.

 

See Liu et al. Nature Biotechnology http://www.nature.com/nbt/journal/v33/n3/full/nbt.3069.html


Via Kamoun Lab @ TSL, Francis Martin
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Equality bias impairs collective decision-making across cultures

Equality bias impairs collective decision-making across cultures | plant cell genetics | Scoop.it
We tend to think that everyone deserves an equal say in a debate. This seemingly innocuous assumption can be damaging when we make decisions together as part of a group. To make optimal decisions, group members should weight their differing opinions according to how competent they are relative to one another; whenever they differ in competence, an equal weighting is suboptimal. Here, we asked how people deal with individual differences in competence in the context of a collective perceptual decision-making task. We developed a metric for estimating how participants weight their partner’s opinion relative to their own and compared this weighting to an optimal benchmark. Replicated across three countries (Denmark, Iran, and China), we show that participants assigned nearly equal weights to each other’s opinions regardless of true differences in their competence—even when informed by explicit feedback about their competence gap or under monetary incentives to maximize collective accuracy. This equality bias, whereby people behave as if they are as good or as bad as their partner, is particularly costly for a group when a competence gap separates its members.
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Plant phenotyping: from bean weighing to image analysis

Plant phenotyping: from bean weighing to image analysis | plant cell genetics | Scoop.it
Plant phenotyping refers to a quantitative description of the plant’s anatomical, ontogenetical, physiological and biochemical properties. Today, rapid developments are taking place in the field of non-destructive, image-analysis -based phenotyping that allow for a characterization of plant traits in high-throughput. During the last decade, ‘the field of image-based phenotyping has broadened its focus from the initial characterization of single-plant traits in controlled conditions towards ‘real-life’ applications of robust field techniques in plant plots and canopies. An important component of successful phenotyping approaches is the holistic characterization of plant performance that can be achieved with several methodologies, ranging from multispectral image analyses via thermographical analyses to growth measurements, also taking root phenotypes into account.
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Suspension Culture of Plant Cells Under Phototrophic Conditions - Industrial Scale Suspension Culture of Living Cells - Niederkrüger - Wiley Online Library

Suspension Culture of Plant Cells Under Phototrophic Conditions - Industrial Scale Suspension Culture of Living Cells - Niederkrüger - Wiley Online Library | plant cell genetics | Scoop.it
The use of plant (cell) suspension cultures in phototrophic mode on an industrially relevant scale is limited to two systems worldwide. These are the moss-based BryoTechnology™ and the duckweed-based SYNLEX™ production systems being developed by greenovation biotech GmbH and Synthon, respectively. Both production platforms make use of intact plants, rather than isolated cells, which are grown in simple salt media to manufacture recombinant, high value pharmaceutical proteins. They exploit unique features of plants like homogenous N-glycosylation, absolute genetic stability, and pathogen safety to create biopharmaceuticals of outstanding quality. On the equipment side, both processes build on single use, disposable solutions bringing about high flexibility and regulatory safety. Despite sharing all of the above-mentioned aspects, these two systems differ remarkably in several details. Physcomitrella patens, the moss behind BryoTechnology™, is unique in its potential for genetic engineering. Resembling yeast systems in that aspect, it allows for rapid generation of product-tailored production platforms. The SYNLEX™-system on the other hand, with Lemna minor as producing organism has a very basic process setup with few controls and good scale-up potential. This chapter discusses strengths and weaknesses of both systems side-by-side, describes their current technological development status, and gives a short future outlook.
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Rapid generation and analysis of expressed sequence tags to uncovering inflorescence secondary metabolism of Bougainvillea spectabilis ‘Speciosas’ by pyrosequencing - Online First - Springer

Rapid generation and analysis of expressed sequence tags to uncovering inflorescence secondary metabolism of Bougainvillea spectabilis ‘Speciosas’ by pyrosequencing - Online First - Springer | plant cell genetics | Scoop.it
Bougainvilleas, are one of the unique plant families with an unusual class of pigments, known as betalains replaced the more common anthocyanins. However, little is known on the molecular mechanism on the mutual exclusion of anthocyanins and betalains. In order to explore the unique phenomena in Bougainvilleas, we used open inflorescences of B. spectabilis ‘Speciosas’ for transcriptome analysis by pyrosequencing, which is the first attempt to obtain the transcriptome of this specific plant. In this study, we obtained 111.9 M raw data, after assembling, 17,728 unigenes sequence with average length of 607 bp long were available, the annotation including Gene Ontology, COG/KOG and associated Kyoto Encyclopedia of Genes and Genomics (KEGG) pathway maps were conducted. Important genes involved in flavonoid/Betalains/anthocyanins motablisms were identified including FLS/F3H, UGT, DFR, DODA, anthocyanidin reductase and Anthocyanidin 3-O-glucosyltransferase, as well as some transcriptional factors (Myb, YABBY, MADS-box, F-box, WD-40 and bHLH) in this study. The obtained unigenes which will provide a database for discovering genes involved in secondary metabolic synthesis pathway. The discovered genes can be used for future bioengineering of various secondary metabolites for health improvement, pigments, medicine and agricultural production, etc. Specially, these genes such as DFR, anthocyanidin reductase and anthocyanidin 3-O-glucosyltransferase, were detected in betalain-synthesizing plants, which is exciting for researchers. Furthermore, a total of 877 simple sequence repeat motifs (SSRs) were identified, among the perfect SSRs, the most abundant repeat units were mononucleotide repeats (61 %) with (A/T)n and the second one is tri-nucleotide repeats (24 %). The obtained EST-SSRs can be used for marker development which will be beneficial for the studies in the aspects of genetic diversity, evolution and phenotype variation of B. spectabilis ‘Speciosas’ as well as its related species.
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