Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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PLOS Genetics: Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis thaliana

PLOS Genetics: Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis thaliana | Plant Gene Seeker -PGS | Scoop.it
PLOS Genetics is an open-access
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PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture.

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Dynamic Transcriptomic Profiles between Tomato and a Wild Relative Reflect Distinct Developmental Architectures

Dynamic Transcriptomic Profiles between Tomato and a Wild Relative Reflect Distinct Developmental Architectures | Plant Gene Seeker -PGS | Scoop.it
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Developmental differences between species commonly result from changes in the tissue-specific expression of genes. Clustering algorithms are a powerful means to detect coexpression across tissues in single species but are not often applied to multidimensional data sets, such as gene expression across tissues in multiple species. As next-generation sequencing approaches enable interspecific analyses, methods to visualize and explore such data sets will be required. Here, we analyze a data set comprising gene expression profiles across six different tissue types in domesticated tomato (Solanum lycopersicum) and a wild relative (Solanum pennellii). We find that self-organizing maps are a useful means to analyze interspecies data, as orthologs can be assigned to independent levels of a “super self-organizing map.” We compare various clustering approaches using a principal component analysis in which the expression of orthologous pairs is indicated by two points. We leverage the expression profile differences between orthologs to look at tissue-specific changes in gene expression between species. Clustering based on expression differences between species (rather than absolute expression profiles) yields groups of genes with large tissue-by-species interactions. The changes in expression profiles of genes we observe reflect differences in developmental architecture, such as changes in meristematic activity between S. lycopersicum and S. pennellii. Together, our results offer a suite of data-exploration methods that will be important to visualize and make biological sense of next-generation sequencing experiments designed explicitly to discover tissue-by-species interactions in gene expression data.


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PLOS ONE: QTL Mapping of Flowering and Fruiting Traits in Olive

PLOS ONE: QTL Mapping of Flowering and Fruiting Traits in Olive | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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One of the challenge fruit growers are facing is to balance between tree production and vegetative growth from year to year. To investigate the existence of genetic determinism for reproductive behaviour in olive tree, we studied an olive segregating population derived from a cross between ‘Olivière’ and ‘Arbequina’ cultivars. Our strategy was based on (i) an annual assessment of individual trees yield, and (ii) a decomposition of adult growth units at the crown periphery into quantitative variables related to both flowering and fruiting process in relation to their growth and branching. Genetic models, including the year, genotype effects and their interactions, were built with variance function and correlation structure of residuals when necessary. Among the progeny, trees were either ‘ON’ or ‘OFF’ for a given year and patterns of regular vs. irregular bearing were revealed. Genotype effect was significant on yield but not for flowering traits at growth unit (GU) scale, whereas the interaction between genotype and year was significant for both traits. A strong genetic effect was found for all fruiting traits without interaction with the year. Based on the new constructed genetic map, QTLs with small effects were detected, revealing multigenic control of the studied traits. Many were associated to alleles from ‘Arbequina’. Genetic correlations were found between Yield and Fruit set at GU scale suggesting a common genetic control, even though QTL co-localisations were in spe`cific years only. Most QTL were associated to flowering traits in specific years, even though reproductive traits at GU scale did not capture the bearing status of the trees in a given year. Results were also interpreted with respect to ontogenetic changes of growth and branching, and an alternative sampling strategy was proposed for capturing tree fruiting behaviour. Regular bearing progenies were identified and could constitute innovative material for selection programs.

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Honey constituents up-regulate detoxification and immunity genes in the western honey bee Apis mellifera

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As a managed pollinator, the honey bee Apis mellifera is critical to the American agricultural enterprise. Recent colony losses have thus raised concerns; possible explanations for bee decline include nutritional deficiencies and exposures to pesticides and pathogens. We determined that constituents found in honey, including p-coumaric acid, pinocembrin, and pinobanksin 5-methyl ether, specifically induce detoxification genes. These inducers are primarily found not in nectar but in pollen in the case of p-coumaric acid (a monomer of sporopollenin, the principal constituent of pollen cell walls) and propolis, a resinous material gathered and processed by bees to line wax cells. RNA-seq analysis (massively parallel RNA sequencing) revealed that p-coumaric acid specifically up-regulates all classes of detoxification genes as well as select antimicrobial peptide genes. This up-regulation has functional significance in that that adding p-coumaric acid to a diet of sucrose increases midgut metabolism of coumaphos, a widely used in-hive acaricide, by ∼60%. As a major component of pollen grains, p-coumaric acid is ubiquitous in the natural diet of honey bees and may function as a nutraceutical regulating immune and detoxification processes. The widespread apicultural use of honey substitutes, including high-fructose corn syrup, may thus compromise the ability of honey bees to cope with pesticides and pathogens and contribute to colony losses.

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Dealing with drought - Research Highlights - RIKEN RESEARCH

Dealing with drought - Research Highlights - RIKEN RESEARCH | Plant Gene Seeker -PGS | Scoop.it
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Today’s crops are subjected to all kinds of stresses. Drought and high salinity are particularly damaging to plant growth and development, limiting crop productivity across the world. Developing crop varieties that can adapt to such stresses has therefore never been more important. A team led by Lam-Son Tran at the RIKEN Center for Sustainable Resource Science has now characterized a key set of genes that transmit signals relating to drought and salinity stresses in the model plant Arabidopsis thaliana.

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Abiotic Stress - Plant Responses and Applications in Agriculture | InTechOpen

Abiotic Stress - Plant Responses and Applications in Agriculture | InTechOpen | Plant Gene Seeker -PGS | Scoop.it
Abiotic Stress - Plant Responses and Applications in Agriculture. Edited by: Kourosh Vahdati and Charles Leslie. ISBN 978-953-51-1024-8, Published 2013-03-13

 

"This book is not intended to cover all known abiotic stresses or every possible technique used to understand plant tolerance but, instead, to describe some of the widely used approaches to addressing such major abiotic stresses as drought, salinity, extreme temperature, cold, light, calcareous soils, excessive irradiation, ozone, ultraviolet radiation, and flooding, and to describe major or newly emerging techniques employed in understanding and improving plant tolerance. Among the strategies for plant stress survival, examples of both avoidance and tolerance are presented in detail and comprehensive case studies of progress and directions in several agricultural crops such as apple, walnut, grape and wheat are included."

  


Via Plant Breeding and Genomics News
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OPEN ACCESS BOOK, GREAT!

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Green Revolution research saved an estimated 18 to 27 million hectares from being brought into agricultural production

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Abstract

New estimates of the impacts of germplasm improvement in the major staple crops between 1965 and 2004 on global land-cover change are presented, based on simulations carried out using a global economic model (Global Trade Analysis Project Agro-Ecological Zone), a multicommodity, multiregional computable general equilibrium model linked to a global spatially explicit database on land use. We estimate the impact of removing the gains in cereal productivity attributed to the widespread adoption of improved varieties in developing countries. Here, several different effects—higher yields, lower prices, higher land rents, and trade effects—have been incorporated in a single model of the impact of Green Revolution research (and subsequent advances in yields from crop germplasm improvement) on land-cover change. Our results generally support the Borlaug hypothesis that increases in cereal yields as a result of widespread adoption of improved crop germplasm have saved natural ecosystems from being converted to agriculture. However, this relationship is complex, and the net effect is of a much smaller magnitude than Borlaug proposed. We estimate that the total crop area in 2004 would have been between 17.9 and 26.7 million hectares larger in a world that had not benefited from crop germplasm improvement since 1965. Of these hectares, 12.0–17.7 million would have been in developing countries, displacing pastures and resulting in an estimated 2 million hectares of additional deforestation. However, the negative impacts of higher food prices on poverty and hunger under this scenario would likely have dwarfed the welfare effects of agricultural expansion.

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Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars

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Abstract

Domesticated crops experience strong human-mediated selection aimed at developing high-yielding varieties adapted to local conditions. To detect regions of the wheat genome subject to selection during improvement, we developed a high-throughput array to interrogate 9,000 gene-associated single-nucleotide polymorphisms (SNP) in a worldwide sample of 2,994 accessions of hexaploid wheat including landraces and modern cultivars. Using a SNP-based diversity map we characterized the impact of crop improvement on genomic and geographic patterns of genetic diversity. We found evidence of a small population bottleneck and extensive use of ancestral variation often traceable to founders of cultivars from diverse geographic regions. Analyzing genetic differentiation among populations and the extent of haplotype sharing, we identified allelic variants subjected to selection during improvement. Selective sweeps were found around genes involved in the regulation of flowering time and phenology. An introgression of a wild relative-derived gene conferring resistance to a fungal pathogen was detected by haplotype-based analysis. Comparing selective sweeps identified in different populations, we show that selection likely acts on distinct targets or multiple functionally equivalent alleles in different portions of the geographic range of wheat. The majority of the selected alleles were present at low frequency in local populations, suggesting either weak selection pressure or temporal variation in the targets of directional selection during breeding probably associated with changing agricultural practices or environmental conditions. The developed SNP chip and map of genetic variation provide a resource for advancing wheat breeding and supporting future population genomic and genome-wide association studies in wheat.

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Architecture and evolution of a minute plant genome : Nature

Architecture and evolution of a minute plant genome : Nature | Plant Gene Seeker -PGS | Scoop.it
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It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

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Spanish National Research Council to grow transgenic wheat for celiacs - Materia (2013)

Slightly edited machine translation: 

 

Scientists of the agency are seeking permission to cultivate a GM wheat suitable for coeliacs on a plot of Córdoba. The harvest, half a ton of grain serve to develop and carry out a clinical trial with patients. Researchers believe that the cereal could reach the market within five years... 

 

CSIC scientists have requested permission to plant there, on a plot of 1,000 square meters, wheat whose genes have been modified so that it can be consumed by people with celiac disease, a currently incurable disease of unknown origin that affects about 1% of the world population.

 

When people with celiac disease consume gluten - a protein found in wheat, barley and rye - their body's defenses react and damage the intestine. As a result, there are diarrhea, vomiting and unexplained weight loss until it is given to the cause. Their only option now is to eat gluten-free foods that are more expensive. Celiacs spent each year 1,600 euros more on food than the other people. In the U.S. alone, the market for gluten-free foods moved 4,200 billion in 2012.

 

To remedy this, a team from the Institute of Sustainable Agriculture Cordoba, led by biologist Francisco Barro, has since 2004 investigating transgenic wheat varieties without gluten. In 2011, researchers announced that they had obtained varieties capable of producing in celiacs "a reaction up to 95% less toxic than natural wheat", according to laboratory results.

 

Now, Barro has asked the National Biosafety Commission for a permit to grow wheat for the first time outdoors. His goal is to harvest half a ton of grain to make crackers that will be used to conduct a clinical trial with celiacs. The test, if all goes as planned, will be held for three months with between 30 and 60 patients, who will be able to taste wheat again, until now forbidden to them, in a trial coordinated by medical Queen Sofía Hospital. The biologist believes his cereal could reach the market within five years.

 

Barro is aware that its GM wheat "has no chance in Europe", the continent most reluctant to genetically modified organisms. Five countries - USA, Canada, Argentina, Brazil and India - grabbing global GM production, with 152 million hectares.

 

Europe only allows the cultivation of two GM crops: modified corn by the U.S. company Monsanto to be resistant to insect infestation and a starch potato from German chemicals company BASF for paper and textile industries. However, following a hypocritical policy, Brussels does support importing about 40 GM products from other countries.

 

The CSIC has sold the license to exploit the patent for its GM wheat, to a British company, Plant Bioscience Limited, based in Norwich. "Possibly, their strategy will be to cultivate our wheat in the U.S., Argentina and China, and they will sell the flour to Spain for the price of gold", speculates Barro.

 

According to preliminary studies, "in the worst case, a celiac can [at least] eat every day three slices of bread made from the modified wheat". Barro team has organized a blind tasting with 11 tasters, who were unable to distinguish the normal wheat bread from the one baked with transgenic cereals.

 

To prevent the escape of genetically modified wheat from the plot... CSIC scientists impose a safety distance of 200 meters to any other plot with cereal. Barro considered very unlikely that there is a leak, because "wheat pollen is heavy" and cannot travel long distances on the wind. 

 

Wheat suitable for coeliacs has its genes modified to suppress the proteins responsible for the allergic response of celiacs, gliadins. "It would be surprising that this feature gave the GM wheat a competitive advantage over the normal wheat [if it escapes]," says Barro... "There are anti-GMO environmentalists, who are celiacs, who called me to try our wheat," says Barro... 

 

Original article in Spanish: 
http://esmateria.com/2013/05/09/el-csic-pide-cultivar-trigo-transgenico-para-celiacos/
 


Via Alexander J. Stein
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AckerbauHalle's curator insight, May 12, 2013 12:50 PM

In Spanien gibt es einen Versuch mit Weizen, der auch für Menschen mit Zöliaki geeignet sein soll. 

sonia ramos's curator insight, May 13, 2013 2:20 AM

Hay mucho trabajo que hacer sobre los trangénicos, unos debemos acercarlos más a la población explicando los controles y la legislación, las pruebas y el tiempo de experimientación sobre su efectos y, otros, abriendo  perspectivas e informándose.

 

Este tema lleva mucha desinformación detrás y se están perdidendo oportunidades de mejora de calidad de vida y salud en el mundo por quedarse sólo en la superficie de este campo de investigación.

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Tiny genes orchestrate plant shape - Research Highlights - RIKEN RESEARCH

Tiny genes orchestrate plant shape - Research Highlights - RIKEN RESEARCH | Plant Gene Seeker -PGS | Scoop.it
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A subset of short genes hidden inside plant genomes may be important in setting plant growth patterns


Although thousands of entire genomes have been sequenced, our understanding of their detailed workings remains far from complete. Researchers continue to find new genes, determine their function, and map how they interact to build organisms. Working on the well-studied model plant Arabidopsis thaliana, Kousuke Hanada and colleagues from the RIKEN Plant Science Center have revealed that a subset of tiny genes scattered through the genome may control the patterning of development1
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The psychology of GMO - Martin (2013) - Current Biology

The psychology of GMO - Martin (2013) - Current Biology | Plant Gene Seeker -PGS | Scoop.it

Despite receiving the seal of approval from scientists, genetically modified food continues to be unpalatable in many parts of the world. As Cyrus Martin reports, a combination of factors, including economics and culture, may help to explain the differences... 

 

Why the difference in the attitude? Keith Lindsey, a plant scientist at Durham University who sits on a panel charged with advising the British government on GMO, points out that the initial reception of GM food in Europe was actually positive, but the relationship quickly soured due to a combination of suspect science and media sensationalism...

 

“Originally in the UK, in the mid 90s, the first GM product (Flavr Savr tomato) was very popular in the UK and elsewhere — I bought some from the local supermarket, and it sold very well at the time. The turning point was later, with some flawed experiments on GM potatoes, not peer-reviewed but seized on by the popular press, which in turn was seized on by environmentalist campaigners.”

 

Indeed, this same scenario seems to have played out in the case of the recent Séralini study as the panel of experts appointed by the EFSA have discredited the paper, citing a combination of small sample sizes and inadequate statistics. Unfortunately for proponents of GM food, reporting on the EFSA findings in the popular media has been scant, in contrast to when the story first broke...

 

The failure of Calgene was followed by a string of successes with GM crops engineered not to improve the quality of the product but to increase yields and lower costs of production. Chief among these developments was the creation of herbicide- and pest-resistant plants... Such crops are planted extensively in the US, and a global survey reveals that they have also been embraced next door in Canada and in certain South American countries. However, as noted above, GM crops are scarcely planted in Europe. [AS: But they are imported at a large scale.] 

 

If the full history of man’s relationship with food is considered, a reasonable question to ask is whether it is rational for the consumer to put GM food in a different category than traditionally cultivated crops. As is clear in the case of the teosinte to maize transformation, our crops have undergone extensive genetic modification over the millennia, long before modern genetic tools emerged. But there seems to have been a line crossed in the consumer’s mind when it comes to transgenic plants, and the media and environmental groups have certainly helped fan these embers of doubt.

 

But other scientists close to the GM debate feel that, at least in Europe, there may be other mitigating factors — the economy for instance. Hanspeter Naegeli, a toxicology expert who sits on a GM advisory panel for the EFSA, says, “since the end of WWII, there has been no major economic, financial or political crisis in Western Europe and in these countries we have a very high quality of life with prosperity and a well implemented welfare system. The cost of food declined enormously when compared to the overall costs of living such that people are not dependent on a cheap agricultural production and can afford to buy more expensive products (i.e. organic food).” 

 

Coupled to a favourable economic climate in which the consumer can afford to turn their nose up at a genetically modified potato, Naegeli senses an anti-big business current running through Europe, explaining, “there is also a negative attitude against large multinational companies. The economies of Western European countries are traditionally built upon small and medium-sized enterprises and larger international companies are considered suspicious.” Ironically, Naegeli thinks that the stranglehold that big business enjoys is also a product of the reforms environmentalists lobbied for, explaining that, “because of the extensive experimental testing required for approval, GM crops are mainly a domain of such large multinationals.” ... 

 

As with any technology, at some point there has to be a cost/benefit analysis done. While all of the food safety scares surrounding GM food continue to be debunked as fast as they materialize, there are no doubt potential risks that are not yet fully understood, as can be seen in the ecology aspect of the debate. And there is nothing to say that new varieties of GM food could, in principle, potentially be harmful. On the other side of the ledger, however, we have the enormous challenge of feeding the world’s population, which is rapidly growing on a planet with finite resources. Of course, malnourishment has many causes, including local politics and war, but agricultural technology will certainly factor importantly.

 

And GM food has lived up to its promise of providing increased yields with less pesticide use and at a lower cost to the consumer. Not only this, but genetic engineering has the potential to provide much needed micronutrients (i.e., vitamins) to the malnourished of the world. A case in point is the recent development of an engineered form of rice that produces a precursor of vitamin A, dubbed ‘golden rice’. This remarkable and easily implementable technology has the potential to mitigate hundreds of thousands of cases of blindness in the developing world, and yet it remains shelved due to unsubstantiated health concerns.

 

Many western consumers can afford to stock their refrigerators with organic produce, but can the rest of the world? Do the potential risks really trump malnourishment and starvation? While the interested parties continue to debate, science marches on. On the horizon are GM crops that can grow in inhospitable corners of the earth, such as the dry and salty environs. And we are now seeing the application of GM technology to animals, such as salmon engineered to reach market weight more quickly through the expression of genes encoding growth hormones. Whether these technologies are taken up or left to gather dust on the shelf will likely depend on the ability of scientists and the government to make a convincing case to the public. If they fail, we potentially handcuff ourselves and will be forced to rely on 20th century technology to solve 21st century problems.

 

 

 

 

 

 


Via Alexander J. Stein, Jennifer Mach
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AckerbauHalle's curator insight, May 7, 2013 11:12 PM

Zur Psychologie der Ablehnung von GVOs. EIn Beitrag, der noch einmal tief in die Historie der ersten Produkte geht und versucht die Entwicklung der letzten  Jahrzehnte zu erklären. 

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BTI scientist co-leads kiwifruit genome sequencing project | BTI

BTI scientist co-leads kiwifruit genome sequencing project | BTI | Plant Gene Seeker -PGS | Scoop.it
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An international team, led by Dr. Zhangjun Fei at the Boyce Thompson Institute for Plant Research, Dr. Yongsheng Liu at Hefei University of Technology and Dr. Hongwen Huang at South China Botanical Garden, has sequenced and assembled a draft genome of kiwifruit (Actinidia chinensis). A heterozygous diploid Chinese kiwifruit variety, called Hongyang, was used to generate the draft genome sequence, which is accessible at the online Kiwifruit Genome Database (http://bioinfo.bti.cornell.edu/kiwi).

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Plant-Plant Interactions, the newest Teaching Tool online

Plant-Plant Interactions, the newest Teaching Tool online | Plant Gene Seeker -PGS | Scoop.it

Online today, the newest Teaching Tool in Plant Biology, "Plant-Plant Interactions", by Ariel Novoplansky and Mary Williams. It's all about how plants sense and respond to their neighbors. Subscription to Plant Cell required. Slides, lecture notes and teaching guide too!
http://www.plantcell.org/site/teachingtools/TTPB25.xhtml


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Mahani Mohamad's curator insight, June 2, 2013 12:35 PM

to be shared with Jr.

Happy Updates's comment, June 3, 2013 12:55 AM
nice share Mary Williams http://icareeradvice.com/
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Plant Cell: Plant Immune Responses Against Viruses: How Does a Virus Cause Disease?

Plant Cell: Plant Immune Responses Against Viruses: How Does a Virus Cause Disease? | Plant Gene Seeker -PGS | Scoop.it

New review article in Plant Cell.

"Recently, significant progress has been made in understanding RNA silencing and how viruses counter this apparently ubiquitous antiviral defense. In addition, plants also induce hypersensitive and systemic acquired resistance responses, which together limit the virus to infected cells and impart resistance to the noninfected tissues."


Via Mary Williams
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Open Access pdf

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María Serrano's curator insight, June 24, 2014 12:30 PM
Respuesta inmune de las plantas frente a los virus.
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PLOS ONE: Going Beyond the Millennium Ecosystem Assessment: An Index System of Human Dependence on Ecosystem Services

PLOS ONE: Going Beyond the Millennium Ecosystem Assessment: An Index System of Human Dependence on Ecosystem Services | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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The Millennium Ecosystem Assessment (MA) estimated that two thirds of ecosystem services on the earth have degraded or are in decline due to the unprecedented scale of human activities during recent decades. These changes will have tremendous consequences for human well-being, and offer both risks and opportunities for a wide range of stakeholders. Yet these risks and opportunities have not been well managed due in part to the lack of quantitative understanding of human dependence on ecosystem services. Here, we propose an index of dependence on ecosystem services (IDES) system to quantify human dependence on ecosystem services. We demonstrate the construction of the IDES system using household survey data. We show that the overall index and sub-indices can reflect the general pattern of households' dependences on ecosystem services, and their variations across time, space, and different forms of capital (i.e., natural, human, financial, manufactured, and social capitals). We support the proposition that the poor are more dependent on ecosystem services and further generalize this proposition by arguing that those disadvantaged groups who possess low levels of any form of capital except for natural capital are more dependent on ecosystem services than those with greater control of capital. The higher value of the overall IDES or sub-index represents the higher dependence on the corresponding ecosystem services, and thus the higher vulnerability to the degradation or decline of corresponding ecosystem services. The IDES system improves our understanding of human dependence on ecosystem services. It also provides insights into strategies for alleviating poverty, for targeting priority groups of conservation programs, and for managing risks and opportunities due to changes of ecosystem services at multiple scales.

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PLOS Pathogens: Plant Virus Ecology

PLOS Pathogens: Plant Virus Ecology | Plant Gene Seeker -PGS | Scoop.it

Viruses have generally been studied either as disease-causing infectious agents that have a negative impact on the host (most eukaryote-infecting viruses), or as tools for molecular biology (especially bacteria-infecting viruses, or phage). Virus ecology looks at the more complex issues of virus-host-environment interactions. For plant viruses this includes studies of plant virus biodiversity, including viruses sampled directly from plants and from a variety of other environments; how plant viruses impact species invasion; interactions between plants, viruses and insects; the large number of persistent viruses in plants that may have epigenetic effects; and viruses that provide a clear benefit to their plant hosts (mutualists). Plants in a non-agricultural setting interact with many other living entities such as animals, insects, and other plants, as well as their physical environment. Wild plants are almost always colonized by a number of microbes, including fungi, bacteria and viruses. Viruses may impact any of these interactions [1].


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The Norway spruce genome sequence and conifer genome evolution - Nature

The Norway spruce genome sequence and conifer genome evolution - Nature | Plant Gene Seeker -PGS | Scoop.it

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.


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PLOS ONE: Bioarchaeological Insights into the Process of Domestication of Grapevine (Vitis vinifera L.) during Roman Times in Southern France

PLOS ONE: Bioarchaeological Insights into the Process of Domestication of Grapevine (Vitis vinifera L.) during Roman Times in Southern France | Plant Gene Seeker -PGS | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
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Abstract

Grapevine (Vitis vinifera), one of the most important fruit species in the Classical Mediterranean world, is thought to have been domesticated first in South-Western Asia, during the Neolithic. However, the domestication process remains largely unknown. Crucial unanswered questions concern the duration of the process (rapid or slow?) and the related geographical area (single or multiple-origins?). Seeds from domesticated grapevine and from its wild ancestor are reported to differ according to shape. Our work aims, first, to confirm this difference and secondly to identify the extent of domestication in the grapes cultivated by Romans in Southern France during the period 50 BCE–500 CE. We had the opportunity to analyze uncharred waterlogged grape pips from 17 archaeological sites. Based on an extended reference sample of modern wild grapevines and cultivars our work shows that both subspecies can be discriminated using simple measurements. The elongation gradient of the pip’s body and stalk may be regarded as an indicator of the strength of the selection pressures undergone by domesticated grapes. Grapevines cultivated during the Roman period included a mix of morphotypes comprising wild, intermediate and moderately selected domesticated forms. Our data point to a relative shift towards more selected types during the Roman period. Domestication of the grapevine appears to have been a slow process. This could result from the recurrent incorporation into cultivation of plants originating from sexual reproduction, when grape cultivation essentially relies on vegetative propagation

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Agricultural Innovation to Protect the Environment Special Feature

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A Special section of PNAS in Agricultural innovation and its interaction with Environmental issues.


 

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JIntegrPlantBiol: The Plant Vascular System: Evolution, Development and Functions (OA)

JIntegrPlantBiol: The Plant Vascular System: Evolution, Development and Functions (OA) | Plant Gene Seeker -PGS | Scoop.it

Sixty seven pages, twenty seven figures, but still very readable. If you ever teach about transport or homeostasis, add this comprehensive update to your folder.

 

As the title indicates, this big review pulls together the latest information on the evolution, development and functions of the plant vascular system (including its role as an effective long-distance communication system).


Via Mary Williams
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Rescooped by Andres Zurita from Plant Breeding and Genomics News
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Online Course- Plant Breeding for Drought Tolerance

Online Course- Plant Breeding for Drought Tolerance | Plant Gene Seeker -PGS | Scoop.it

Colorado State University will offer a one-credit online course in Plant Breeding for Drought Tolerance August 26 to December 13, 2013. Course instructor is Dr. Patrick Byrne, Department of Soil and Crop Sciences.

TARGET AUDIENCE

This distance course is targeted to graduate students in the plant sciences, as well as to professionals in the public and private sectors who want to increase their knowledge in this area. It will provide one transferable graduate-level credit.

CONTENT

The course will focus on plant breeding strategies and practices directed toward improving plant performance under drought stress. Concepts for this intensive, one-credit graduate level course include:
• Analyzing the target environment 
• Understanding plant response to drought stress and plant adaptation strategies 
• Using wild species and landraces as sources of drought tolerance 
• Determining which phenotypic traits to use in selection practices 
• Detecting marker-trait associations for relevant traits 
• Understanding transgenic approaches to drought tolerance 
• Learning from successful examples of improving drought tolerance in a variety of crops

 

The 15-week curriculum is divided into 15 lessons. Each lesson's content will be delivered via a voice-over PowerPoint presentation, a video, a reading assignment, or combinations of these media. Some lessons will require student participation in an online discussion, completion of an online quiz, or submission of a homework assignment. The compiled homework assignments will comprise a portfolio of documents describing an analysis and breeding strategy for a specific crop and environment. There will be a comprehensive final exam administered during the week of December 16.

PREREQUISITES

Participants should have a basic understanding of genetics, plant breeding, and plant physiology. Prior to the beginning of the course, students will review online material on these topics to provide a common background in breeding and physiology concepts.

PROGRAM COSTS AND REQUIREMENTS

The cost of student tuition is US $549 plus a $20 technology fee. Word processing, spreadsheet, and presentation software (e.g., Microsoft Word, Excel, and PowerPoint) is required, as is Adobe Reader. Students are required to have access to a computer and Internet access that meet the general CSU recommendations.

 


Via Plant Breeding and Genomics News
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Macoto Murayama’s Intricate Blueprints of Flowers

Macoto Murayama’s Intricate Blueprints of Flowers | Plant Gene Seeker -PGS | Scoop.it
The Japanese artist depicts blossoms from various plant species in fastidious detail

Via Meristemi
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Impressive!

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New Phytol. (OA) Emerging trends in strigolactone research

New Phytol. (OA) Emerging trends in strigolactone research | Plant Gene Seeker -PGS | Scoop.it

Via Mary Williams
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Fine-tuning plant growth - Research Highlights - RIKEN RESEARCH

Fine-tuning plant growth - Research Highlights - RIKEN RESEARCH | Plant Gene Seeker -PGS | Scoop.it

Figure 1: Mutant rice plants without the CYP714B1 andCYP714B2 genes (right) show enhanced uppermost node lengths, indicating that these genes are negative regulators of growth.

Andres Zurita's insight:

Finding the missing genes in a hormone-biosynthesis pathway hints at subtle control of growth in rice


The plant hormones known as gibberellins (GAs) are growth promoters that are involved in a wide range of processes from seed germination to flower development. The details of the biosynthesis of GAs, however, have yet to be fully clarified. Hiroshi Magome and colleagues of the Gene Discovery Research Group at the RIKEN Center for Sustainable Resource Science have now identified genes for two ‘cytochrome P450’ enzymes involved in GA biosynthesis in rice1. 1. Magome, H., Nomura, T., Hanada, A., Takeda-Kamiya, N., Ohnishi, T., Shinma, Y., Katsumata, T., Kawaide, H., Kamiya, Y. & Yamaguchi, S. CYP714B1 and CYP714B2 encode gibberellin 13-oxidases that reduce gibberellin activity in rice. Proceedings of the National Academy of Sciences USA 110, 1947–1952 (2013).
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