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Curated by Andres Zurita
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Molecular breeding for the development of multiple disease resistance in Basmati rice

Background and aims Basmati rice grown in the Indian subcontinent is highly valued for its unique culinary qualities. Production is, however, often constrained by diseases such as bacterial blight (BB), blast and sheath blight (ShB). The present study developed Basmati rice with inbuilt resistance to BB, blast and ShB using molecular marker-assisted selection.

Methodology The rice cultivar ‘Improved Pusa Basmati 1’ (carrying the BB resistance genes xa13 and Xa21) was used as the recurrent parent and cultivar ‘Tetep’ (carrying the blast resistance gene Pi54 and ShB resistance quality trait loci (QTL), qSBR11-1) was the donor. Marker-assisted foreground selection was employed to identify plants possessing resistance alleles in the segregating generations along with stringent phenotypic selection for faster recovery of the recurrent parent genome (RPG) and phenome (RPP). Background analysis with molecular markers was used to estimate the recovery of RPG in improved lines.

Principal results Foreground selection coupled with stringent phenotypic selection identified plants homozygous for xa13, Xa21 and Pi54, which were advanced to BC2F5 through pedigree selection. Marker-assisted selection for qSBR11-1 in BC2F5 using flanking markers identified seven homozygous families. Background analysis revealed that RPG recovery was up to 89.5%. Screening with highly virulent isolates of BB, blast and ShB showed that the improved lines were resistant to all three diseases and were on a par with ‘Improved Pusa Basmati 1’ for yield, duration and Basmati grain quality.

Conclusions This is the first report of marker-assisted transfer of genes conferring resistance to three different diseases in rice wherein genes xa13 and Xa21 for BB resistance, Pi54 for blast resistance, and a major QTL qSBR11-1 have been combined through marker-assisted backcross breeding. In addition to offering the potential for release as cultivars, the pyramided lines will serve as useful donors of gene(s) for BB, blast and ShB in future Basmati rice breeding programmes.

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México: Científicos comprometen al gobierno a apoyar CyT - SciDev.Net

México: Científicos comprometen al gobierno a apoyar CyT - SciDev.Net | Plant Gene Seeker -PGS | Scoop.it
Comunidad científica mexicana presentó una agenda con más de cien acciones para impulsar la CyT+i y aumentar los recursos a partir de 2013.
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Genomic tillage and the harvest of fungal phytopathogens - Oliver - 2012 - New Phytologist - Wiley Online Library

Genomic tillage and the harvest of fungal phytopathogens - Oliver - 2012 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

Summary
Genome sequencing has been carried out on a small selection of major fungal ascomycete pathogens. These studies show that simple models whereby pathogens evolved from phylogenetically related saprobes by the acquisition or modification of a small number of key genes cannot be sustained.The genomes show that pathogens cannot be divided into three clearly delineated classes (biotrophs, hemibiotrophs and necrotrophs) but rather into a complex matrix of categories each with subtly different properties. It is clear that the evolution of pathogenicity is ancient, rapid and ongoing. Fungal pathogens have undergone substantial genomic rearrangements that can be appropriately described as ‘genomic tillage’. Genomic tillage underpins the evolution and expression of large families of genes – known as effectors – that manipulate and exploit metabolic and defence processes of plants so as to allow the proliferation of pathogens.

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S. Diez de Medina's comment, November 6, 2012 7:58 AM
Excelent!!! thanks for sharing it
Andres Zurita's comment, November 6, 2012 8:23 AM
You welcome Sergio! Peer surveillance is always useful ;)
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Trends in Plant Science - Gateway vectors for transformation of cereals

Summary

Until now, the availability of vectors for transgenic research in cereal crops has been rather limited. We present a novel collection of Agrobacterium tumefaciens binary T-DNA vectors compatible with Gateway recombinational cloning that facilitate the modular assembly of genes of interest together with new regulatory sequences, such as strong constitutive or endosperm-specific Brachypodium distachyon promoters. This resource aims at streamlining the creation of vectors and transgenes designed to explore gene functions in vital monocotyledonous crops.

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Pollination patterns and plant breeding systems in the Galápagos: a review

Pollination patterns and plant breeding systems in the Galápagos: a review | Plant Gene Seeker -PGS | Scoop.it

Background

Despite the importance of the Galápagos Islands for the development of central concepts in ecology and evolution, the understanding of many ecological processes in this archipelago is still very basic. One such process is pollination, which provides an important service to both plants and their pollinators. The rather modest level of knowledge on this subject has so far limited our predictive power on the consequences of the increasing threat of introduced plants and pollinators to this unique archipelago.

Scope

As a first step toward building a unified view of the state of pollination in the Galápagos, a thorough literature search was conducted on the breeding systems of the archipelago's flora and compiled all documented flower–visitor interactions. Based on 38 studies from the last 100 years, we retrieved 329 unique interactions between 123 flowering plant species (50 endemics, 39 non-endemic natives, 26 introduced and eight of unknown origin) from 41 families and 120 animal species from 13 orders. We discuss the emergent patterns and identify promising research avenues in the field.

Conclusions

Although breeding systems are known for <20 % of the flora, most species in our database were self-compatible. Moreover, the incidence of autogamy among endemics, non-endemic natives and alien species did not differ significantly, being high in all groups, which suggests that a poor pollinator fauna does not represent a constraint to the integration of new plant species into the native communities. Most interactions detected (approx. 90 %) come from a single island (most of them from Santa Cruz). Hymenopterans (mainly the endemic carpenter bee Xylocopa darwinii and ants), followed by lepidopterans, were the most important flower visitors. Dipterans were much more important flower visitors in the humid zone than in the dry zone. Bird and lizard pollination has been occasionally reported in the dry zone. Strong biases were detected in the sampling effort dedicated to different islands, time of day, focal plants and functional groups of visitors. Thus, the existing patterns need to be confronted with new and less biased data. The implementation of a community-level approach could greatly increase our understanding of pollination on the islands and our ability to predict the consequences of plant invasions for the natural ecosystems of the Galápagos.

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Dienekes' Anthropology Blog: A thousand (and ninety two) genomes

Dienekes' Anthropology Blog: A thousand (and ninety two) genomes | Plant Gene Seeker -PGS | Scoop.it
This is an open access paper describing the phase1 data of the 1000 Genomes Project. There is plenty of interest in the paper and supplement, but look at Figure S8 (left). This indicates the median shared haplotype length ...
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Iskandar Malaysia: City of the future

Iskandar Malaysia: City of the future | Plant Gene Seeker -PGS | Scoop.it
ISKANDAR Malaysia in Johor is the pilot region for a smart city model for Malaysia.THE aim of a smart city programme is to enhance the people's quality of life, and to achieve a sustainable economic and technological ecosystem that would ultimately create smart, connected and inclusive communities.

 


Via S. Diez de Medina
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NASA Maps How Nutrients Affect Plant Productivity - NASA Jet Propulsion Laboratory

NASA Maps How Nutrients Affect Plant Productivity - NASA Jet Propulsion Laboratory | Plant Gene Seeker -PGS | Scoop.it
A new analysis led by NASA's Jet Propulsion Laboratory has estimated how much the growth of plants worldwide is limited by the amount of nutrients available in their soil.

Via R K Upadhyay
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Invited perspective: bryophytes as models for understanding the evolution of sexual systems

Invited perspective: bryophytes as models for understanding the evolution of sexual systems | Plant Gene Seeker -PGS | Scoop.it
Stuart F. McDaniel and Pierre-François Perroud (2012) Invited perspective: bryophytes as models for understanding the evolution of sexual systems. The Bryologist: Vol. 115, No. 1, pp. 1-11.

One of the first life history characters that students of bryology learn is the bryophyte life cycle. Roughly half of the bryophytes have separate sexes (dioicous) and half are hermaphroditic (monoicous). This variation is important for taxonomic purposes but also has major consequences for nearly every aspect of bryophyte biology. For example, dioicous species generally reproduce less frequently than monoicous species (Longton & Schuster 1983) but harbor more genetic variation than monoicous species (Eppley et al. 2006). More broadly, however, the maintenance of both sexual systems at nearly equal frequencies in the bryophytes is quite unusual among the eukaryotes. This situation makes bryophytes an important model system for studying the evolutionary consequences of changes in sexual system.


Via Jean-Pierre Zryd
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Science key to global food future

Science key to global food future | Plant Gene Seeker -PGS | Scoop.it
SCIENCE will be the key to feeding the global population as demand for food begins to outstrip supply, the head of an international agricultural group has said.

Via CIMMYT, Int.
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Approaches towards nitrogen- and phosphorus-efficient rice

Abstract

Background and aims Food production has to increase to meet the demand of a growing population. In light of the high energy costs and increasingly scarce resources, future agricultural systems have to be more productive and more efficient in terms of inputs such as fertilizer and water. The development of rice varieties with high yield under low-nutrient conditions has therefore become a breeding priority. The rapid progress made in sequencing and molecular-marker technology is now beginning to change the way breeding is done, providing new opportunities.

Scope Nitrogen (N) and phosphorus (P) are applied to agricultural systems in large quantities and a deficiency of either nutrient leads to yield losses and triggers complex molecular and physiological responses. The underlying genes are now being identified and studied in detail, and an increasing number of quantitative trait loci (QTLs) related to N and P uptake and utilization are being reported. Here, we provide an overview of the different aspects related to N and P in rice production systems, and apply a breeder's perspective on the potential of relevant genes and pathways for breeding applications.

Main points For the development of nutrient-efficient rice, a holistic approach should be followed combining optimized fertilizer management with enhanced nutrient uptake via a vigorous root system, leading to increased grain filling and yield. Despite an increasing number of N- and P-related genes and QTLs being reported, very few are actively used in molecular breeding programmes. The complex regulation of N- and P-related pathways challenges breeders and the research community to identify large-effect genes/QTLs. For this it will be important to focus more on the analysis of tolerant genotypes rather than model plants, since tolerance pathways may employ a different set of genes.

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Barley's giant genome could breed better beer | Genome Engineering

Barley's giant genome could breed better beer | Genome Engineering | Plant Gene Seeker -PGS | Scoop.it
The International Barley Genome Sequencing Consortium (IBSC) has sequenced the barley (Hordeum vulgare L.) genome – a huge 5.3 billion bases.
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Report examines the many effects of climate change on agriculture, urges action now

Report examines the many effects of climate change on agriculture, urges action now | Plant Gene Seeker -PGS | Scoop.it
A new report from the CGIAR Research Program on Climate Change, Agriculture and Food Security calls for the need to “recalibrate” food production in the developing world.

Via Luigi Guarino
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A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers |BMC Biology |

Background
Seed plants are composed of angiosperms and gymnosperms, which diverged around 300 Mya from each other. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meager for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling.

Results
To gain insight into the macro-organization and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyze gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms out-numbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organized in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 Mya.

Conclusions
Taken altogether, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.

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Dramatic genotypic difference in, and effect of genetic crossing on, tissue culture-induced mobility of retrotransposon Tos17 in rice - Springer

Dramatic genotypic difference in, and effect of genetic crossing on, tissue culture-induced mobility of retrotransposon Tos17 in rice - Springer | Plant Gene Seeker -PGS | Scoop.it

We show for the first time that intraspecific crossing may impact mobility of the prominent endogenous retrotransposon Tos17 under tissue culture conditions in rice.
Abstract
Tos17, an endogenous copia retrotransposon of rice, is transpositionally active in tissue culture. To study whether there exists fundamental genotypic difference in the tissue culture-induced mobility of Tos17, and if so, whether the difference is under genetic and/or epigenetic control, we conducted this investigation. We show that dramatic difference in tissue culture-induced Tos17 mobility exists among different rice pure-line cultivars sharing the same maternal parent: of the three lines studied that harbor Tos17, two showed mobilization of Tos17, which accrued in proportion to subculture duration, while the third line showed total quiescence (immobility) of the element and the fourth line did not contain the element. In reciprocal F1 hybrids between Tos17-mobile and -immobile (or absence) parental lines, immobility was dominant over mobility. In reciprocal F1 hybrids between both Tos17-mobile parental lines, an additive or synergistic effect on mobility of the element was noticed. In both types of reciprocal F1 hybrids, clear difference in the extent of Tos17 mobility was noted between crossing directions. Given that all lines share the same maternal parent, this observation indicates the existence of epigenetic parent-of-origin effect. We conclude that the tissue culture-induced mobility of Tos17 in rice is under complex genetic and epigenetic control, which can be either enhanced or repressed by intraspecific genetic crossing.


Via Jean-Pierre Zryd
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Metabolic engineering of novel lignin in biomass crops - Vanholme - 2012 - New Phytologist - Wiley Online Library

Metabolic engineering of novel lignin in biomass crops - Vanholme - 2012 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it

Summary
Lignin, a phenolic polymer in the secondary wall, is the major cause of lignocellulosic biomass recalcitrance to efficient industrial processing. From an applications perspective, it is desirable that second-generation bioenergy crops have lignin that is readily degraded by chemical pretreatments but still fulfill its biological role in plants. Because plants can tolerate large variations in lignin composition, often without apparent adverse effects, substitution of some fraction of the traditional monolignols by alternative monomers through genetic engineering is a promising strategy to tailor lignin in bioenergy crops. However, successful engineering of lignin incorporating alternative monomers requires knowledge about phenolic metabolism in plants and about the coupling properties of these alternative monomers. Here, we review the current knowledge about lignin biosynthesis and the pathways towards the main phenolic classes. In addition, the minimal requirements are defined for molecules that, upon incorporation into the lignin polymer, make the latter more susceptible to biomass pretreatment. Numerous metabolites made by plants meet these requirements, and several have already been tested as monolignol substitutes in biomimetic systems. Finally, the status of detection and identification of compounds by phenolic profiling is discussed, as phenolic profiling serves in pathway elucidation and for the detection of incorporation of alternative lignin monomers.

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Advances in ethylene signalling: protein complexes at the endoplasmic reticulum membrane

The gaseous plant hormone ethylene plays critical roles in plant responses to environmental and endogenous signals that modulate growth and development. Over the past 25 years, great progress has been made in elucidating the ethylene signalling pathway. Genetic studies in Arabidopsis thaliana have identified key components of the pathway, and subcellular localization studies have shown that most of these components, other than transcription factors and protein turnover machinery, are associated with or lie within the endoplasmic reticulum (ER) membrane. The ethylene receptors are found in high-molecular-mass protein complexes and interact with the CTR1 serine/threonine protein kinase and the genetically downstream EIN2 Nramp-like protein. To more fully understand the ethylene signalling pathway, recent research has focused on examining the molecular connections between these components and how they are regulated. Here, we review recent advances and remaining gaps in our understanding of the early steps in the ethylene signalling pathway taking place at the ER.

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The Homeobox BcHOX8 Gene in Botrytis Cinerea Regulates Vegetative Growth and Morphology PLOS ONE

The Homeobox BcHOX8 Gene in Botrytis Cinerea Regulates Vegetative Growth and Morphology PLOS ONE | Plant Gene Seeker -PGS | Scoop.it

Abstract
Filamentous growth and the capacity at producing conidia are two critical aspects of most fungal life cycles, including that of many plant or animal pathogens. Here, we report on the identification of a homeobox transcription factor encoding gene that plays a role in these two particular aspects of the development of the phytopathogenic fungus Botrytis cinerea. Deletion of the BcHOX8 gene in both the B. cinerea B05-10 and T4 strains causes similar phenotypes, among which a curved, arabesque-like, hyphal growth on hydrophobic surfaces; the mutants were hence named Arabesque. Expression of the BcHOX8 gene is higher in conidia and infection cushions than in developing appressorium or mycelium. In the Arabesque mutants, colony growth rate is reduced and abnormal infection cushions are produced. Asexual reproduction is also affected with abnormal conidiophore being formed, strongly reduced conidia production and dramatic changes in conidial morphology. Finally, the mutation affects the fungus ability to efficiently colonize different host plants. Analysis of the B. cinerea genome shows that BcHOX8 is one member of a nine putative homeobox genes family. Available gene expression data suggest that these genes are functional and sequence comparisons indicate that two of them would be specific to B. cinerea and its close relative Sclerotinia sclerotiorum.

 

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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NextGen Science essay survey: Using science to address your county's problems

NextGen Science essay survey: Using science to address your county's problems | Plant Gene Seeker -PGS | Scoop.it

Young scientists!

"You've just been elected to your nation's highest office! In your inaugural address, announce the biggest challenge facing your country today and how you will use science to address it."

Submit your essay by 16 November for a chance to be featured in Science -


Via Mary Williams
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Desert farming forms bacterial communities that promote drought resistance

Desert farming forms bacterial communities that promote drought resistance | Plant Gene Seeker -PGS | Scoop.it

When there is little water available for plants to grow, their roots form alliances with soil microbes that can promote plant growth even under water-limiting conditions


Via R K Upadhyay
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Los productos naturales ¡vaya timo!: Amigos antitransgénicos: esto no es ciencia.

Los productos naturales ¡vaya timo!: Amigos antitransgénicos: esto no es ciencia. | Plant Gene Seeker -PGS | Scoop.it

Via Isabel Etayo
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Plant interaction with friendly bacteria gives pathogens their break | News from the John Innes Centre

Plant interaction with friendly bacteria gives pathogens their break | News from the John Innes Centre | Plant Gene Seeker -PGS | Scoop.it

Professor Giles Oldroyd of the John Innes Centre explains how plant roots form beneficial interactions with soil microbes. Almost all plants associate with mycorrhizal fungi to help in the uptake of nutrients such as phosphate. Some plants, particularly legumes, also associate with bacteria that ‘fix’ atmospheric nitrogen into a form the plant can use as fertiliser.


Via John Innes Centre
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Australian Wheat Exports Plunging Most in Six Years

Australian Wheat Exports Plunging Most in Six Years | Plant Gene Seeker -PGS | Scoop.it
The deepest slump in Australian
wheat shipments in six years will exacerbate the biggest
contraction in global exports in a generation after droughts
withered crops around the world.

 

Pass along - no, we're not making this stuff up - food production (and water resources) are not secure, and neither are we. Rising food prices leads to political instability and worse, yet most governments fail to support the very plant science research that's needed to maintain food production. Plant research gets a tiny fraction of the money spent on bioscience research. Governments and taxpayers must wake up to the fact that plant science needs more support, otherwise diseases of old age will be the least of our concerns.


Via CIMMYT, Int., Mary Williams
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Recalibrating Food Production in the Developing World: Global Warming Will Change More Than Just the Climate

Recalibrating Food Production in the Developing World: Global Warming Will Change More Than Just the Climate | Plant Gene Seeker -PGS | Scoop.it

An analysis of the effects of climate change on 22 critical agricultural commodities and three important natural resources in the developing world reveals a number of cross-cutting themes: The world’s agricultural systems face an uphill struggle in feeding a projected nine to ten billion people by 2050. Climate change introduces a significant hurdle in this struggle. - Securing and maintaining necessary levels of calories, protein and nutrients for populations around the world will be an exceptional challenge. - Recalibrating agriculture in the face of climate change is more than planting crops that can tolerate warmer weather. Some commodities, for example, can grow in warm weather but cannot resist the insects and diseases whose prevalence will increase. Others can tolerate a lack of water but not the sporadic flooding that occurs with more common weather extremes. - Even as global deforestation continues, trees continue to be valued as a provider of agricultural commodities like nuts and fruit; as a mitigating resource that removes carbon dioxide from the atmosphere; and also as a staple of adaptation—trees help stabilize soil erosion, better regulate water, as well as provide shade, firewood and fodder. - Production of the most common commodity staples—wheat, maize and rice—will be challenged by new weather patterns. Adjustments in production, replacement with commodities that can tolerate the new conditions in different regions, and innovations in technology are key elements of adaptation. - Raising livestock and catching fish and other aquatic products—two of the more common sources of protein—will also be challenged by a new climate. In some areas, different plants, breeds and species can provide substitutions, but in others, adaptation is critical. - This recalibration of agriculture will eventually extend beyond what is grown and raised. The world’s many cultures must adapt to the changing dinner menu forced upon them due to climate change.

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European programme places renewed emphasis on research and innovation

European programme places renewed emphasis on research and innovation | Plant Gene Seeker -PGS | Scoop.it
The European Technology Platform (ETP) ‘Food for Life’ yesterday launched its new Strategic Research & Innovation Agenda (SRIA), which focuses upon improving food safety standards.
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