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Scientists develop 200 GM crops, await govt nod for trials - Times of India (2013)

Scientists develop 200 GM crops, await govt nod for trials - Times of India (2013) | Plant Gene Seeker -PGS | Scoop.it

Do you think only 'Monsanto' (or any multi-national seed company) has the capacity to develop transgenic crops? The answer is a clear 'no'. Indian scientists, working with public sector research institutions and universities, too have developed many genetically engineered varieties which, in fact, could not move beyond lab or 'restricted' trials... 

Indian scientists have over the years developed more than 200 genetically modified (GM) varieties of as many as 15 crops including cotton, brinjal, castor, groundnut, mustard, papaya, potato, rice, rubber, sugarcane, wheat and tomato. These varieties... have all the traits — resistance to insect, fungal, drought and virus — which may bring them in the league of Bt cotton by increasing productivity and export earnings. 

Indigenous transgenic varieties include a high salt-tolerant rice which can grow in salty water near coast. This variety is developed using genes of mangrove. Similarly, Indian scientists have developed a tomato variety having shelf life of over 50 days. The farmers will, however, reap the benefit of these findings only when government allows the scientists to go for extensive field trials and eventually for commercial production... 

 

A green signal to commercial production of such crops will affect the Indian farmers due to monopolistic control of seed business by multi-national companies (MNCs). "The solution to this problem is to encourage competition among the GM seed companies and even more importantly to have mission-mode programmes for the development of genetically modified seeds in the public sector", said N K Singh, professor at National Research Centre on Plant Biotechnology... "The Seed Act and the Monopoly and Restrictive Trade Practices Act should be used effectively to ensure competition and control of seed prices in addition to the bio-safety". 

It is true that the MNCs are far ahead in the development of GM crop varieties due to heavy investment and focused attempts by the companies. But, Indian research data show that the public sector transgenic crops can compete if allowed to grow. Expressing his confidence over what the Indian scientists have developed over the years, Asis Datta, former vice-chancellor of Jawaharlal Nehru University, said, "GM crop is going to be an essential part of our life today or tomorrow. If we don't realize it now, it will only push the country back. It will be difficult to recover later due to intense global competition"... 


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Form matters: morphological aspects of lateral root development

Form matters: morphological aspects of lateral root development | Plant Gene Seeker -PGS | Scoop.it
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Background The crucial role of roots in plant nutrition, and consequently in plant productivity, is a strong motivation to study the growth and functioning of various aspects of the root system. Numerous studies on lateral roots, as a major determinant of the root system architecture, mostly focus on the physiological and molecular bases of developmental processes. Unfortunately, little attention is paid either to the morphological changes accompanying the formation of a lateral root or to morphological defects occurring in lateral root primordia. The latter are observed in some mutants and occasionally in wild-type plants, but may also result from application of external factors.

Scope and Conclusions In this review various morphological aspects of lateral branching in roots are analysed. Morphological events occurring during the formation of a typical lateral root are described. This process involves dramatic changes in the geometry of the developing organ that at early stages are associated with oblique cell divisions, leading to breaking of the symmetry of the cell pattern. Several types of defects in the morphology of primordia are indicated and described. Computer simulations show that some of these defects may result from an unstable field of growth rates. Significant changes in both primary and lateral root morphology may also be a consequence of various mutations, some of which are auxin-related. Examples reported in the literature are considered. Finally, lateral root formation is discussed in terms of mechanics. In this approach the primordium is considered as a physical object undergoing deformation and is characterized by specific mechanical properties.

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Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance.
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Results

A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient.


Conclusions

Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.

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Water Filtration Using Plant Xylem

Water Filtration Using Plant Xylem | 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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Effective point-of-use devices for providing safe drinking water are urgently needed to reduce the global burden of waterborne disease. Here we show that plant xylem from the sapwood of coniferous trees – a readily available, inexpensive, biodegradable, and disposable material – can remove bacteria from water by simple pressure-driven filtration. Approximately 3 cm3 of sapwood can filter water at the rate of several liters per day, sufficient to meet the clean drinking water needs of one person. The results demonstrate the potential of plant xylem to address the need for pathogen-free drinking water in developing countries and resource-limited settings.

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Miya Ando: "Obon"

Miya Ando: "Obon" | Plant Gene Seeker -PGS | Scoop.it

“Obon” Artist Miya Ando released 1,000 non-toxic resin leaves coated w/ phosphorescence into a small pond in Puerto Rico. During the day the leaves would “recharge”, & by night, give off a ghostly, ethereal glow. The installation “Obon” was inspired by a Japanese Buddhist festival of the same name, & to simulate Puerto Rico’s bioluminescent bays, a natural phenomenon caused by dinoflagellates, photosynthetic underwater organisms that emit light when agitated. 2013

 

http://www.spoon-tamago.com/2012/06/14/obon-miya-ando-1000-floating-leaves/ ;


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A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing : Scientific Reports

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing : Scientific Reports | Plant Gene Seeker -PGS | Scoop.it
RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341[emsp14]Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.
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ROS homeostasis in halophytes in the context of salinity stress tolerance

ROS homeostasis in halophytes in the context of salinity stress tolerance | Plant Gene Seeker -PGS | Scoop.it
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Halophytes are defined as plants that are adapted to live in soils containing high concentrations of salt and benefiting from it, and thus represent an ideal model to understand complex physiological and genetic mechanisms of salinity stress tolerance. It is also known that oxidative stress signalling and reactive oxygen species (ROS) detoxification are both essential components of salinity stress tolerance mechanisms. This paper comprehensively reviews the differences in ROS homeostasis between halophytes and glycophytes in an attempt to answer the questions of whether stress-induced ROS production is similar between halophytes and glycophytes; is the superior salinity tolerance in halophytes attributed to higher antioxidant activity; and is there something special about the specific ‘pool’ of enzymatic and non-enzymatic antioxidants in halophytes. We argue that truly salt-tolerant species possessing efficient mechanisms for Na+ exclusion from the cytosol may not require a high level of antioxidant activity, as they simply do not allow excessive ROS production in the first instance. We also suggest that H2O2 ‘signatures’ may operate in plant signalling networks, in addition to well-known cytosolic calcium ‘signatures’. According to the suggested concept, the intrinsically higher superoxide dismutase (SOD) levels in halophytes are required for rapid induction of the H2O2 ‘signature’, and to trigger a cascade of adaptive responses (both genetic and physiological), while the role of other enzymatic antioxidants may be in decreasing the basal levels of H2O2, once the signalling has been processed. Finally, we emphasize the importance of non-enzymatic antioxidants as the only effective means to prevent detrimental effects of hydroxyl radicals on cellular structures.

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miRNAs in the crosstalk between phytohormone signalling pathways

miRNAs in the crosstalk between phytohormone signalling pathways | Plant Gene Seeker -PGS | Scoop.it
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Abstract

Phytohormones are signal molecules produced within the plant that control its growth and development through the regulation of gene expression. Interaction between different phytohormone pathways is essential in coordinating tissue outgrowth in response to environmental changes, such as the adaptation of root development to water deficit or the initiation of seed germination during imbibition. Recently, microRNAs (miRNAs) have emerged as key regulators of phytohormone response pathways in planta by affecting their metabolism, distribution, and perception. Here we review current knowledge on the miRNA-mediated regulations involved in phytohormone crosstalk. We focus on the miRNAs exhibiting regulatory links with more than one phytohormone pathway and discuss their possible implication in coordinating multiple phytohormone responses during specific developmental processes.

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BMC Genomics | Finding the missing honey bee genes: lessons learned from a genome upgrade

The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.
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AbstractResults

Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.

Conclusions

Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

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Genome and transcriptome analysis of the grapevine (Vitis vinifera L.) WRKY gene family

Genome and transcriptome analysis of the grapevine (Vitis vinifera L.) WRKY gene family | Plant Gene Seeker -PGS | Scoop.it
Horticulture Research, Published online: 26 March 2014; | doi:10.1038/hortres.2014.16
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The plant WRKY gene family represents an ancient and complex class of zinc-finger transcription factors (TFs) that are involved in the regulation of various physiological processes, such as development and senescence, and in plant response to many biotic and abiotic stresses. Despite the growing number of studies on the genomic organisation of WRKY gene family in different species, little information is available about this family in grapevine (Vitis vinifera L.). In the present study, a total number of 59 putative grapevine WRKY transcription factors (VvWRKYs) were identified based on the analysis of various genomic and proteomic grapevine databases. According to their structural and phylogentic features, the identified grapevine WRKY transcription factors were classified into three main groups. In order to shed light into their regulatory roles in growth and development as well as in response to biotic and abiotic stress in grapevine, theVvWRKYs expression profiles were examined in publicly available microarray data. Bioinformatics analysis of these data revealed distinct temporal and spatial expression patterns of VvWRKYs in various tissues, organs and developmental stages, as well as in response to biotic and abiotic stresses. To also extend our analysis to situations not covered by the arrays and to validate our results, the expression profiles of selected VvWRKYs in response to drought stress, Erysiphe necator (powdery mildew) infection, and hormone treatments (salicilic acid and ethylene), were investigated by quantitative real-time reverse transcription PCR (qRT-PCR). The present study provides a foundation for further comparative genomics and functional studies of this important class of transcriptional regulators in grapevine.

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Increasing homogeneity in global food supplies and the implications for food security

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Abstract

The narrowing of diversity in crop species contributing to the world’s food supplies has been considered a potential threat to food security. However, changes in this diversity have not been quantified globally. We assess trends over the past 50 y in the richness, abundance, and composition of crop species in national food supplies worldwide. Over this period, national per capita food supplies expanded in total quantities of food calories, protein, fat, and weight, with increased proportions of those quantities sourcing from energy-dense foods. At the same time the number of measured crop commodities contributing to national food supplies increased, the relative contribution of these commodities within these supplies became more even, and the dominance of the most significant commodities decreased. As a consequence, national food supplies worldwide became more similar in composition, correlated particularly with an increased supply of a number of globally important cereal and oil crops, and a decline of other cereal, oil, and starchy root species. The increase in homogeneity worldwide portends the establishment of a global standard food supply, which is relatively species-rich in regard to measured crops at the national level, but species-poor globally. These changes in food supplies heighten interdependence among countries in regard to availability and access to these food sources and the genetic resources supporting their production, and give further urgency to nutrition development priorities aimed at bolstering food security.

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Trends in Plant Science - Root architecture and root and tuber crop productivity

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Summary

It is becoming increasingly evident that optimization of root architecture for resource capture is vital for enabling the next green revolution. Although cereals provide half of the calories consumed by humans, root and tuber crops are the second major source of carbohydrates globally. Yet, knowledge of root architecture in root and tuber species is limited. In this opinion article, we highlight what is known about the root system in root and tuber crops, and mark new research directions towards a better understanding of the relation between root architecture and yield. We believe that unraveling the role of root architecture in root and tuber crop productivity will improve global food security, especially in regions with marginal soil fertility and low-input agricultural systems.

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ETHYLENE RESPONSE FACTOR070 Regulates Root Development and Phosphate Starvation-Mediated Responses

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Inorganic phosphate (Pi) availability is a major factor determining growth and consequently the productivity of crops. However, it is one of the least available macronutrients due to its high fixation in the rhizospheres. To overcome this constraint, plants have developed adaptive responses to better acquire, utilize, and recycle Pi. Molecular determinants of these adaptive mechanisms include transcription factors (TFs) that play a major role in transcriptional control, thereby regulating genome-scale networks. In this study, we have characterized the biological role of Arabidopsis thaliana Ethylene Response Factor070 (AtERF070), aPi starvation-induced TF belonging to the APETALA2/ETHYLENE RESPONSE FACTOR family of TFs in Arabidopsis (Arabidopsis thaliana). It is localized to the nucleus and induced specifically in Pi-deprived roots and shoots. RNA interference-mediated suppression of AtERF070 led to augmented lateral root development resulting in higher Pi accumulation, whereas there were reductions in both primary root length and lateral root number in 12-d-old transgenic seedlings overexpressing AtERF070. When the overexpressing lines were grown to maturity under greenhouse conditions, they revealed a stunted bushy appearance that could be rescued by gibberellic acid application. Furthermore, a number of Pistarvation-responsive genes were modulated in AtERF070-overexpressing and RNA interference lines, thereby suggesting a potential role for this TF in maintaining Pi homeostasis.

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Widespread and frequent horizontal transfers of transposable elements in plants

Vertical, transgenerational transmission of genetic material occurs through reproduction of living organisms. In addition to vertical inheritance, horizontal gene transfer between reproductively-isolated species has recently been shown to be an important, if not dominant, mechanism in the evolution of prokaryotic genomes. In contrast, only a few horizontal transfer (HTs) events have been characterized so far in eukaryotes and mainly concern transposable elements (TEs). Whether these are frequent and have a significant impact on genome evolution remains largely unknown. We performed a computational search for highly conserved LTR-retrotransposons among 40 sequenced eukaryotic genomes representing the major plant families. We found that 26 genomes (65%) harbor at least one case of horizontal TE transfer (HTT) . These transfers concern species as distantly related as palm and grapevine, tomato and bean or poplar and peach. In total, we identified 32 cases of HTTs, which could translate into more than two millions among the 13,551 monocot and dicot genera. Moreover, we show that these TEs have remained functional after their transfer, occasionally causing a transpositional burst. This suggests that plants can frequently exchange genetic material through horizontal transfers and that this mechanism may be important in TE-driven genome evolution.

 

 


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Economic and physical determinants of the global distributions of crop pests and pathogens - Bebber - 2014 - New Phytologist - Wiley Online Library

Economic and physical determinants of the global distributions of crop pests and pathogens - Bebber - 2014 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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SummaryCrop pests and pathogens pose a significant and growing threat to food security, but their geographical distributions are poorly understood. We present a global analysis of pest and pathogen distributions, to determine the roles of socioeconomic and biophysical factors in determining pest diversity, controlling for variation in observational capacity among countries.Known distributions of 1901 pests and pathogens were obtained from CABI. Linear models were used to partition the variation in pest species per country amongst predictors.Reported pest numbers increased with per capita gross domestic product (GDP), research expenditure and research capacity, and the influence of economics was greater in micro-organisms than in arthropods. Total crop production and crop diversity were the strongest physical predictors of pest numbers per country, but trade and tourism were insignificant once other factors were controlled. Islands reported more pests than mainland countries, but no latitudinal gradient in species richness was evident.Country wealth is likely to be a strong indicator of observational capacity, not just trade flow, as has been interpreted in invasive species studies. If every country had US levels of per capita GDP, then 205 ± 9 additional pests per country would be reported, suggesting that enhanced investment in pest observations will reveal the hidden threat of crop pests and pathogens.

 

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Identification and Characterization of an Arabidopsis Mutant with Altered Localization of NIP5;1, a Plasma Membrane Boric Acid Channel, Reveals the Requirement for d-Galactose in Endomembrane Organ...

Identification and Characterization of an Arabidopsis Mutant with Altered Localization of NIP5;1, a Plasma Membrane Boric Acid Channel, Reveals the Requirement for d-Galactose in Endomembrane Organ... | Plant Gene Seeker -PGS | Scoop.it
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Endomembrane organization is important for various aspects of cell physiology, including membrane protein trafficking. To explore the molecular mechanisms regulating the trafficking of plasma membrane-localized proteins in plants, we screened for Arabidopsis mutants with defective localization of green fluorescent protein (GFP)–nodulin 26-like intrinsic protein (NIP)5;1. Fluorescence imaging-based screening led to the isolation of a mutant which accumulated abnormal intracellular aggregates labeled by GFP–NIP5;1. The aggregates appeared in epidermal cells in the root elongation zone and included the trans-Golgi network/early endosomes. Rough mapping and whole-genome sequencing identified the mutant as an allele of UDP-glucose 4-epimerase 4 (uge4)/root hair defective 1 (rhd1) /root epidermal bulgar 1 (reb 1), which was originally defined as a cell wall mutant. The responsible gene encodes UDP-glucose 4-epimerase 4 (UGE4), which functions in the biosynthesis of D-galactose, especially for the synthesis of the cell wall polysaccharide xyloglucan and arabinogalactan proteins (AGPs). The endomembrane aggregates in the mutants were absent in the presence of D-galactose, indicative of a requirement for a D-galactose-containing component in endomembrane organization. Genetic and pharmacological analyses suggested that the aggregates were not caused by the disruption of cell wall polysaccharides or the cytoskeleton. Overall, our results suggest that UGE4 activity in D-galactose synthesis is required for the structure of cell wall polysaccharides and endomembrane organization.

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Cell Wall, Cytoskeleton, and Cell Expansion in Higher Plants

Cell Wall, Cytoskeleton, and Cell Expansion in Higher Plants | Plant Gene Seeker -PGS | Scoop.it
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To accommodate two seemingly contradictory biological roles in plant physiology, providing both the rigid structural support of plant cells and the adjustable elasticity needed for cell expansion, the composition of the plant cell wall has evolved to become an intricate network of cellulosic, hemicellulosic, and pectic polysaccharides and protein. Due to its complexity, many aspects of the cell wall influence plant cell expansion, and many new and insightful observations and technologies are forthcoming. The biosynthesis of cell wall polymers and the roles of the variety of proteins involved in polysaccharide synthesis continue to be characterized. The interactions within the cell wall polymer network and the modification of these interactions provide insight into how the plant cell wall provides its dual function. The complex cell wall architecture is controlled and organized in part by the dynamic intracellular cytoskeleton and by diverse trafficking pathways of the cell wall polymers and cell wall-related machinery. Meanwhile, the cell wall is continually influenced by hormonal and integrity sensing stimuli that are perceived by the cell. These many processes cooperate to construct, maintain, and manipulate the intricate plant cell wall—an essential structure for the sustaining of the plant stature, growth, and life.

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Yield Trends Are Insufficient to Double Global Crop Production by 2050

Yield Trends Are Insufficient to Double Global Crop Production by 2050 | 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.


Via Luigi Guarino
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Several studies have shown that global crop production needs to double by 2050 to meet the projected demands from rising population, diet shifts, and increasing biofuels consumption. Boosting crop yields to meet these rising demands, rather than clearing more land for agriculture has been highlighted as a preferred solution to meet this goal. However, we first need to understand how crop yields are changing globally, and whether we are on track to double production by 2050. Using ~2.5 million agricultural statistics, collected for ~13,500 political units across the world, we track four key global crops—maize, rice, wheat, and soybean—that currently produce nearly two-thirds of global agricultural calories. We find that yields in these top four crops are increasing at 1.6%, 1.0%, 0.9%, and 1.3% per year, non-compounding rates, respectively, which is less than the 2.4% per year rate required to double global production by 2050. At these rates global production in these crops would increase by ~67%, ~42%, ~38%, and ~55%, respectively, which is far below what is needed to meet projected demands in 2050. We present detailed maps to identify where rates must be increased to boost crop production and meet rising demands.

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Frontiers | Generation of boron-deficiency-tolerant tomato by overexpressing an Arabidopsis thaliana borate transporter AtBOR1 | Plant Nutrition

Nutrient deficiency in soil poses a widespread agricultural problem. Boron (B) is an essential micronutrient in plants, and its deficiency causes defects in both vegetative and reproductive growth in various crops in the field. In Arabidopsis thaliana, increased expression of a major borate transporter gene AtBOR1 or boric acid channel gene AtNIP5;1 improves plant growth under B-deficient conditions. In this study, we examined whether high expression of a borate transporter gene increases B accumulation in shoots and improves the growth of tomato plant, a model of fruit-bearing crops, under B-deficient conditions. We established three independent transgenic tomato plants lines expressing AtBOR1 using Agrobacterium-mediated transformation of tomato (Solanum lycopersicum L. cv. Micro-Tom). Reverse transcription-polymerase chain reaction (RT-PCR) analysis confirmed that two lines (Line 1 and Line 2) more strongly expressed AtBOR1 than Line 3. Wild-type plants and the transgenic plants were grown hydroponically under B-sufficient and B-deficient conditions. Wild-type and Line 3 (weakly expressing transgenic line) showed a defect in shoot growth under B-deficient conditions, especially in the development of new leaves. However, seedlings of Line 1 and Line 2, the transgenic lines showing strong AtBOR1 expression, did not show the B-deficiency phenotype in newly developing leaves. In agreement with this phenotype, shoot biomass under low-B conditions was higher in the strongly expressing AtBOR1 line. B concentrations in leaves or fruits were also higher in Line 2 and Line 1. The present study demonstrates that strong expression of AtBOR1 improved growth in tomato under B-deficient conditions.
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ROS as key players in plant stress signalling

ROS as key players in plant stress signalling | Plant Gene Seeker -PGS | Scoop.it
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Reactive oxygen species (ROS) play an integral role as signalling molecules in the regulation of numerous biological processes such as growth, development, and responses to biotic and/or abiotic stimuli in plants. To some extent, various functions of ROS signalling are attributed to differences in the regulatory mechanisms of respiratory burst oxidase homologues (RBOHs) that are involved in a multitude of different signal transduction pathways activated in assorted tissue and cell types under fluctuating environmental conditions. Recent findings revealed that stress responses in plants are mediated by a temporal–spatial coordination between ROS and other signals that rely on production of stress-specific chemicals, compounds, and hormones. In this review we will provide an update of recent findings related to the integration of ROS signals with an array of signalling pathways aimed at regulating different responses in plants. In particular, we will address signals that confer systemic acquired resistance (SAR) or systemic acquired acclimation (SAA) in plants.

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Translational research: from pot to plot - Plant Biotechnology Journal

Translational research: from pot to plot - Plant Biotechnology Journal | Plant Gene Seeker -PGS | Scoop.it
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Summary

Plant molecular biology has been the key driver to elucidate molecular pathways underlying plant growth, development and stress responses during the past decades. Although this has led to a plethora of available data, the translation to crop improvement is lagging behind. Here, we argue that plant scientists should become more involved in converting basic knowledge into applications in crops to sustainably support food security and agriculture. As the translatability from model species to crops is rather poor, this kind of translational research requires diligence and a thorough knowledge of the investigated trait in the crop. In addition, the robustness of a trait depends on the genotype and environmental conditions, demanding a holistic approach, which cannot always be evaluated under growth chamber and greenhouse conditions. To date, the improved resolution of many genome-wide technologies and the emerging expertise in canopy imaging, plant phenotyping and field monitoring make it very timely to move from the pathway specifics to important agronomical realizations, thus from pot to plot. Despite the availability of scientific know-how and expertise, the translation of new traits to applications using a transgene approach is in some regions of the world, such as Europe, seriously hampered by heavy and nontranslucent legislation for biotech crops. Nevertheless, progress in crop improvement will remain highly dependent on our ability to evaluate improved varieties in field conditions. Here, we plead for a network of protected sites for field trials across the different European climates to test improved biotech traits directly in crops.

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Effects of halving pesticide use on wheat production : Scientific Reports : Nature Publishing Group

Effects of halving pesticide use on wheat production : Scientific Reports : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it

SCIENTIFIC REPORTS | ARTICLE | OPEN

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Pesticides pose serious threats to both human health and the environment. In Europe, farmers are encouraged to reduce their use, and in France a recent environmental policy fixed a target of halving the pesticide use by 2018. Organic and integrated cropping systems have been proposed as possible solutions for reducing pesticide use, but the effect of reducing pesticide use on crop yield remains unclear. Here we use a set of cropping system experiments to quantify the yield losses resulting from a reduction of pesticide use for winter wheat in France. Our estimated yield losses resulting from a 50% reduction in pesticide use ranged from 5 to 13% of the yield obtained with the current pesticide use. At the scale of the whole country, these losses would decrease the French wheat production by about 2 to 3 millions of tons, which represent about 15% of the French wheat export.

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Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

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As an economic crop, pepper satisfies people’s spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.

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Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes

Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes | Plant Gene Seeker -PGS | Scoop.it
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Cytosine methylation is an important base modification that is inherited across mitotic and meiotic cell divisions in plant genomes. Heritable methylation variants can contribute to within-species phenotypic variation. Few methylation variants were known until recently, making it possible to begin to address major unanswered questions: the extent of natural methylation variation within plant genomes, its effects on phenotypic variation, its degree of dependence on genotype, and how it fits into an evolutionary context. Techniques like whole-genome bisulfite sequencing (WGBS) make it possible to determine cytosine methylation states at single-base resolution across entire genomes and populations. Application of this method to natural and novel experimental populations is revealing answers to these long-standing questions about the role of DNA methylation in plant genomes.

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Nitric oxide function in plant biology: a redox cue in deconvolution - Yu - 2014 - New Phytologist - Wiley Online Library

Nitric oxide function in plant biology: a redox cue in deconvolution - Yu - 2014 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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Nitric oxide (NO), a gaseous, redox-active small molecule, is gradually becoming established as a central regulator of growth, development, immunity and environmental interactions in plants. A major route for the transfer of NO bioactivity is S-nitrosylation, the covalent attachment of an NO moiety to a protein cysteine thiol to form an S-nitrosothiol (SNO). This chemical transformation is rapidly emerging as a prototypic, redox-based post-translational modification integral to the life of plants. Here we review the myriad roles of NO and SNOs in plant biology and, where known, the molecular mechanisms underpining their activity.

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Economic and physical determinants of the global distributions of crop pests and pathogens - Bebber - 2014 - New Phytologist - Wiley Online Library

Economic and physical determinants of the global distributions of crop pests and pathogens - Bebber - 2014 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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SummaryCrop pests and pathogens pose a significant and growing threat to food security, but their geographical distributions are poorly understood. We present a global analysis of pest and pathogen distributions, to determine the roles of socioeconomic and biophysical factors in determining pest diversity, controlling for variation in observational capacity among countries.Known distributions of 1901 pests and pathogens were obtained from CABI. Linear models were used to partition the variation in pest species per country amongst predictors.Reported pest numbers increased with per capita gross domestic product (GDP), research expenditure and research capacity, and the influence of economics was greater in micro-organisms than in arthropods. Total crop production and crop diversity were the strongest physical predictors of pest numbers per country, but trade and tourism were insignificant once other factors were controlled. Islands reported more pests than mainland countries, but no latitudinal gradient in species richness was evident.Country wealth is likely to be a strong indicator of observational capacity, not just trade flow, as has been interpreted in invasive species studies. If every country had US levels of per capita GDP, then 205 ± 9 additional pests per country would be reported, suggesting that enhanced investment in pest observations will reveal the hidden threat of crop pests and pathogens.

 

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