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Responses of foliar antioxidative and photoprotective defence systems of trees to drought: a meta-analysis

Responses of foliar antioxidative and photoprotective defence systems of trees to drought: a meta-analysis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Current climate change predictions hint to more frequent extreme weather events, including extended droughts, making better understanding of the impacts of water stress on trees even more important. At the individual plant level, stomatal closure as a result of water deficit leads to reduced CO2 availability in the leaf, which can lead to photo-oxidative stress. Photorespiration and the Mehler reaction can maintain electron transport rates under low internal CO2, but result in production of reactive oxygen species (ROS). If electron consumption is decreased, upstream photochemical processes can be affected and light energy is absorbed in excess of photochemical requirements. Trees evolved to cope with excess energy and elevated concentration of ROS by activating photoprotective and antioxidative defence systems. The meta-analysis we present here assessed responses of these defence systems reported in 50 studies. We found responses to vary depending on stress intensity, foliage type and habitat, and on whether experiments were done in the field or in controlled environments. In general, drought increased concentrations of antioxidants and photoprotective pigments. However, severe stress caused degradation of antioxidant concentrations and oxidation of antioxidant pools. Evergreen trees seemed to preferentially reinforce membrane-bound protection systems zeaxanthin and tocopherol, whereas deciduous species showed greater responses in water-soluble antioxidants ascorbic acid and glutathione. Trees and shrubs from arid versus humid habitats vary in their antioxidative and photoprotective defence responses. In field experiments, drought had greater effects on some defence compounds than under controlled conditions.

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Exploring the Genes of Yerba Mate (Ilex paraguariensis A. St.-Hil.) by NGS and De Novo Transcriptome Assembly

Exploring the Genes of Yerba Mate (Ilex paraguariensis A. St.-Hil.) by NGS and De Novo Transcriptome Assembly | 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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Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ~32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ~1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.

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A reference genome for common bean and genome-wide analysis of dual domestications

A reference genome for common bean and genome-wide analysis of dual domestications | Plant Gene Seeker -PGS | Scoop.it

Nature Genetics

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Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.


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The CLE40 and CRN/CLV2 Signaling Pathways Antagonistically Control Root Meristem Growth in Arabidopsis

The CLE40 and CRN/CLV2 Signaling Pathways Antagonistically Control Root Meristem Growth in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Differentiation processes in the primary root meristem are controlled by several signaling pathways that are regulated by phytohormones or by secreted peptides. Long-term maintenance of an active root meristem requires that the generation of new stem cells and the loss of these from the meristem due to differentiation are precisely coordinated. Via phenotypic and large-scale transcriptome analyses of mutants, we show that the signaling peptide CLE40 and the receptor proteins CLV2 and CRN act in two genetically separable pathways that antagonistically regulate cell differentiation in the proximal root meristem. CLE40 inhibits cell differentiation throughout the primary root meristem by controlling genes with roles in abscisic acid, auxin, and cytokinin signaling. CRN and CLV2jointly control target genes that promote cell differentiation specifically in the transition zone of the proximal root meristem. While CRN and CLV2 are not acting in the CLE40 signaling pathway under normal growth conditions, both proteins are required when the levels of CLE40 or related CLE peptides increase. We show here that two antagonistically acting pathways controlling root meristem differentiation can be activated by the same peptide in a dosage-dependent manner.

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SPX1 is a phosphate-dependent inhibitor of PHOSPHATE STARVATION RESPONSE 1 in Arabidopsis

SPX1 is a phosphate-dependent inhibitor of PHOSPHATE STARVATION RESPONSE 1 in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
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Significance

When P levels are low, plants activate an array of adaptive responses to increase efficient acquisition and use of phosphate (Pi), the form in which P is preferentially absorbed, and to protect themselves from Pi starvation stress. Considerable progress has been made recently in dissecting the plant Pi starvation signaling pathway. Nonetheless, little is known as to how Pi levels are perceived by plants. Here, we identify the nuclear protein SPX1 as a Pi-dependent inhibitor of DNA binding by PHOSPHATE STARVATION RESPONSE 1 (PHR1), a master regulator of Pi starvation responses. We show that the Pi dependence of SPX1 inhibition of PHR1 activity can be recreated in vitro using purified proteins, which indicates that the SPX1/PHR1 module links Pi sensing and signaling.

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Strategies for optimization of mineral nutrient transport in plants: multi-level regulation of nutrient-dependent dynamics of root architecture and transporter activity

Strategies for optimization of mineral nutrient transport in plants: multi-level regulation of nutrient-dependent dynamics of root architecture and transporter activity | Plant Gene Seeker -PGS | Scoop.it

PCP Plant Cell Physiology

Andres Zurita's insight:

How do sessile plants cope with irregularities in soil nutrient availability? The uptake of essential minerals from the soil influences plant growth and development. However, most environments do not provide sufficient nutrients; rather nutrient distribution in the soil can be uneven and change temporally according to environmental factors. To maintain mineral nutrient homeostasis in their tissues, plants have evolved sophisticated systems for coping with spatial and temporal variability in soil nutrient concentrations. Among these are mechanisms for modulating root system architectures in response to nutrient availability. This review discusses recent advances in knowledge of the two important strategies for optimizing nutrient uptake and translocation in plants: root architecture modification and transporter expression control in response to nutrient availability. Recent studies have determined (i) nutrient-specific root patterns, (ii) their physiological consequences, and (iii) the molecular mechanisms underlying these modulation systems that operate to facilitate efficient nutrient acquisition. Another mechanism employed by plants in nutrient-heterogeneous soils involves modification of nutrient transport activities in a nutrient-concentration-dependent manner. In recent years, considerable progress has been made in characterizing the diverse functions of transporters for specific nutrients; it is now clear that the expression and activities of nutrient transporters are finely regulated in multiple steps at both the transcriptional and post-transcriptional levels for adaptation to a wide range of nutrient conditions.

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A Meta-Analysis of the Impacts of Genetically Modified Crops - Klümper & Qaim (2014) - PLOS One

A Meta-Analysis of the Impacts of Genetically Modified Crops - Klümper & Qaim (2014) - PLOS One | Plant Gene Seeker -PGS | Scoop.it

Despite the rapid adoption of genetically modified (GM) crops by farmers in many countries, controversies about this technology continue. Uncertainty about GM crop impacts is one reason for widespread public suspicion. 

 

We carry out a meta-analysis of the agronomic and economic impacts of GM crops to consolidate the evidence... Studies were included when they build on primary data from farm surveys or field trials anywhere in the world, and when they report impacts of GM soybean, maize, or cotton on crop yields, pesticide use, and/or farmer profits... 

 

 

On average, GM technology adoption has reduced chemical pesticide use by 37%, increased crop yields by 22%, and increased farmer profits by 68%. Yield gains and pesticide reductions are larger for insect-resistant crops than for herbicide-tolerant crops. Yield and profit gains are higher in developing countries than in developed countries...


The meta-analysis reveals robust evidence of GM crop benefits for farmers in developed and developing countries. Such evidence may help to gradually increase public trust in this technology.

 

http://dx.doi.org/10.1371/journal.pone.0111629

 


Via Alexander J. Stein
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AckerbauHalle's curator insight, November 4, 4:52 PM

Meta-Analyse zum Einsatz von transgenen Pflanzen

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The roles of histone acetylation in seed performance and plant development

The roles of histone acetylation in seed performance and plant development | Plant Gene Seeker -PGS | Scoop.it
Abstract
Histone acetylation regulates gene transcription by chromatin modifications and plays a crucial role in the plant development and response to environment cues. The homeostasis of histone acetylation is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in different plant tissues and development stages. The vigorous knowledge of the function and co-factors about HATs (e.g. GCN5) and HDACs (e.g. HDA19, HDA6) has been obtained from model plant Arabidopsis. However, understanding individual role of other HATs and HDACs require more work, especially in the major food crops such as rice, maize and wheat. Many co-regulators have been recently identified to function as a component of HAT or HDAC complex in some specific developmental processes. The described findings show a distinctive and interesting epigenetic regulation network composed of HATs, HDACs and co-regulators playing crucial roles in the seed performance, flowering time, plant morphogenesis, plant response to stresses etc. In this review, we summarized the recent progresses and suggested the perspective of histone acetylation research, which might provide us a new window to understand the epigenetic code of plant development and to improve the crop production and quality.
Andres Zurita's insight:
Highlights

• Increasing knowledges about histone acetylation give new clues for plant epigenetics.

• Histone acetylation plays roles in seed development, performance and plant growth.• Co-regulators determine the function specificity of histone (de)acetylation complex.
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Flowers under pressure: ins and outs of turgor regulation in development

Flowers under pressure: ins and outs of turgor regulation in development | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Background Turgor pressure is an essential feature of plants; however, whereas its physiological importance is unequivocally recognized, its relevance to development is often reduced to a role in cell elongation.

Scope This review surveys the roles of turgor in development, the molecular mechanisms of turgor regulation and the methods used to measure turgor and related quantities, while also covering the basic concepts associated with water potential and water flow in plants. Three key processes in flower development are then considered more specifically: flower opening, anther dehiscence and pollen tube growth.

Conclusions Many molecular determinants of turgor and its regulation have been characterized, while a number of methods are now available to quantify water potential, turgor and hydraulic conductivity. Data on flower opening, anther dehiscence and lateral root emergence suggest that turgor needs to be finely tuned during development, both spatially and temporally. It is anticipated that a combination of biological experiments and physical measurements will reinforce the existing data and reveal unexpected roles of turgor in development.

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PLOS Collections : Article collections published by the Public Library of Science

PLOS Collections : Article collections published by the Public Library of Science | Plant Gene Seeker -PGS | Scoop.it
PLOS Collections: Article collections published by the Public Library of Science
Andres Zurita's insight:

As the world's human population continues to expand, and as water resources come under increasing pressure and pathogens that cause devastating crop losses continue to spread in the face of increased global commerce and climate change, there is a pressing need for plant research to contribute solutions to improving food security in a sustainable and safe way. 

 

Plant translational research - the development of basic plant research discoveries into technologies or approaches that improve agriculture - has a vital role to play in meeting these challenges, and given the importance of research in this field, PLOS believes that such work should be published in open access journals, ensuring that it reaches the widest possible audience without any barriers to access.

 

The technical advances highlighted in this PLOS Collection exemplify how basic research discoveries are being translated into methods to develop and improve, both agriculturally and environmentally, important crop traits.

 

The Collection was produced with the support of  The Bill & Melinda Gates Foundation.

 

The Collection will be updated periodically with new Plant Translational Research.

 

www.ploscollections.org/planttranslationalresearch

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Genomic analyses provide insights into the history of tomato breeding

Genomic analyses provide insights into the history of tomato breeding | Plant Gene Seeker -PGS | Scoop.it

Nature Genetics : Nature Publishing Group

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The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ~100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

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The Potential of Transcription Factor-Based Genetic Engineering in Improving Crop Tolerance to Drought

OMICS: A Journal of Integrative Biology
Andres Zurita's insight:

Drought is one of the major constraints in crop production and has an effect on a global scale. In order to improve crop production, it is necessary to understand how plants respond to stress. A good understanding of regulatory mechanisms involved in plant responses during drought will enable researchers to explore and manipulate key regulatory points in order to enhance stress tolerance in crops. Transcription factors (TFs) have played an important role in crop improvement from the dawn of agriculture. TFs are therefore good candidates for genetic engineering to improve crop tolerance to drought because of their role as master regulators of clusters of genes. Many families of TFs, such as CCAAT, homeodomain, bHLH, NAC, AP2/ERF, bZIP, and WRKY have members that may have the potential to be tools for improving crop tolerance to drought. In this review, the roles of TFs as tools to improve drought tolerance in crops are discussed. The review also focuses on current strategies in the use of TFs, with emphasis on several major TF families in improving drought tolerance of major crops. Finally, many promising transgenic lines that may have improved drought responses have been poorly characterized and consequently their usefulness in the field is uncertain. New advances in high-throughput phenotyping, both greenhouse and field based, should facilitate improved phenomics of transgenic lines. Systems biology approaches should then define the underlying changes that result in higher yields under water stress conditions. These new technologies should help show whether manipulating TFs can have effects on yield under field conditions.

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Origin and Evolution of Plastids and Photosynthesis in Eukaryotes

Origin and Evolution of Plastids and Photosynthesis in Eukaryotes | Plant Gene Seeker -PGS | Scoop.it
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Recent progress in understanding the origins of plastids from endosymbiotic cyanobacteria is reviewed. Establishing when during geological time the endosymbiosis occurred remains elusive, but progress has been made in defining the cyanobacterial lineage most closely related to plastids, and some mechanistic insight into the possible existence of cryptic endosymbioses perhaps involving Chlamydia-like infections of the host have also been presented. The phylogenetic affinities of the host remain obscure. The existence of a second lineage of primary plastids in euglyphid amoebae has now been confirmed, but the quasipermanent acquisition of plastids by animals has been shown to be more ephemeral than initially suspected. A new understanding of how plastids have been integrated into their hosts by transfer of photosynthate, by endosymbiotic gene transfer and repatriation of gene products back to the endosymbiont, and by regulation of endosymbiont division is presented in context.

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Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World | Plant Gene Seeker -PGS | Scoop.it

Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique.

Andres Zurita's insight:

To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.

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Arabidopsis gulliver1/superroot2-7 identifies a metabolic basis for auxin and brassinosteroid synergy

Arabidopsis gulliver1/superroot2-7 identifies a metabolic basis for auxin and brassinosteroid synergy | Plant Gene Seeker -PGS | Scoop.it

Maharjan - 2014 - The Plant Journal - Wiley Online Library

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Phytohormone homeostasis is essential for proper growth and development of plants. To understand the growth mechanisms mediated by hormonal levels, we isolated a gulliver1 (gul1) mutant that had tall stature in the presence of both brassinazole and the light. The gul1phenotype depended on functional BR biosynthesis; the genetic introduction of dwarf4, a BR biosynthetic mutation, masked the long hypocotyl phenotype of gul1. Furthermore, BR biosynthesis was dramatically enhanced, such that the level of 22-hydroxy campesterol was 5.8-fold greater in gul1. Molecular cloning revealed that gul1 was a missense mutation, resulting in a glycine to arginine change at amino acid 116 in SUPERROOT2 (CYP83B1), which converts indole acetaldoxime to an S-alkyl thiohydroximate adduct in the indole glucosinolate pathway. Auxin metabolite profiling coupled with quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis of auxin biosynthetic genes revealed that gul1/sur2-7 activated multiple alternative branches of tryptophan-dependent auxin biosynthetic pathways. Furthermore, exogenous treatment of gul1/sur2-7 with BRs caused adventitious roots from hypocotyls, indicative of an increased response to BRs relative to wild-type. Different from severe alleles of sur2, gul1/sur2-7 lacked ‘high-auxin’ phenotypes that include stunted growth and callus-like disintegration of hypocotyl tissues. The auxin level in gul1/sur2-7 was only 1.6-fold greater than in the wild-type, whereas it was 4.2-fold in a severe allele like sur2-8. Differences in auxin content may account for the range of phenotypes observed among the sur2 alleles. This unusual allele provides long-sought evidence for a synergistic interaction between auxin and BRs in promoting growth in Arabidopsis at the level of their biosynthetic enzymes.

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Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice

Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice | Plant Gene Seeker -PGS | Scoop.it
Significance

Flowering time is one of the best studied ecologically important traits under natural or human selection for adaptation of plants to specific local environments. Photoperiodic sensitivity is a major agronomic trait that tailors vegetative and reproductive growth to local climates and is thus particularly important for crop yield and quality. This study not only identifies a major quantitative trait locus underlying photoperiod sensitivity in rice (Days to heading 7, DTH7) but also demonstrates that various haplotype combinations of DTH7 with Grain number, plant height, and heading date 7 (Ghd7) and DTH8 correlate well with the flowering time and grain yield of rice varieties under diverse cultivating conditions. Our results build a foundation for breeding of high-yield rice varieties with desired photosensitivity and optimum adaptation to the target environments.
Andres Zurita's insight:

Success of modern agriculture relies heavily on breeding of crops with maximal regional adaptability and yield potentials. A major limiting factor for crop cultivation is their flowering time, which is strongly regulated by day length (photoperiod) and temperature. Here we report identification and characterization of Days to heading 7(DTH7), a major genetic locus underlying photoperiod sensitivity and grain yield in rice. Map-based cloning reveals that DTH7 encodes a pseudo-response regulator protein and its expression is regulated by photoperiod. We show that in long days DTH7 acts downstream of the photoreceptor phytochrome B to repress the expression of Ehd1, an up-regulator of the “florigen” genes (Hd3a and RFT1), leading to delayed flowering. Further, we find that haplotype combinations of DTH7 with Grain number, plant height, and heading date 7 (Ghd7) and DTH8 correlate well with the heading date and grain yield of rice under different photoperiod conditions. Our data provide not only a macroscopic view of the genetic control of photoperiod sensitivity in rice but also a foundation for breeding of rice cultivars better adapted to the target environments using rational design.

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Capturing Arabidopsis Root Architecture Dynamics with root-fit Reveals Diversity in Responses to Salinity

Andres Zurita's insight:

The plant root is the first organ to encounter salinity stress, but the effect of salinity on root system architecture (RSA) remains elusive. Both the reduction in main root (MR) elongation and the redistribution of the root mass between MRs and lateral roots (LRs) are likely to play crucial roles in water extraction efficiency and ion exclusion. To establish which RSA parameters are responsive to salt stress, we performed a detailed time course experiment in which Arabidopsis (Arabidopsis thaliana) seedlings were grown on agar plates under different salt stress conditions. We captured RSA dynamics with quadratic growth functions (ROOT-FIT) and summarized the salt-induced differences in RSA dynamics in three growth parameters: MR elongation, average LR elongation, and increase in number of LRs. In the ecotype Columbia-0 accession of Arabidopsis, salt stress affected MR elongation more severely than LR elongation and an increase in LRs, leading to a significantly altered RSA. By quantifying RSA dynamics of 31 different Arabidopsis accessions in control and mild salt stress conditions, different strategies for regulation of MR and LR meristems and root branching were revealed. Different RSA strategies partially correlated with natural variation in abscisic acid sensitivity and different Na+/K+ ratios in shoots of seedlings grown under mild salt stress. Applying ROOT-FIT to describe the dynamics of RSA allowed us to uncover the natural diversity in root morphology and cluster it into four response types that otherwise would have been overlooked.

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What is the World's Biggest Cash Crop? - Information Is Beautiful

What is the World's Biggest Cash Crop? - Information Is Beautiful | Plant Gene Seeker -PGS | Scoop.it
Information Is Beautiful
ideas, issues, knowledge, data — visualized!
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Via Loïc Lepiniec
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Long-term relationships among pesticide applications, mobility, and soil erosion in a vineyard watershed

Long-term relationships among pesticide applications, mobility, and soil erosion in a vineyard watershed | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Agricultural pesticide use has increased worldwide during the last several decades, but the long-term fate, storage, and transfer dynamics of pesticides in a changing environment are poorly understood. Many pesticides have been progressively banned, but in numerous cases, these molecules are stable and may persist in soils, sediments, and ice. Many studies have addressed the question of their possible remobilization as a result of global change. In this article, we present a retro-observation approach based on lake sediment records to monitor micropollutants and to evaluate the long-term succession and diffuse transfer of herbicides, fungicides, and insecticide treatments in a vineyard catchment in France. The sediment allows for a reliable reconstruction of past pesticide use through time, validated by the historical introduction, use, and banning of these organic and inorganic pesticides in local vineyards. Our results also revealed how changes in these practices affect storage conditions and, consequently, the pesticides' transfer dynamics. For example, the use of postemergence herbicides (glyphosate), which induce an increase in soil erosion, led to a release of a banned remnant pesticide (dichlorodiphenyltrichloroethane, DDT), which had been previously stored in vineyard soil, back into the environment. Management strategies of ecotoxicological risk would be well served by recognition of the diversity of compounds stored in various environmental sinks, such as agriculture soil, and their capability to become sources when environmental conditions change.

 
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Receptors, repressors, PINs: a playground for strigolactone signaling

Receptors, repressors, PINs: a playground for strigolactone signaling | Plant Gene Seeker -PGS | Scoop.it

Highlights

• Strigolactones are now recognized as a new group of plant hormones.
• Strigolactones are sensed via a cell-specific reception system.
• Strigolactone activity is partially conducted in a non-cell-autonomous fashion.
• Strigolactones interact with other plant hormones by regulating PIN proteins.

Andres Zurita's insight:

Strigolactones, previously identified as active stimuli of seed germination in parasitic plants, are now recognized as a new group of plant hormones that are active in both shoots and roots. Here, we review recent insights into the concepts of strigolactones-signal transduction and their mode of action. Although strigolactones are sensed via a cell-specific reception system, at least some aspects of their activity are conducted in a non-cell-autonomous fashion. Strigolactones also affect trafficking and plasma-membrane localization of the auxin transporter PIN, thereby regulating auxin flux. We present a model for strigolactone-signal transduction that might also explain the integration of strigolactones into other hormone-signaling pathways via the regulation of PIN auxin transporters.

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Nature Outlook : Rice

Nature Outlook : Rice | Plant Gene Seeker -PGS | Scoop.it

Nature Supplement

Free full access

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A simple grain with global impact, rice has helped to build empires and fed revolutions. Now, scientists are starting a rice revolution of their own to feed a hungry world. By decoding genetics, improving breeding and, perhaps, reshaping the plant's biology, researchers are working to take the world’s most vital crop into the future.

 

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Current trends and future directions in flower development research

Current trends and future directions in flower development research | Plant Gene Seeker -PGS | Scoop.it

ANNALS OF BOTANY

Andres Zurita's insight:

Flowers, the reproductive structures of the approximately 400 000 extant species of flowering plants, exist in a tremendous range of forms and sizes, mainly due to developmental differences involving the number, arrangement, size and form of the floral organs of which they consist. However, this tremendous diversity is underpinned by a surprisingly robust basic floral structure in which a central group of carpels forms on an axis of determinate growth, almost invariably surrounded by two successive zones containing stamens and perianth organs, respectively. Over the last 25 years, remarkable progress has been achieved in describing the molecular mechanisms that control almost all aspects of flower development, from the phase change that initiates flowering to the final production of fruits and seeds. However, this work has been performed almost exclusively in a small number of eudicot model species, chief among which is Arabidopsis thaliana. Studies of flower development must now be extended to a much wider phylogenetic range of flowering plants and, indeed, to their closest living relatives, the gymnosperms. Studies of further, more wide-ranging models should provide insights that, for various reasons, cannot be obtained by studying the major existing models alone. The use of further models should also help to explain how the first flowering plants evolved from an unknown, although presumably gymnosperm-like ancestor, and rapidly diversified to become the largest major plant group and to dominate the terrestrial flora. The benefits for society of a thorough understanding of flower development are self-evident, as human life depends to a large extent on flowering plants and on the fruits and seeds they produce. In this preface to the Special Issue, we introduce eleven articles on flower development, representing work in both established and further models, including gymnosperms. We also present some of our own views on current trends and future directions of the flower development field.

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OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis

OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it

Water is crucial to plant growth and development. Environmental water deficiency triggers an osmotic stress signalling cascade, which induces short-term cellular responses to reduce water loss and long-term responses to remodel the transcriptional network and physiological and developmental processes1, 2, 3, 4. Several signalling components that have been identified by extensive genetic screens for altered sensitivities to osmotic stress seem to function downstream of the perception of osmotic stress. It is known that hyperosmolality and various other stimuli trigger increases in cytosolic free calcium concentration ([Ca2+]i)5, 6. Considering that in bacteria and animals osmosensing Ca2+channels serve as osmosensors7, 8, hyperosmolality-induced [Ca2+]i increases have been widely speculated to be involved in osmosensing in plants1, 9. However, the molecular nature of corresponding Ca2+ channels remain unclear6, 10, 11. Here we describe a hyperosmolality-gated calcium-permeable channel and its function in osmosensing in plants. Using calcium-imaging-based unbiased forward genetic screens we isolatedArabidopsis mutants that exhibit low hyperosmolality-induced [Ca2+]i increases. These mutants were rescreened for their cellular, physiological and developmental responses to osmotic stress, and those with clear combined phenotypes were selected for further physical mapping. One of the mutants, reduced hyperosmolality-induced [Ca2+]i increase 1(osca1), displays impaired osmotic Ca2+ signalling in guard cells and root cells, and attenuated water transpiration regulation and root growth in response to osmotic stress. OSCA1 is identified as a previously unknown plasma membrane protein and forms hyperosmolality-gated calcium-permeable channels, revealing that OSCA1 may be an osmosensor. OSCA1 represents a channel responsible for [Ca2+]i increases induced by a stimulus in plants, opening up new avenues for studying Ca2+ machineries for other stimuli and providing potential molecular genetic targets for engineering drought-resistant crops.


Via Jennifer Mach
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The osmosensing mechanism in plants finally found?

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De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits | Plant Gene Seeker -PGS | Scoop.it

NATURE BIOTECHNOLOGY | RESEARCH | ARTICLE | OPEN

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Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novoassembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.

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The Maize TFome – development of a transcription factor open reading frame collection for functional genomics

The Maize TFome – development of a transcription factor open reading frame collection for functional genomics | Plant Gene Seeker -PGS | Scoop.it
Summary
Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/).
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Multiscale digital Arabidopsis predicts individual organ and whole-organism growth

Multiscale digital Arabidopsis predicts individual organ and whole-organism growth | Plant Gene Seeker -PGS | Scoop.it
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Significance

Plants respond to environmental change by triggering biochemical and developmental networks across multiple scales. Multiscale models that link genetic input to the whole-plant scale and beyond might therefore improve biological understanding and yield prediction. Authors report a modular approach to build such models, validated by a framework model of Arabidopsis thaliana comprising four existing mathematical models. Our model brings together gene dynamics, carbon partitioning, organ growth, shoot architecture, and development in response to environmental signals. It predicted the biomass of each leaf in independent data, demonstrated flexible control of photosynthesis across photoperiods, and predicted the pleiotropic phenotype of a developmentally misregulated transgenic line. Systems biology, crop science, and ecology might thus be linked productively in a community-based approach to modeling.

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