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PIN-driven polar auxin transport in plant developmental plasticity: a key target for environmental and endogenous signals - Habets - 2014 - New Phytologist - Wiley Online Library

PIN-driven polar auxin transport in plant developmental plasticity: a key target for environmental and endogenous signals - Habets - 2014 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
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Plants master the art of coping with environmental challenges in two ways: on the one hand, through their extensive defense systems, and on the other, by their developmental plasticity. The plant hormone auxin plays an important role in a plant's adaptations to its surroundings, as it specifies organ orientation and positioning by regulating cell growth and division in response to internal and external signals. Important in auxin action is the family of PIN-FORMED (PIN) auxin transport proteins that generate auxin maxima and minima by driving polar cell-to-cell transport of auxin through their asymmetric subcellular distribution. Here, we review how regulatory proteins, the cytoskeleton, and membrane trafficking affect PIN expression and localization. Transcriptional regulation of PIN genes alters protein abundance, provides tissue-specific expression, and enables feedback based on auxin concentrations and crosstalk with other hormones. Post-transcriptional modification, for example by PIN phosphorylation or ubiquitination, provides regulation through protein trafficking and degradation, changing the direction and quantity of the auxin flow. Several plant hormones affect PIN abundance, resulting in another means of crosstalk between auxin and these hormones. In conclusion, PIN proteins are instrumental in directing plant developmental responses to environmental and endogenous signals.

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Pectins, ROS homeostasis and UV-B responses in plant roots

Pectins, ROS homeostasis and UV-B responses in plant roots | Plant Gene Seeker -PGS | Scoop.it
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Abstract

Light from the sun contains far-red, visible and ultra violet (UV) wavelength regions. Almost all plant species have been evolved under the light environment. Interestingly, several photoreceptors, expressing both in shoots and roots, process the light information during the plant life cycle. Surprisingly, Arabidopsis root apices express besides the UVR8 UV-B receptor, also root-specific UV-B sensing proteins RUS1 and RUS2 linked to the polar cell–cell transport of auxin. In this mini-review, we focus on reactive oxygen species (ROS) signaling and possible roles of pectins internalized via endocytic vesicle recycling system in the root-specific UV-B perception and ROS homeostasis.

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Environmental perception and epigenetic memory: mechanistic insight through FLC

Environmental perception and epigenetic memory: mechanistic insight through FLC | Plant Gene Seeker -PGS | Scoop.it

Berry - 2015 - The Plant Journal - Wiley Online Library

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Chromatin plays a central role in orchestrating gene regulation at the transcriptional level. However, our understanding of how chromatin states are altered in response to environmental and developmental cues, and then maintained epigenetically over many cell divisions, remains poor. The floral repressor gene FLOWERING LOCUS C (FLC) in Arabidopsis thaliana is a useful system to address these questions. FLC is transcriptionally repressed during exposure to cold temperatures, allowing studies of how environmental conditions alter expression states at the chromatin level. FLC repression is also epigenetically maintained during subsequent development in warm conditions, so that exposure to cold may be remembered. This memory depends on molecular complexes that are highly conserved among eukaryotes, making FLC not only interesting as a paradigm for understanding biological decision-making in plants, but also an important system for elucidating chromatin-based gene regulation more generally. In this review, we summarize our understanding of how cold temperature induces a switch in the FLC chromatin state, and how this state is epigenetically remembered. We also discuss how the epigenetic state of FLC is reprogrammed in the seed to ensure a requirement for cold exposure in the next generation.

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Stress physiology functions of the Arabidopsis histidine kinase cytokinin receptors

Stress physiology functions of the Arabidopsis histidine kinase cytokinin receptors | Plant Gene Seeker -PGS | Scoop.it

Kumar - 2014 - Physiologia Plantarum - Wiley Online Library

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Cytokinin signaling has complex effects on abiotic stress responses that remain to be fully elucidated. The Arabidopsis histidine kinases (AHKs), AHK2, AHK3 and CRE1 (cytokinin response1/AHK4) are the principle cytokinin receptors of Arabidopsis. Using a set of ahk mutants, we found dramatic differences in response to low water potential and salt stress among the AHKs. ahk3-3 mutants had increased root elongation after transfer to low water potential media. Conversely ahk2-2 was hypersensitive to salt stress in terms of root growth and fresh weight and accumulated higher than wild-type levels of proline specifically under salt stress. Strongly reduced proline accumulation in ahkdouble mutants after low water potential treatment indicated a more general role of cytokinin signaling in proline metabolism. Reduced P5CS1(Δ1-pyrroline-5-carboxylate synthetase1) gene expression may have contributed to this reduced proline accumulation. Low water potential phenotypes of ahk mutants were not caused by altered abscisic acid (ABA) accumulation as all ahk mutants had wild-type ABA levels, despite the observation that ahk double mutants had reduced NCED3 (9-cis-epoxycartenoid dioxygenase3) expression when exposed to low water potential. No difference in osmoregulatory solute accumulation was detected in any of the ahk mutants indicating that they do not affect drought responsive osmotic adjustment. Overall, our examination of ahk mutants found specific phenotypes associated with AHK2 and AHK3 as well as a general function of cytokinin signaling in proline accumulation and low water potential induction of P5CS1 and NCED3expression. These results show the stress physiology function of AHKs at a new level of detail.

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Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens | BMC Genomics | Full Text

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens | BMC Genomics | Full Text | Plant Gene Seeker -PGS | Scoop.it
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AbstractBackground

Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.

Results

The integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.

Conclusions

This study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management.

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An integrated database of wood-formation related genes in plants

An integrated database of wood-formation related genes in plants | Plant Gene Seeker -PGS | Scoop.it

Scientific Reports : Nature Publishing Group

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Wood, which consists mainly of plant cell walls, is an extremely important resource in daily lives. Genes whose products participate in the processes of cell wall and wood formation are therefore major subjects of plant science research. The Wood-Formation Related Genes database (WFRGdb, http://me.lzu.edu.cn/woodformation/) serves as a data resource center for genes involved in wood formation. To create this database, we collected plant genome data published in other online databases and predicted all cell wall and wood formation related genes using BLAST and HMMER. To date, 47 gene families and 33 transcription factors from 57 genomes (28 herbaceous, 22 woody and 7 non-vascular plants) have been covered and more than 122,000 genes have been checked and recorded. To provide easy access to these data, we have developed several search methods, which make it easy to download targeted genes or groups of genes free of charge in FASTA format. Sequence and phylogenetic analyses are also available online. WFRGdb brings together cell wall and wood formation related genes from all available plant genomes, and provides an integrative platform for gene inquiry, downloading and analysis. This database will therefore be extremely useful for those who focuses on cell wall and wood research.

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Root phenotyping: from component trait in the lab to breeding

Root phenotyping: from component trait in the lab to breeding | Plant Gene Seeker -PGS | Scoop.it
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Abstract

In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential.

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The radish genome and comprehensive gene expression profile of tuberous root formation and development

The radish genome and comprehensive gene expression profile of tuberous root formation and development | Plant Gene Seeker -PGS | Scoop.it

Scientific Reports : Nature Publishing Group

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Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

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Differential Roles of PIN1 and PIN2 in Root Meristem Maintenance Under Low-B Conditions in Arabidopsis thaliana

Differential Roles of PIN1 and PIN2 in Root Meristem Maintenance Under Low-B Conditions in Arabidopsis thaliana | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Boron (B) is an essential element for plants; its deficiency causes rapid cessation of root elongation. In addition, B influences auxin accumulation in plants. To assess the importance of auxin transport in B-dependent root elongation, Arabidopsis thaliana pin1–pin4 mutants were grown under low-B conditions. Among them, only the pin2/eir1-1 mutant showed a significantly shorter root under low-B conditions than under control conditions. Moreover, the root meristem size of pin2/eir1-1 was reduced under low-B conditions. Among the PIN-FORMED (PIN) family, PIN1 and PIN2 are important for root meristem growth/maintenance under normal conditions. To investigate the differential response of pin1 and pin2 mutants under low-B conditions, the effect of low-B on PIN1–green fluorescent protein (GFP) and PIN2–GFP accumulation and localization was examined. Low-B did not affect PIN2–GFP, while it reduced the accumulation of PIN1–GFP. Moreover, no signal from DII-VENUS, an auxin sensor, was detected under the low-B condition in the stele of wild-type root meristems. Taken together, these results indicate that under low-B conditions PIN1 is down-regulated and PIN2 plays an important role in root meristem maintenance.

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Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis | Plant Gene Seeker -PGS | Scoop.it

DOWNIE - 2014

Plant, Cell & Environment

Wiley Online Library

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Abstract

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.

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Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding

Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding | Plant Gene Seeker -PGS | Scoop.it

Molecular Plant

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Abstract

The temperate-tropical division of early maize germplasms to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from examining 558 529 single nucleotide polymorphisms, expression data of 28 769 genes, and 662 traits collected from 368 diverse temperate and tropical maize inbred lines in this study. This is a new attempt to systematically exploit the mechanisms of the adaptation process in maize. Our results indicate that divergence between tropical and temperate lines apparently occurred 3400–6700 years ago. Seven hundred and one genomic selection signals and transcriptomic variants including 2700 differentially expressed individual genes and 389 rewired co-expression network genes were identified. These candidate signals were found to be functionally related to stress responses, and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. Our study also clearly indicates that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. The latter process may be a more flexible and dynamic way for maize to adapt to environmental changes along its short evolutionary history.

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Root Hair Development in the Grasses: What We Already Know and What We Still Need to Know

Root Hair Development in the Grasses: What We Already Know and What We Still Need to Know | Plant Gene Seeker -PGS | Scoop.it
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Abstract

A priority in many crop improvement programs for a long time has been to enhance the tolerance level of plants to both abiotic and biotic stress. Recognition that the root system is the prime determinant of a plant’s ability to extract both water and minerals from the soil implies that its architecture is an important variable underlying a cultivar’s adaptation. The density and/or length of the root hairs (RHs) that are formed are thought to have a major bearing on the plant’s performance under stressful conditions. Any attempt to improve a crop’s root system will require a detailed understanding of the processes of RH differentiation. Recent progress in uncovering the molecular basis of root epidermis specialization has been recorded in the grasses. This review seeks to present the current view of RH differentiation in grass species. It combines what has been learned from molecular-based analyses, histological studies, and observation of the phenotypes of both laboratory- and field-grown plants.

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What plant hydraulics can tell us about responses to climate-change droughts

What plant hydraulics can tell us about responses to climate-change droughts | Plant Gene Seeker -PGS | Scoop.it

New Phytologist - Wiley Online Library

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Summary

Climate change exposes vegetation to unusual drought, causing declines in productivity and increased mortality. Drought responses are hard to anticipate because canopy transpiration and diffusive conductance (G) respond to drying soil and vapor pressure deficit (D) in complex ways. A growing database of hydraulic traits, combined with a parsimonious theory of tree water transport and its regulation, may improve predictions of at-risk vegetation. The theory uses the physics of flow through soil and xylem to quantify how canopy water supply declines with drought and ceases by hydraulic failure. This transpiration ‘supply function’ is used to predict a water ‘loss function’ by assuming that stomatal regulation exploits transport capacity while avoiding failure. Supply–loss theory incorporates root distribution, hydraulic redistribution, cavitation vulnerability, and cavitation reversal. The theory efficiently defines stomatal responses to D, drying soil, and hydraulic vulnerability. Driving the theory with climate predicts drought-induced loss of plant hydraulic conductance (k), canopy G, carbon assimilation, and productivity. Data lead to the ‘chronic stress hypothesis’ wherein > 60% loss of k increases mortality by multiple mechanisms. Supply–loss theory predicts the climatic conditions that push vegetation over this risk threshold. The theory's simplicity and predictive power encourage testing and application in large-scale modeling.

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Cytokinin is required for escape but not release from auxin mediated apical dominance

Cytokinin is required for escape but not release from auxin mediated apical dominance | Plant Gene Seeker -PGS | Scoop.it

Müller - 2015 - The Plant Journal -

OPEN

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Summary

Auxin produced by an active primary shoot apex is transported down the main stem and inhibits the growth of the axillary buds below it, contributing to apical dominance. Here we use Arabidopsis thaliana cytokinin (CK) biosynthetic and signalling mutants to probe the role of CK in this process. It is well established that bud outgrowth is promoted by CK, and that CK synthesis is inhibited by auxin, leading to the hypothesis that release from apical dominance relies on an increased supply of CK to buds. Our data confirm that decapitation induces the expression of at least one ISOPENTENYLTRANSFERASE (IPT) CK biosynthetic gene in the stem. We further show that transcript abundance of a clade of the CK-responsive type-A Arabidopsis response regulator (ARR) genes increases in buds following CK supply, and that, contrary to their typical action as inhibitors of CK signalling, these genes are required for CK-mediated bud activation. However, analysis of the relevant arr and ipt multiple mutants demonstrates that defects in bud CK response do not affect auxin-mediated bud inhibition, and increased IPT transcript levels are not needed for bud release following decapitation. Instead, our data suggest that CK acts to overcome auxin-mediated bud inhibition, allowing buds to escape apical dominance under favourable conditions, such as high nitrate availability.

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Chromatin dynamics during cellular differentiation in the female reproductive lineage of flowering plants

Chromatin dynamics during cellular differentiation in the female reproductive lineage of flowering plants | Plant Gene Seeker -PGS | Scoop.it

Baroux - 2015 - The Plant Journal - Wiley Online Library

Open Access

Andres Zurita's insight:

Sexual reproduction in flowering plants offers a number of remarkable aspects to developmental biologists. First, the spore mother cells – precursors of the plant reproductive lineage – are specified late in development, as opposed to precocious germline isolation during embryogenesis in most animals. Second, unlike in most animals where meiosis directly produces gametes, plant meiosis entails the differentiation of a multicellular, haploid gametophyte, within which gametic as well as non-gametic accessory cells are formed. These observations raise the question of the factors inducing and modus operandi of cell fate transitions that originate in floral tissues and gametophytes, respectively. Cell fate transitions in the reproductive lineage imply cellular reprogramming operating at the physiological, cytological and transcriptome level, but also at the chromatin level. A number of observations point to large-scale chromatin reorganization events associated with cellular differentiation of the female spore mother cells and of the female gametes. These include a reorganization of the heterochromatin compartment, the genome-wide alteration of the histone modification landscape, and the remodeling of nucleosome composition. The dynamic expression of DNA methyltransferases and actors of small RNA pathways also suggest additional, global epigenetic alterations that remain to be characterized. Are these events a cause or a consequence of cellular differentiation, and how do they contribute to cell fate transition? Does chromatin dynamics induce competence for immediate cellular functions (meiosis, fertilization), or does it also contribute long-term effects in cellular identity and developmental competence of the reproductive lineage? This review attempts to review these fascinating questions.

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Chromatin and epigenetics at the nexus between cell division, differentiation and development

Chromatin and epigenetics at the nexus between cell division, differentiation and development | Plant Gene Seeker -PGS | Scoop.it
Special Issue: Chromatin and epigenetics at the nexus between cell division, differentiation and development
Andres Zurita's insight:

It is now approximately 40 years since chromatin studies changed drastically with the first visualization of ‘nu bodies’, that we now know as nucleosomes. The ‘beads on a string’ that appeared in electron micrographs (Olins and Olins, 1974) showed the structural units of chromatin and provided the foundation for a field that has been expanding ever since then. One of the major advances in chromatin studies has been the identification of numerous connections between nucleosome organization, including the plethora of histone post-translational modifications, and gene function. Studies in an apparently different field, development of multicellular organisms, have also revealed that developmental transitions and organogenesis are strictly dependent on the establishment, maintenance and modification of highly regulated gene expression patterns. Therefore, efforts to learn about chromatin organization and function, gene expression and developmental transitions converge, contributing to provide a complete picture. In this Special Issue on ‘Chromatin and epigenetics at the nexus between cell division, differentiation and development’ we have gathered articles from leading scientists in their fields discussing a broad spectrum of topics relating chromatin structure and function with developmental transitions: the special organization and functional properties of centromeres and telomeres, genome maintenance and integrity, nucleosome remodeling and modification complexes, histone dynamics, epigenetic memory and chromatin during gametophyte development.

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German authorities approve genome edited rape seed (canola) as non GMO

German authorities approve genome edited rape seed (canola) as non GMO | Plant Gene Seeker -PGS | Scoop.it

Via Saclay Plant Sciences
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Saclay Plant Sciences's curator insight, June 20, 3:03 AM

German authorities approve genome edited rape seed (canola) as non GMO,

 http://www.testbiotech.org/sites/default/files/BVL%20Cibus.pdf

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Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana (L.) Heynh

Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana (L.) Heynh | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

A balanced supply of essential nutrients is an important factor influencing root architecture in many plants, yet data related to the interactive effects of two nutrients on root growth are limited. Here, we investigated the interactive effect between phosphorus (P) and magnesium (Mg) on root growth of Arabidopsis grown in pH-buffered agar medium at different P and Mg levels. The results showed that elongation and deviation of primary roots were directly correlated with the amount of P added to the medium but could be modified by the Mg level, which was related to the root meristem activity and stem-cell division. High P enhanced while low P decreased the tip-focused fluorescence signal of auxin biosynthesis, transport, and redistribution during elongation of primary roots; these effects were greater under low Mg than under high Mg. The altered root growth in response to P and Mg supply was correlated with AUX1, PIN2, and PIN3 mRNA abundance and expression and the accumulation of the protein. Application of either auxin influx inhibitor or efflux inhibitor inhibited the elongation and increased the deviation angle of primary roots, and decreased auxin level in root tips. Furthermore, the auxin-transport mutants aux1-22 and eir1-1 displayed reduced root growth and increased the deviation angle. Our data suggest a profound effect of the combined supply of P and Mg on the development of root morphology in Arabidopsis through auxin signals that modulate the elongation and directional growth of primary root and the expression of root differentiation and development genes.

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Global Synthesis of Drought Effects on Food Legume Production

Global Synthesis of Drought Effects on Food Legume Production | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:
AbstractFood legume crops play important roles in conservation farming systems and contribute to food security in the developing world. However, in many regions of the world, their production has been adversely affected by drought. Although water scarcity is a severe abiotic constraint of legume crops productivity, it remains unclear how the effects of drought co-vary with legume species, soil texture, agroclimatic region, and drought timing. To address these uncertainties, we collected literature data between 1980 and 2014 that reported monoculture legume yield responses to drought under field conditions, and analyzed this data set using meta-analysis techniques. Our results showed that the amount of water reduction was positively related with yield reduction, but the extent of the impact varied with legume species and the phenological state during which drought occurred. Overall, lentil (Lens culinaris), groundnut (Arachis hypogaea), and pigeon pea (Cajanus cajan) were found to experience lower drought-induced yield reduction compared to legumes such as cowpea (Vigna unguiculata) and green gram (Vigna radiate). Yield reduction was generally greater when legumes experienced drought during their reproductive stage compared to during their vegetative stage. Legumes grown in soil with medium texture also exhibited greater yield reduction compared to those planted on soil of either coarse or fine texture. In contrast, regions and their associated climatic factors did not significantly affect legume yield reduction. In the face of changing climate, our study provides useful information for agricultural planning and research directions for development of drought-resistant legume species to improve adaptation and resilience of agricultural systems in the drought-prone regions of the world.
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Producing a road map that enables plants to cope with future climate change

Producing a road map that enables plants to cope with future climate change | Plant Gene Seeker -PGS | Scoop.it
If the worst predictions of climate change are correct, global warming could cause changes in temperature at a rate unmatched over the last 50 million years, as well as an increase in the frequency and severity of extreme weather events. The potential impact of such events on food production can already be seen in the effects of the severe droughts in Australia in 2007–8, Russia in 2010, and South-East China in 2013, all of which contributed to steep rises in crop commodity prices and helped push food security to the top of the global agenda.

As well as dealing with a changing and increasingly extreme climate, agriculture will have to meet the demands of a growing population and increasing per capita consumption while contending with rising energy costs, the approach of peak oil, the use of crop products for biofuel and renewable raw materials, competition for fresh water and land, soil degradation, and pollution. It will also be required to do its bit to reduce greenhouse gas emissions. Plant breeding and the sciences that underpin it will have a major part to play in meeting these challenges, and this volume comprises a series of papers from leading researchers in the field.
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A Special Issue of Journal of Experimental Botany, with the focus on "Breeding Plants to Cope with Future Climate Change". Nice reviews and research articles, specially in 

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Getting the ‘MOST’ out of crop improvement

Getting the ‘MOST’ out of crop improvement | Plant Gene Seeker -PGS | Scoop.it

Trends in Plant Science

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Highlights

 

We propose ‘molecular strengthening’ (MOST) to improve crop performance.MOST treatments help to maximize trait expression for any given genotype and counteract environmental conditions.Detailed molecular genetic information is essential for development of MOST treatments.MOST treatments can be combined with current breeding methods like marker aided selection, transgenics, and genomic selection.

 

Unraveling the function of genes affecting agronomic traits is accelerating due to progress in DNA sequencing and other high-throughput genomic approaches. Characterized genes can be exploited by plant breeders by using either marker-aided selection (MAS) or transgenic procedures. Here, we propose a third ‘outlet’, ‘molecular strengthening’ (MOST), as alternative option for exploiting detailed molecular understanding of trait expression, which is comparable to the pharmaceutical treatment of human diseases. MOST treatments can be used to enhance yield stability. Alternatively, they can be used to control traits temporally, such as flowering time to facilitate crosses for plant breeders. We also discuss the essence for developing MOST treatments, their prospects, and limitations.

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Omics Approaches Toward Defining the Comprehensive Abscisic Acid Signaling Network in Plants

Omics Approaches Toward Defining the Comprehensive Abscisic Acid Signaling Network in Plants | Plant Gene Seeker -PGS | Scoop.it
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ABA is a plant hormone that plays crucial roles in controlling cellular and physiological responses to osmotic stress and in developmental processes. Endogenous ABA levels are increased in response to a decrease in water availability in cells, and ABA sensing and signaling are thought to be mediated according to the current model established in Arabidopsis thaliana, which involves pyrabactin resistance 1 (PYR)/PYR1-like (PYL)/regulatory components of ABA receptor (RCAR), protein phosphatase 2C (PP2C) and sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2). These core components of ABA signaling have a pivotal role in stress-responsive gene expression and stomatal regulation. However, because a limited number of their upstream and downstream factors have been characterized, it is still difficult to define the comprehensive network of ABA signaling in plants. This review focuses on current progress in the study of PYR/PYL/RCARs, PP2Cs and SnRK2s, with particular emphasis on omics approaches, such as interactome and phosphoproteome studies. Moreover, the role of ABA in plant growth and development is discussed based on recent metabolomic profiling studies.

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Plant signalling mechanisms in response to the environment

Plant signalling mechanisms in response to the environment | Plant Gene Seeker -PGS | Scoop.it
Editorial Plant signalling mechanisms in response to the environmentEnvironmental and Experimental Botany
 
Andres Zurita's insight:

Being sessile organisms, plants are faced with multiple and changing environmental stimuli and stressors which have to be intercepted, interpreted to generate appropriate responses for continued development, growth and ultimate survival of the species. All of these processes involve plant signalling mechanisms, these ranging from environmental sensors of biotic and abiotic factors, multiple signal transduction pathways involving a plethora of molecules that govern not only individual processes at the subcellular, organ and whole plant level but which are involved in cross talk between them. It is no surprise that the field of plant signalling is emerging as one indispensable in the study of biological processes, and understanding of these complex interactions is of increasing importance in managing plant productivity for food security purposes in a time when predictions from climate change models propose that increasing temperatures, UV emissions and considerably altered precipitation patterns inter alia will preclude agricultural practices commonly used today.

This special edition on Plant Signalling brings together 14 papers on various aspects of plant signalling, including responses to abiotic factors of water availability, temperature, light, hypoxia, macro and micro nutrient status, and biotic stimuli/stresses imposed by micro-, meso and macro organisms, at the cellar, organ and whole plant level. The roles of plant hormones, phospholipid signalling, redox balance, transcription factors and other regulatory elements such as microRNAs, heterotrimeric G-proteins and ubiquitination-mediated protein regulation are presented for a number of plant species and mechanisms of action (chemical and electrical) and cross talk among these in control of multiple simultaneous external stimuli are discussed.

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Domestication: Sweet! A naturally transgenic crop

Domestication: Sweet! A naturally transgenic crop | Plant Gene Seeker -PGS | Scoop.it
Strains of bacteria from the genus Agrobacterium have a well-characterized and widely utilized capacity to introduce DNA into plant cells1. The transferred DNA (T-DNA) is specified by short left and right border sequences, and is delivered from the bacterium into plant cells by a mechanism that evolved from bacterial conjugation2. Essentially, the bacteria have sex with the plant. The bacteria-derived genes perturb plant hormonal balances causing tumour-like galls, and also modify plant metabolism to support bacterial growth, by forcing the plant to produce sugar–amino acid conjugates called opines that can only be used as nutrients by agrobacteria. Previously, using less-refined methods, some evidence was found for Agrobacterium-derived sequences inherited in the germ lines of Nicotiana glauca and Linaria vulgaris species, so heritable genetic modification of plants without human intervention is not new3,4. But these plants are not important food crops. Now, Kyndt et al.5 report in Proceedings of the National Academy of Sciences USA that during or prior to domestication, Agrobacterium-derived T-DNA became incorporated into the genome of one of the world's staple crops, the hexaploid sweet potato (Ipomoea batatas).
Andres Zurita's insight:

One of the world's most important staple crops, the sweet potato, is a naturally transgenic plant that was genetically modified thousands of years ago by a soil bacterium. This surprising discovery may influence the public view of GM crops.

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Root anatomical phenes predict root penetration ability and biomechanical properties in maize (Zea Mays)

Root anatomical phenes predict root penetration ability and biomechanical properties in maize (Zea Mays) | Plant Gene Seeker -PGS | Scoop.it
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The ability of roots to penetrate hard soil is important for crop productivity but specific root phenes contributing to this ability are poorly understood. Root penetrability and biomechanical properties are likely to vary in the root system dependent on anatomical structure. No information is available to date on the influence of root anatomical phenes on root penetrability and biomechanics. Root penetration ability was evaluated using a wax layer system. Root tensile and bending strength were evaluated in plant roots grown in the greenhouse and in the field. Root anatomical phenes were found to be better predictors of root penetrability than root diameter per se and associated with smaller distal cortical region cell size. Smaller outer cortical region cells play an important role in stabilizing the root against ovalization and reducing the risk of local buckling and collapse during penetration, thereby increasing root penetration of hard layers. The use of stele diameter was found to be a better predictor of root tensile strength than root diameter. Cortical thickness, cortical cell count, cortical cell wall area and distal cortical cell size were stronger predictors of root bend strength than root diameter. Our results indicate that root anatomical phenes are important predictors for root penetrability of high-strength layers and root biomechanical properties.

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The paralogous R3 MYB proteins CAPRICE, TRIPTYCHON and ENHANCER OF TRY AND CPC1 play pleiotropic and partly non-redundant roles in the phosphate starvation response of Arabidopsis roots

The paralogous R3 MYB proteins CAPRICE, TRIPTYCHON and ENHANCER OF TRY AND CPC1 play pleiotropic and partly non-redundant roles in the phosphate starvation response of Arabidopsis roots | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq. The data show that in an intricate interplay between the three MYBs regulate several developmental, physiological and metabolic processes that are putatively located in different tissues. When grown on media with a low Pi concentration, all three TFs acquire additional functions that are related to the Pi starvation response, including transition metal transport, membrane lipid remodelling, and the acquisition, uptake and storage of Pi. Control of gene activity is partly mediated through the regulation of potential antisense transcripts. The current dataset extends the known functions of R3 MYB proteins, provides a suite of novel candidates with critical function in root hair development under both control and Pi-deficient conditions, and challenges the definition of genetic redundancy by demonstrating that environmental perturbations may confer specific functions to orthologous proteins that could have similar roles under control conditions.

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