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The Brassinosteroid Signaling Pathway - New Key Players and Interconnections with Other Signaling Networks Crucial for Plant Development and Stress Tolerance

The Brassinosteroid Signaling Pathway - New Key Players and Interconnections with Other Signaling Networks Crucial for Plant Development and Stress Tolerance | Plant Gene Seeker -PGS | Scoop.it

Recent studies clearly indicated that some of the components of BR signaling pathway act as multifunctional proteins involved in other signaling networks regulating diverse physiological processes, such as photomorphogenesis, cell death control, stomatal development, flowering, plant immunity to pathogens and metabolic responses to stress conditions, including salinity. Regulation of some of these processes is mediated through a crosstalk between BR signalosome and the signaling cascades of other hormones, including auxin, abscisic acid, ethylene and salicylic acid. Unravelling the complicated mechanisms of BR signaling and its interconnections with other molecular networks may be of great importance for future practical applications in agriculture.


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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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Andres Zurita's insight:
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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A novel highly differentially expressed gene in wheat endosperm associated with bread quality

A novel highly differentially expressed gene in wheat endosperm associated with bread quality | Plant Gene Seeker -PGS | Scoop.it

Scientific Reports : Nature Publishing Group

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Analysis of gene expression in developing wheat seeds was used to identify a gene, wheat bread making (wbm), with highly differential expression (~1000 fold) in the starchy endosperm of genotypes varying in bread making quality. Several alleles differing in the 5’-upstream region (promoter) of this gene were identified, with one present only in genotypes with high levels of wbm expression. RNA-Seq analysis revealed low or no wbm expression in most genotypes but high expression (0.2-0.4% of total gene expression) in genotypes that had good bread loaf volume. The wbm gene is predicted to encode a mature protein of 48 amino acids (including four cysteine residues) not previously identified in association with wheat quality, possibly because of its small size and low frequency in the wheat gene pool. Genotypes with high wbm expression all had good bread making quality but not always good physical dough qualities. The predicted protein was sulphur rich suggesting the possibility of a contribution to bread loaf volume by supporting the crossing linking of proteins in gluten. Improved understanding of the molecular basis of differences in bread making quality may allow more rapid development of high performing genotypes with acceptable end-use properties and facilitate increased wheat production.

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Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines

Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

MADS-box transcription factors are involved in many aspects of plant growth and development, such as floral organ determination, fruit ripening, and embryonic development. Yet not much is known about grape (Vitis vinifera) MADS-box genes in a relatively comprehensive genomic and functional way during ovule development. Accordingly, we identified 54 grape MADS-box genes, aiming to enhance our understanding of grape MADS-box genes from both evolutionary and functional perspectives. Synteny analysis indicated that both segmental and tandem duplication events contributed to the expansion of the grape MADS-box family. Furthermore, synteny analysis between the grape and Arabidopsis genomes suggested that several grape MADS-box genes arose before divergence of the two species. Phylogenetic analysis and comparisons of exon–intron structures provided further insight into the evolutionary relationships between the genes, as well as their putative functions. Based on phylogenetic tree analysis, grape MADS-box genes were divided into type I and type II subgroups. Tissue-specific expression analysis suggested roles in both vegetative and reproductive tissue development. Expression analysis of the MADS-box genes following gibberellic acid (GA3) treatment revealed their response to GA3 treatment and that seedlessness caused by GA3 treatment underwent a different mechanism from that of normal ovule abortion. Expression profiling of MADS-box genes from six cultivars suggests their function in ovule development and may represent potential ovule identity genes involved in parthenocarpy. The results presented provide a few candidate genes involved in ovule development for future study, which may be useful in seedlessness-related molecular breeding programs.

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Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past

Chemical messages in 170-year-old champagne bottles from the Baltic Sea: Revealing tastes from the past | Plant Gene Seeker -PGS | Scoop.it
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Abstract

Archaeochemistry as the application of the most recent analytical techniques to ancient samples now provides an unprecedented understanding of human culture throughout history. In this paper, we report on a multiplatform analytical investigation of 170-y-old champagne bottles found in a shipwreck at the bottom of the Baltic Sea, which provides insight into winemaking practices used at the time. Organic spectroscopy-based nontargeted metabolomics and metallomics give access to the detailed composition of these wines, revealing, for instance, unexpected chemical characteristics in terms of small ion, sugar, and acid contents as well as markers of barrel aging and Maillard reaction products. The distinct aroma composition of these ancient champagne samples, first revealed during tasting sessions, was later confirmed using state-of-the-art aroma analysis techniques. After 170 y of deep sea aging in close-to-perfect conditions, these sleeping champagne bottles awoke to tell us a chapter of the story of winemaking and to reveal their extraordinary archaeometabolome and elemental diversity in the form of chemical signatures related to each individual step of champagne production.

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The Pepper Lipoxygenase CaLOX1 Plays a Role in Osmotic, Drought and High Salinity Stress Response

The Pepper Lipoxygenase CaLOX1 Plays a Role in Osmotic, Drought and High Salinity Stress Response | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

In plants, lipoxygenases (LOXs) are involved in various physiological processes, including defense responses to biotic and abiotic stresses. Our previous study had shown that the pepper 9-LOX gene, CaLOX1, plays a crucial role in cell death due to pathogen infection. Here, the function of CaLOX1 in response to osmotic, drought and high salinity stress was examined using CaLOX1-overexpressing (CaLOX1-OX) Arabidopsis plants. Changes in the temporal expression pattern of the CaLOX1 gene were observed when pepper leaves were treated with drought and high salinity, but not when treated with ABA, the primary hormone in response to drought stress. During seed germination and seedling development, CaLOX1-OX plants were more tolerant to ABA, mannitol and high salinity than wild-type plants. In contrast, expression of the ABA-responsive marker genes RAB18 and RD29B was higher in CaLOX1-OX Arabidopsis plants than in wild-type plants. In response to high salinity, CaLOX1-OX plants exhibited enhanced tolerance, compared with the wild type, which was accompanied by decreased accumulation of H2O2 and high levels of RD20, RD29A, RD29B and P5CS gene expression. Similarly, CaLOX1-OX plants were also more tolerant than wild-type plants to severe drought stress. H2O2 production and the relative increase in lipid peroxidation were lower, and the expression of COR15A, DREB2A, RD20, RD29A and RD29B was higher in CaLOX1-OX plants, relative to wild-type plants. Taken together, our results indicate that CaLOX1 plays a crucial role in plant stress responses by modulating the expression of ABA- and stress-responsive marker genes, lipid peroxidation and H2O2 production.

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Interplay between reactive oxygen species and hormones in the control of plant development and stress tolerance

Interplay between reactive oxygen species and hormones in the control of plant development and stress tolerance | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

As a consequence of a sessile lifestyle, plants are continuously exposed to changing environmental conditions and often life-threatening stresses caused by exposure to excessive light, extremes of temperature, limiting nutrient or water availability, and pathogen/insect attack. The flexible coordination of plant growth and development is necessary to optimize vigour and fitness in a changing environment through rapid and appropriate responses to such stresses. The concept that reactive oxygen species (ROS) are versatile signalling molecules in plants that contribute to stress acclimation is well established. This review provides an overview of our current knowledge of how ROS production and signalling are integrated with the action of auxin, brassinosteroids, gibberellins, abscisic acid, ethylene, strigolactones, salicylic acid, and jasmonic acid in the coordinate regulation of plant growth and stress tolerance. We consider the local and systemic crosstalk between ROS and hormonal signalling pathways and identify multiple points of reciprocal control, as well as providing insights into the integration nodes that involve Ca2+-dependent processes and mitogen-activated protein kinase phosphorylation cascades.

 
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The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration

The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

“Drying without dying” is an essential trait in land plant evolution. Unraveling how a unique group of angiosperms, the Resurrection Plants, survive desiccation of their leaves and roots has been hampered by the lack of a foundational genome perspective. Here we report the ∼1,691-Mb sequenced genome of Boea hygrometrica, an important resurrection plant model. The sequence revealed evidence for two historical genome-wide duplication events, a compliment of 49,374 protein-coding genes, 29.15% of which are unique (orphan) to Boea and 20% of which (9,888) significantly respond to desiccation at the transcript level. Expansion of early light-inducible protein (ELIP) and 5S rRNA genes highlights the importance of the protection of the photosynthetic apparatus during drying and the rapid resumption of protein synthesis in the resurrection capability of Boea. Transcriptome analysis reveals extensive alternative splicing of transcripts and a focus on cellular protection strategies. The lack of desiccation tolerance-specific genome organizational features suggests the resurrection phenotype evolved mainly by an alteration in the control of dehydration response genes.


Significance

The genome analysis presented here represents a major step forward in the field of desiccation tolerance and a much-anticipated resource that will have a far-reaching effect in many areas of plant biology and agriculture. We present the ∼1.69-Gb draft genome of Boea hygrometrica, an important plant model for understanding responses to dehydration. To our knowledge, this is the first genome sequence of a desiccation-tolerant extremophile, offering insight into the evolution of this important trait and a first look, to our knowledge, into the genome organization of desiccation tolerance. The underpinning genome architecture and response in relation to the hydration state of the plant and its role in the preservation of cellular integrity has important implications for developing drought tolerance improvement strategies for our crops.


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Engineering plants to reflect light: strategies for engineering water-efficient plants to adapt to a changing climate

Engineering plants to reflect light: strategies for engineering water-efficient plants to adapt to a changing climate | Plant Gene Seeker -PGS | Scoop.it

Population growth and globally increasing standards of living have put a significant strain on the energy-food-water nexus. Limited water availability particularly affects agriculture, as it accounts for over 70% of global freshwater withdrawals.

 

This study outlines the fundamental nature of plant water consumption and suggests a >50% reduction in renewable freshwater demand is possible by engineering more reflective crops. Furthermore, the decreased radiative forcing resulting from the greater reflectivity of crops would be equivalent to removing 10-50 ppm CO2 from the atmosphere.

 

Recent advances in engineering optical devices and a greater understanding of the mechanisms of biological reflectance suggest such a strategy may now be viable... While the local benefits may be straightforward, determining the global externalities will require careful modelling efforts and gradually scaled field trials.

 

http://dx.doi.org/10.1111/pbi.12382

 


Via Alexander J. Stein
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Differentiating phosphate-dependent and phosphate-independent systemic phosphate-starvation response networks in Arabidopsis thaliana through the application of phosphite

Differentiating phosphate-dependent and phosphate-independent systemic phosphate-starvation response networks in Arabidopsis thaliana through the application of phosphite | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Phosphite is a less oxidized form of phosphorus than phosphate. Phosphite is considered to be taken up by the plant through phosphate transporters. It can mimic phosphate to some extent, but it is not metabolized into organophosphates. Phosphite could therefore interfere with phosphorus signalling networks. Typical physiological and transcriptional responses to low phosphate availability were investigated and the short-term kinetics of their reversion by phosphite, compared with phosphate, were determined in both roots and shoots of Arabidopsis thaliana. Phosphite treatment resulted in a strong growth arrest. It mimicked phosphate in causing a reduction in leaf anthocyanins and in the expression of a subset of the phosphate-starvation-responsive genes. However, the kinetics of the response were slower than for phosphate, which may be due to discrimination against phosphite by phosphate transporters PHT1;8 and PHT1;9 causing delayed shoot accumulation of phosphite. Transcripts encoding PHT1;7, lipid-remodelling enzymes such as SQD2, and phosphocholine-producing NMT3 were highly responsive to phosphite, suggesting their regulation by a direct phosphate-sensing network. Genes encoding components associated with the ‘PHO regulon’ in plants, such as At4, IPS1, and PHO1;H1, generally responded more slowly to phosphite than to phosphate, except for SPX1 in roots and MIR399d in shoots. Two uncharacterized phosphate-responsive E3 ligase genes, PUB35 and C3HC4, were also highly phosphite responsive. These results show that phosphite is a valuable tool to identify network components directly responsive to phosphate.

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Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement | Plant Gene Seeker -PGS | Scoop.it

NATURE BIOTECHNOLOGY | RESEARCH ARTICLE OPEN

Andres Zurita's insight:

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

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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
Andres Zurita's insight:

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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Modified CTAB and TRIzol Protocols Improve RNA Extraction from Chemically Complex Embryophyta

Modified CTAB and TRIzol Protocols Improve RNA Extraction from Chemically Complex Embryophyta | Plant Gene Seeker -PGS | Scoop.it
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Premise of the study: Here we present a series of protocols for RNA extraction across a diverse array of plants; we focus on woody, aromatic, aquatic, and other chemically complex taxa.

Methods and Results: Ninety-one taxa were subjected to RNA extraction with three methods presented here: (1) TRIzol/TURBO DNA-free kits using the manufacturer's protocol with the addition of sarkosyl; (2) a combination method using cetyltrimethylammonium bromide (CTAB) and TRIzol/sarkosyl/TURBO DNA-free; and (3) a combination of CTAB and QIAGEN RNeasy Plant Mini Kit. Bench-ready protocols are given.

Conclusions: After an iterative process of working with chemically complex taxa, we conclude that the use of TRIzol supplemented with sarkosyl and the TURBO DNA-free kit is an effective, efficient, and robust method for obtaining RNA from 100 mg of leaf tissue of land plant species (Embryophyta) examined. Our protocols can be used to provide RNA of suitable stability, quantity, and quality for transcriptome sequencing.

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A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system– and sperm motility–related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.

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Genes and networks regulating root anatomy and architecture

Genes and networks regulating root anatomy and architecture | Plant Gene Seeker -PGS | Scoop.it

Wachsman - 2015 - New Phytologist - Wiley Online Library

OPEN ACCESS

Andres Zurita's insight:

The root is an excellent model for studying developmental processes that underlie plant anatomy and architecture. Its modular structure, the lack of cell movement and relative accessibility to microscopic visualization facilitate research in a number of areas of plant biology. In this review, we describe several examples that demonstrate how cell type-specific developmental mechanisms determine cell fate and the formation of defined tissues with unique characteristics. In the last 10 yr, advances in genome-wide technologies have led to the sequencing of thousands of plant genomes, transcriptomes and proteomes. In parallel with the development of these high-throughput technologies, biologists have had to establish computational, statistical and bioinformatic tools that can deal with the wealth of data generated by them. These resources provide a foundation for posing more complex questions about molecular interactions, and have led to the discovery of new mechanisms that control phenotypic differences. Here we review several recent studies that shed new light on developmental processes, which are involved in establishing root anatomy and architecture. We highlight the power of combining large-scale experiments with classical techniques to uncover new pathways in root development.

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The genome sequence of the orchid Phalaenopsis equestris : Nature Genetics : Nature Publishing Group

The genome sequence of the orchid Phalaenopsis equestris : Nature Genetics : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

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Trafficking of Plant Plasma Membrane Aquaporins: Multiple Regulation Levels and Complex Sorting Signals

Trafficking of Plant Plasma Membrane Aquaporins: Multiple Regulation Levels and Complex Sorting Signals | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Aquaporins are small channel proteins which facilitate the diffusion of water and small neutral molecules across biological membranes. Compared with animals, plant genomes encode numerous aquaporins, which display a large variety of subcellular localization patterns. More specifically, plant aquaporins of the plasma membrane intrinsic protein (PIP) subfamily were first described as plasma membrane (PM)-resident proteins, but recent research has demonstrated that the trafficking and subcellular localization of these proteins are complex and highly regulated. In the past few years, PIPs emerged as new model proteins to study subcellular sorting and membrane dynamics in plant cells. At least two distinct sorting motifs (one cytosolic, the other buried in the membrane) are required to direct PIPs to the PM. Hetero-oligomerization and interaction with SNAREs (soluble N-ethylmaleimide-sensitive factor protein attachment protein receptors) also influence the subcellular trafficking of PIPs. In addition to these constitutive processes, both the progression of PIPs through the secretory pathway and their dynamics at the PM are responsive to changing environmental conditions.

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Breeding and characterization of soybean Triple Null; a stack of recessive alleles of Kunitz Trypsin Inhibitor, Soybean Agglutinin, and P34 allergen nulls

Breeding and characterization of soybean Triple Null; a stack of recessive alleles of Kunitz Trypsin Inhibitor, Soybean Agglutinin, and P34 allergen nulls | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Soybean (Glycine max) seeds contain bioactive proteins with antinutritional and immunological properties that affect metabolism and assimilation of nutrients. The presence of antinutritional proteins requires soybeans to be heat-treated resulting in input energy costs. Nulls for bioactive seed proteins have been previously isolated from the USDA soybean collection, including Kunitz trypsin inhibitor (TI), soybean agglutinin (LE) and immunodominant soybean allergen P34 protein. Each of these nulls has the potential to partially address the concerns of soybean feed/food consumption. A stack of recessive nulls of TI, LE and P34 was created in a cv ‘Williams 82’ background termed ‘Triple Null’. Triple Null has a slight reduction of total protein compared with ‘Williams 82’ corresponding to aggregate contribution of TI, LE and P34 in the seed proteome. Triple Null's proteome analysis revealed P34 and TI nulls are frame-shift mutants able to accumulate small amounts of authentic P34 and TI proteins. Triple Null has possible application as a conventional feed/food source and for immunotherapy to mitigate soybean allergenic response.

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Sugar demand of ripening grape berries leads to recycling of surplus phloem water via the xylem

Sugar demand of ripening grape berries leads to recycling of surplus phloem water via the xylem | Plant Gene Seeker -PGS | Scoop.it

KELLER - 2014 - Plant, Cell & Environment - Wiley Online Library

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Abstract

We tested the common assumption that fleshy fruits become dependent on phloem water supply because xylem inflow declines at the onset of ripening. Using two distinct grape genotypes exposed to drought stress, we found that a sink-driven rise in phloem inflow at the beginning of ripening was sufficient to reverse drought-induced berry shrinkage. Rewatering accelerated berry growth and sugar accumulation concurrently with leaf photosynthetic recovery. Interrupting phloem flow through the peduncle prevented the increase in berry growth after rewatering, but interrupting xylem flow did not. Nevertheless, xylem flow in ripening berries, but not berry size, remained responsive to root or shoot pressurization. A mass balance analysis on ripening berries sampled in the field suggested that phloem water inflow may exceed growth and transpiration water demands. Collecting apoplastic sap from ripening berries showed that osmotic pressure increased at distinct rates in berry vacuoles and apoplast. Our results indicate that the decrease in xylem inflow at the onset of ripening may be a consequence of the sink-driven increase in phloem inflow. We propose a conceptual model in which surplus phloem water bypasses the fruit cells and partly evaporates from the berry surface and partly moves apoplastically to the xylem for outflow.

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qRT9, a quantitative trait locus controlling root thickness and root length in upland rice

qRT9, a quantitative trait locus controlling root thickness and root length in upland rice | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Breeding for strong root systems is an important strategy for improving drought avoidance in rice. To clone genes responsible for strong root traits, an upland rice introgression line IL392 with thicker and longer roots than the background parent lowland rice Yuefu was selected. A quantitative trait locus (QTL), qRT9, controlling root thickness and root length was detected under hydroponic culture using 203 F2:3 populations derived from a cross between Yuefu and IL392. The qRT9 locus explained 32.5% and 28.1% of the variance for root thickness and root length, respectively. Using 3185 F2 plants, qRT9 was ultimately narrowed down to an 11.5kb region by substitution mapping. One putative basic helix–loop–helix (bHLH) transcription factor gene, LOC_Os09g28210 (named OsbHLH120), is annotated in this region. Sequences of OsbHLH120 in 11 upland rice and 13 lowland rice indicated that a single nucleotide polymorphism (SNP) at position 82 and an insertion/deletion (Indel) at position 628–642 cause amino acid changes and are conserved between upland rice and lowland rice. Phenotypic analysis indicated that the two polymorphisms were significantly associated with root thickness and root length under hydroponic culture. Quantitative real-time PCR showed that OsbHLH120 was strongly induced by polyethylene glycol (PEG), salt, and abscisic acid, but higher expression was present in IL392 roots than in Yuefu under PEG and salt stress. The successfully isolated locus, qRT9, enriches our knowledge of the genetic basis for drought avoidance and provides an opportunity for breeding drought avoidance varieties by utilizing valuable genes in the upland rice germplasm.

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Roots to Global Food Security. J of Experimental Botany

Roots to Global Food Security. J of Experimental Botany | Plant Gene Seeker -PGS | Scoop.it
Special Issue: Roots to Global Food Security
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This special issue, originating from the ‘Roots to Global Food Security’ meeting at the SEB Annual Meeting in Manchester (2–4 July 2014), not only showcases fundamental science in root growth regulation, root-to-shoot signalling, and crop management, but also demonstrates its importance in securing global food supplies. Many of the authors of the articles collected herein conducted their PhD studies or research within Bill Davies’ group, and a significant feature of this group is the number of PhD graduates who have gone on to forge significant scientific and publishing careers of their own throughout the world. This meeting provided not only an opportunity to discuss issues of scientific importance to Bill, but, once again, to draw together colleagues who have benefited from his friendship and guidance over the years.

 
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