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Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis

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Significance

Cellular signals evoke rapid and broad changes in gene regulatory networks. To uncover these network dynamics, we developed an approach able to monitor primary targets of a transcription factor (TF) based solely on gene regulation, in the absence of detectable binding. This enabled us to follow the transient propagation of a nitrogen (N) nutrient signal as a direct impact of the master TF Basic Leucine Zipper 1 (bZIP1). Unexpectedly, the largest class of primary targets that exhibit transient associations with bZIP1 is uniquely relevant to the rapid and dynamic propagation of the N signal. Our ability to uncover this transient network architecture has revealed the “dark matter” of dynamic N nutrient signaling in plants that has previously eluded detection.

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Plant Gene Seeker -PGS
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Root adaptations to soils with low fertility and aluminium toxicity

Root adaptations to soils with low fertility and aluminium toxicity | Plant Gene Seeker -PGS | Scoop.it

Background 

Plants depend on their root systems to acquire the water and nutrients necessary for their survival in nature, and for their yield and nutritional quality in agriculture. Root systems are complex and a variety of root phenes have been identified as contributors to adaptation to soils with low fertility and aluminium (Al) toxicity. Phenotypic characterization of root adaptations to infertile soils is enabling plant breeders to develop improved cultivars that not only yield more, but also contribute to yield stability and nutritional security in the face of climate variability.

Scope 

In this review the adaptive responses of root systems to soils with low fertility and Al toxicity are described. After a brief introduction, the purpose and focus of the review are outlined. This is followed by a description of the adaptive responses of roots to low supply of mineral nutrients [with an emphasis on low availability of nitrogen (N) and phosphorus (P) and on toxic levels of Al]. We describe progress in developing germplasm adapted to soils with low fertility or Al toxicity using selected examples from ongoing breeding programmes on food (maize, common bean) and forage/feed (Brachiaria spp.) crops. A number of root architectural, morphological, anatomical and metabolic phenes contribute to the superior performance and yield on soils with low fertility and Al toxicity. Major advances have been made in identifying root phenes in improving adaptation to low N (maize), low P (common bean) or high Al [maize, common bean, species and hybrids of brachiariagrass, bulbous canarygrass (Phalaris aquatica) and lucerne (Medicago sativa)].

Conclusions 

Advanced root phenotyping tools will allow dissection of root responses into specific root phenes that will aid both conventional and molecular breeders to develop superior cultivars. These new cultivars will play a key role in sustainable intensification of crop–livestock systems, particularly in smallholder systems of the tropics. Development of these new cultivars adapted to soils with low fertility and Al toxicity is needed to improve global food and nutritional security and environmental sustainability.

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Origins of food crops connect countries worldwide

Origins of food crops connect countries worldwide | Plant Gene Seeker -PGS | Scoop.it
Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.
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Tales and mysteries of fungal fruiting: How morphological and physiological traits affect a pileate lifestyle

Tales and mysteries of fungal fruiting: How morphological and physiological traits affect a pileate lifestyle | Plant Gene Seeker -PGS | Scoop.it

Highlights
• Functionality of the agaricoid fruit body design and its adaptive potential.
• Ecological functions of morphological and physiological fruit body traits.
• Trade-offs among protecting and attracting traits.
• Fruit body development and phenology.

Abstract
Mushroom-forming fungi exhibit a tremendous variety of morphological, physiological and behavioural traits. Though science had taken up the challenge to relate these traits to functions in the 20th century, such deliberations became much rarer in recent decades. In the review presented here we aim at reviving this research area, particularly in regard to ecological implications. We have therefore compiled fruit body traits with their evidenced or suggested functions. Some traits have no immediate functional meaning, but many are suggestive of some ecological importance. Many traits serve more than one function, and traits interact in the sense of trade-offs, patterns that reflect the economy of fungal design. In conclusion, the review comes up with well and little-known mushroom properties, and the numerous gaps in attributing traits to functions.


Via Steve Marek, Francis Martin, Christophe Jacquet
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BMC Genomics

BMC Genomics | Plant Gene Seeker -PGS | Scoop.it

Background 

In wine grape production, management practices have been adopted to optimize grape and wine quality attributes by producing, or screening for, berries of smaller size. Fruit size and composition are influenced by numerous factors that include both internal (e.g. berry hormone metabolism) and external (e.g. environment and cultural practices) factors. Combined physiological, biochemical, and transcriptome analyses were performed to improve our current understanding of metabolic and transcriptional pathways related to berry ripening and composition in berries of different sizes. 

Results 

The comparison of berry physiology between small and large berries throughout development (from 31 to 121 days after anthesis, DAA) revealed significant differences in firmness, the rate of softening, and sugar accumulation at specific developmental stages. Small berries had significantly higher skin to berry weight ratio, lower number of seeds per berry, and higher anthocyanin concentration compared to large berries. RNA-sequencing analyses of berry skins at 47, 74, 103, and 121 DAA revealed a total of 3482 differentially expressed genes between small and large berries. Abscisic acid, auxin, and ethylene hormone pathway genes were differentially modulated between berry sizes. Fatty acid degradation and stilbenoid pathway genes were upregulated at 47 DAA while cell wall degrading and modification genes were downregulated at 74 DAA in small compared to large berries. In the late ripening stage, concerted upregulation of the general phenylpropanoid and stilbenoid pathway genes and downregulation of flavonoid pathway genes were observed in skins of small compared to large berries. Cis-regulatory element analysis of differentially expressed hormone, fruit texture, flavor, and aroma genes revealed an enrichment of specific regulatory motifs related to bZIP, bHLH, AP2/ERF, NAC, MYB, and MADS-box transcription factors. 

Conclusions

The study demonstrates that physiological and compositional differences between berries of different sizes parallel transcriptome changes that involve fruit texture, flavor, and aroma pathways. These results suggest that, in addition to direct effects brought about by differences in size, key aspects involved in the regulation of ripening likely contribute to different quality profiles between small and large berries.

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The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots

The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots | Plant Gene Seeker -PGS | Scoop.it
Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance.
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Conventional Breeding Creates Safer Foods Than Genetic Engineering: Fact or Assumption?

Conventional Breeding Creates Safer Foods Than Genetic Engineering: Fact or Assumption? | Plant Gene Seeker -PGS | Scoop.it

Scientists recognize that there is always the possibility of a GE plant that has some unintended, negative effect on a consuming animal or human. However, the same risk applies to conventionally bred crops, for which harmful cases have been documented [50, 51]. Thus, what matters to food safety is not the process used to create a plant, but the properties of the resulting plant [11, 52-55]. In fact, instead of posing a routine food-safety risk, the reverse is true: GE traits can actually increase food safety as compared to conventional crops (see [56] and citations in [57]).

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Image Harvest: an open-source platform for high-throughput plant image processing and analysis

Image Harvest: an open-source platform for high-throughput plant image processing and analysis | Plant Gene Seeker -PGS | Scoop.it
High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets.
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Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin - Rowe - 2016 - New Phytologist - Wiley Online Library

Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin - Rowe - 2016 - New Phytologist - Wiley Online Library | Plant Gene Seeker -PGS | Scoop.it
Understanding the mechanisms regulating root development under drought conditions is an important question for plant biology and world agriculture. 
We examine the effect of osmotic stress on abscisic acid (ABA), cytokinin and ethylene responses and how they mediate auxin transport, distribution and root growth through effects on PIN proteins. We integrate experimental data to construct hormonal crosstalk networks to formulate a systems view of root growth regulation by multiple hormones. 
Experimental analysis shows: that ABA-dependent and ABA-independent stress responses increase under osmotic stress, but cytokinin responses are only slightly reduced; inhibition of root growth under osmotic stress does not require ethylene signalling, but auxin can rescue root growth and meristem size; osmotic stress modulates auxin transporter levels and localization, reducing root auxin concentrations; PIN1 levels are reduced under stress in an ABA-dependent manner, overriding ethylene effects; and the interplay among ABA, ethylene, cytokinin and auxin is tissue-specific, as evidenced by differential responses of PIN1 and PIN2 to osmotic stress. 
Combining experimental analysis with network construction reveals that ABA regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin.
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Long-Sought Vacuolar Phosphate Transporters Identified: Trends in Plant Science

Long-Sought Vacuolar Phosphate Transporters Identified: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
The vacuole is an important subcellular compartment that serves as main phosphate storage in plants among other functions. Three recent studies shed light on the underlying molecular mechanisms for vacuolar phosphate transport that had long remained unknown.
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The bright side of microbial dark matter: lessons learned from the uncultivated majority - Current Opinion in Microbiology

The bright side of microbial dark matter: lessons learned from the uncultivated majority - Current Opinion in Microbiology | Plant Gene Seeker -PGS | Scoop.it
Microorganisms are the most diverse and abundant life forms on Earth. Yet, in many environments, only 0.1–1% of them have been cultivated greatly hindering our understanding of the microbial world. However, today cultivation is no longer a requirement for gaining access to information from the uncultivated majority. New genomic information from metagenomics and single cell genomics has provided insights into microbial metabolic cooperation and dependence, generating new avenues for cultivation efforts. Here we summarize recent advances from uncultivated phyla and discuss how this knowledge has influenced our understanding of the topology of the tree of life and metabolic diversity.

Via Max-Bernhard Ballhausen
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Max-Bernhard Ballhausen's curator insight, May 20, 3:07 AM
An update on hitherto uncultured bacteria. Good Friday morning read ;)
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Transcription co-activator Arabidopsis ANGUSTIFOLIA3 (AN3) regulates water-use efficiency and drought tolerance by modulating stomatal density and improving root architecture by the transrepression...

Transcription co-activator Arabidopsis ANGUSTIFOLIA3 (AN3) regulates water-use efficiency and drought tolerance by modulating stomatal density and improving root architecture by the transrepression... | Plant Gene Seeker -PGS | Scoop.it
One goal of modern agriculture is the improvement of plant drought tolerance and water-use efficiency (WUE). Although stomatal density has been linked to WUE, the causal molecular mechanisms and engineered alternations of this relationship are not yet fully understood. Moreover, YODA (YDA), which is a MAPKK kinase gene, negatively regulates stomatal development. BR-INSENSITIVE 2 interacts with phosphorylates and inhibits YDA. However, whether YDA is modulated in the transcriptional level is still unclear. Plants lacking ANGUSTIFOLIA3 (AN3) activity have high drought stress tolerance because of low stomatal densities and improved root architecture. Such plants also exhibit enhanced WUE through declining transpiration without a demonstrable reduction in biomass accumulation. AN3 negatively regulated YDA expression at the transcriptional level by target-gene analysis. Chromatin immunoprecipitation analysis indicated that AN3 was associated with a region of the YDA promoter in vivo. YDA mutation significantly decreased the stomatal density and root length of an3 mutant, thus proving the participation of YDA in an3 drought tolerance and WUE enhancement. These components form an AN3–YDA complex, which allows the integration of water deficit stress signalling into the production or spacing of stomata and cell proliferation, thus leading to drought tolerance and enhanced WUE.
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Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell | Plant Gene Seeker -PGS | Scoop.it

Background 

Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress.

Scope 

The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution | Plant Gene Seeker -PGS | Scoop.it
Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events.
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Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir.
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An ecophysiological and developmental perspective on variation in vessel diameter - Hacke - 2016 - Plant, Cell & Environment 

An ecophysiological and developmental perspective on variation in vessel diameter - Hacke - 2016 - Plant, Cell & Environment  | Plant Gene Seeker -PGS | Scoop.it
Variation in xylem vessel diameter is one of the most important parameters when evaluating plant water relations. This review provides a synthesis of the ecophysiological implications of variation in lumen diameter together with a summary of our current understanding of vessel development and its endogenous regulation. We analyzed inter-specific variation of the mean hydraulic vessel diameter (Dv) across biomes, intra-specific variation of Dv under natural and controlled conditions, and intra-plant variation. We found that the Dv measured in young branches tends to stay below 30 µm in regions experiencing winter frost, whereas it is highly variable in the tropical rainforest. Within a plant, the widest vessels are often found in the trunk and in large roots; smaller diameters have been reported for leaves and small lateral roots. Dv varies in response to environmental factors and is not only a function of plant size. Despite the wealth of data on vessel diameter variation, the regulation of diameter is poorly understood. Polar auxin transport through the vascular cambium is a key regulator linking foliar and xylem development. Limited evidence suggests that auxin transport is also a determinant of vessel diameter. The role of auxin in cell expansion and in establishing longitudinal continuity during secondary growth deserve further study.
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Unique Cellular Organization in the Oldest Root Meristem

Unique Cellular Organization in the Oldest Root Meristem | Plant Gene Seeker -PGS | Scoop.it
Summary 
Roots and shoots of plant bodies develop from meristems—cell populations that self-renew and produce cells that undergo differentiation—located at the apices of axes [1].The oldest preserved root apices in which cellular anatomy can be imaged are found in nodules of permineralized fossil soils called coal balls [2], which formed in the Carboniferous coal swamp forests over 300 million years ago [3, 4, 5, 6, 7, 8 and 9]. However, no fossil root apices described to date were actively growing at the time of preservation [3, 4, 5, 6, 7, 8, 9 and 10]. Because the cellular organization of meristems changes when root growth stops, it has been impossible to compare cellular dynamics as stem cells transition to differentiated cells in extinct and extant taxa [11]. We predicted that meristems of actively growing roots would be preserved in coal balls. Here we report the discovery of the first fossilized remains of an actively growing root meristem from permineralized Carboniferous soil with detail of the stem cells and differentiating cells preserved. The cellular organization of the meristem is unique. The position of the Körper-Kappe boundary, discrete root cap, and presence of many anticlinal cell divisions within a broad promeristem distinguish it from all other known root meristems. This discovery is important because it demonstrates that the same general cellular dynamics are conserved between the oldest extinct and extant root meristems. However, its unique cellular organization demonstrates that extant root meristem organization and development represents only a subset of the diversity that has existed since roots first evolved.
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Plant Ionomics: From Elemental Profiling to Environmental Adaptation: Molecular Plant

Plant Ionomics: From Elemental Profiling to Environmental Adaptation: Molecular Plant | Plant Gene Seeker -PGS | Scoop.it
Ionomics is a high-throughput elemental profiling approach to study the molecular mechanistic basis underlying mineral nutrient and trace element composition (also known as the ionome) of living organisms. Since the concept of ionomics was first introduced more than 10 years ago, significant progress has been made in the identification of genes and gene networks that control the ionome. In this update, we summarize the progress made in using the ionomics approach over the last decade, including the identification of genes by forward genetics and the study of natural ionomic variation. We further discuss the potential application of ionomics to the investigation of the ecological functions of ionomic alleles in adaptation to the environment.
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Root phenology in a changing climate

Root phenology in a changing climate | Plant Gene Seeker -PGS | Scoop.it
Plant phenology is one of the strongest indicators of ecological responses to climate change, and altered phenology can have pronounced effects on net primary production, species composition in local communities, greenhouse gas fluxes, and ecosystem processes. Although many studies have shown that aboveground plant phenology advances with warmer temperatures, demonstration of a comparable association for belowground phenology has been lacking because the factors that influence root phenology are poorly understood. Because roots can constitute a large fraction of plant biomass, and root phenology may not respond to warming in the same way as shoots, this represents an important knowledge gap in our understanding of how climate change will influence phenology and plant performance. We review studies of root phenology and provide suggestions to direct future research. Only 29% of examined studies approached root phenology quantitatively, strongly limiting interpretation of results across studies. Therefore, we suggest that researchers emphasize quantitative analyses in future phenological studies. We suggest that root initiation, peak growth, and root cessation may be under different controls. Root initiation and cessation may be more constrained by soil temperature and the timing of carbon availability, whereas the timing of peak root growth may represent trade-offs among competing plant sinks. Roots probably do not experience winter dormancy in the same way as shoots: 89% of the studies that examined winter phenology found evidence of growth during winter months. More research is needed to observe root phenology, and future studies should be careful to capture winter and early season phenology. This should be done quantitatively, with direct observations of root growth utilizing rhizotrons or minirhizotrons.
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Transcriptional regulation of receptor-like protein genes by environmental stresses and hormones and their overexpression activities in Arabidopsis thaliana

Transcriptional regulation of receptor-like protein genes by environmental stresses and hormones and their overexpression activities in Arabidopsis thaliana | Plant Gene Seeker -PGS | Scoop.it
Receptor-like proteins (RLPs) have been implicated in multiple biological processes, including plant development and immunity to microbial infection. Fifty-seven AtRLP genes have been identified in Arabidopsis, whereas only a few have been functionally characterized. This is due to the lack of suitable physiological screening conditions and the high degree of functional redundancy among AtRLP genes. To overcome the functional redundancy and further understand the role of AtRLP genes, we studied the evolution of AtRLP genes and compiled a comprehensive profile of the transcriptional regulation of AtRLP genes upon exposure to a range of environmental stresses and different hormones. These results indicate that the majority of AtRLP genes are differentially expressed under various conditions that were tested, an observation that will help to select certain AtRLP genes involved in a specific biological process for further experimental studies to eventually dissect their function. A large number of AtRLP genes were found to respond to more than one treatment, suggesting that one single AtRLP gene may be involved in multiple physiological processes. In addition, we performed a genome-wide cloning of the AtRLP genes, and generated and characterized transgenic Arabidopsis plants overexpressing the individual AtRLP genes, presenting new insight into the roles of AtRLP genes, as exemplified by AtRLP3, AtRLP11 and AtRLP28. Our study provides an overview of biological processes in which AtRLP genes may be involved, and presents valuable resources for future investigations into the function of these genes.
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Making plant science purposeful and relevant to all

Making plant science purposeful and relevant to all | Plant Gene Seeker -PGS | Scoop.it
Every scientist wants their research to have impact at some level, even if only realized far in the future. But a sense of vision and clear planning are needed today, to inspire everyone from potential investors to schoolchildren contemplating higher education options. Here, the case is made for roadmapping as a critically important way forward for plant science, and a practice that all scientists should take seriously.
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Plant Hormone Homeostasis, Signaling, and Function during Adventitious Root Formation in Cuttings | Frontiers in Plant Science

Plant Hormone Homeostasis, Signaling, and Function during Adventitious Root Formation in Cuttings | Frontiers in Plant Science | Plant Gene Seeker -PGS | Scoop.it
Adventitious root (AR) formation in cuttings is a multiphase developmental process, resulting from wounding at the cutting site and isolation from the resource and signal network of the whole plant. Though, promotive effects of auxins are widely used for clonal plant propagation, the regulation and function of plant hormones and their intricate signaling networks during AR formation in cuttings are poorly understood. In this focused review, we discuss our recent publications on the involvement of polar auxin transport (PAT) and transcriptional regulation of auxin and ethylene action during AR formation in petunia cuttings in a broad context. Integrating new findings on cuttings of other plant species and general models on plant hormone networks, a model on the regulation and function of auxin, ethylene, and jasmonate in AR formation of cuttings is presented. PAT and cutting off from the basipetal auxin drain are considered as initial principles generating early accumulation of IAA in the rooting zone. This is expected to trigger a self-regulatory process of auxin canalization and maximization to responding target cells, there inducing the program of AR formation. Regulation of auxin homeostasis via auxin influx and efflux carriers, GH3 proteins and peroxidases, of flavonoid metabolism, and of auxin signaling via AUX/IAA proteins, TOPLESS, ARFs, and SAUR-like proteins are postulated as key processes determining the different phases of AR formation. NO and H2O2 mediate auxin signaling via the cGMP and MAPK cascades. Transcription factors of the GRAS-, AP2/ERF-, and WOX-families link auxin signaling to cell fate specification. Cyclin-mediated governing of the cell cycle, modifications of sugar metabolism and microtubule and cell wall remodeling are considered as important implementation processes of auxin function. Induced by the initial wounding and other abiotic stress factors, up-regulation of ethylene biosynthesis, and signaling via ERFs and early accumulation of jasmonic acid stimulate AR formation, while both pathways are linked to auxin. Future research on the function of candidate genes should consider their tissue-specific role and regulation by environmental factors. Furthermore, the whole cutting should be regarded as a system of physiological units with diverse functions specifically responding to the environment and determining the rooting response.
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Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science

Phosphorus: The Underrated Element for Feeding the World: Trends in Plant Science | Plant Gene Seeker -PGS | Scoop.it
Predictions on the lifetime of phosphate (Pi) reserves usually take into account only the need for crop production. A recent report predicts the global need of chemical Pi fertilizer for sustaining productivity in cropland and grassland. Here we discuss the implications of these predictions for the lifetime of Pi reserves.
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The race to create super-crops

The race to create super-crops | Plant Gene Seeker -PGS | Scoop.it

Jonathan Lynch likes to look beneath the surface. In his quest to breed better crops, the plant physiologist spends a lot of time digging up roots to work out what makes some varieties extremely good at extracting nutrients from the ground. Lynch wants to use this knowledge to develop plants with extra-efficient roots — crops that grow well in the nutrient-starved soils of the developing world. These plants could also reduce the use of fertilizers in richer nations.



Last year, Lynch's forays into the dirt paid off. He and his team at Pennsylvania State University in University Park reported1 that they had produced a variety of common bean, or string bean (Phaseolus vulgaris), with a combination of root traits that allows it to take up phosphorus from the soil with improved efficiency. In experimental plots, the plants produced three times the bean yield of typical varieties.

That result has raised hopes in Africa, where common beans are one of the most important sources of protein for poor people. Researchers in Mozambique are testing how Lynch's beans perform in the country's ecological zones, and they expect to win regulatory approval to bring the crop to market by next year.

Lynch's beans are among the first successful attempts in a global race to develop crops that grow well in soils depleted of nutrients. “Low availability of nitrogen, phosphorus and water are the main limitations of plant growth on Earth. We desperately need this technology,” says Lynch.

His work stands out because he has taken an old-school approach. He is leading a renaissance in some conventional crop-breeding techniques that rely on laboriously examining plants' physical characteristics and then selecting for desirable traits, such as growth or the length of fine roots...


Via Christophe Jacquet
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Expanding the Regulatory Network for Meristem Size in Plants: Trends in Genetics

Expanding the Regulatory Network for Meristem Size in Plants: Trends in Genetics | Plant Gene Seeker -PGS | Scoop.it
The remarkable plasticity of post-embryonic plant development is due to groups of stem-cell-containing structures called meristems. In the shoot, meristems continuously produce organs such as leaves, flowers, and stems. Nearly two decades ago the WUSCHEL/CLAVATA (WUS/CLV) negative feedback loop was established as being essential for regulating the size of shoot meristems by maintaining a delicate balance between stem cell proliferation and cell recruitment for the differentiation of lateral primordia. Recent research in various model species (Arabidopsis, tomato, maize, and rice) has led to discoveries of additional components that further refine and improve the current model of meristem regulation, adding new complexity to a vital network for plant growth and productivity.
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The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato | Plant Gene Seeker -PGS | Scoop.it

Background 

Solanum sect. Basarthrum is phylogenetically very close to potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon), two groups with great economic importance, and for which Solanum sect. Basarthrum represents a tertiary gene pool for breeding. This section includes the important regional cultigen, the pepino (Solanum muricatum), and several wild species. Among the wild species, S. caripense is prominent due to its major involvement in the origin of pepino and its wide geographical distribution. Despite the value of the pepino as an emerging crop, and the potential for gene transfer from both the pepino and S. caripense to potatoes and tomatoes, there has been virtually no genomic study of these species. 


Results 

Using Illumina HiSeq 2000, RNA-Seq was performed with a pool of three tissues (young leaf, flowers in pre-anthesis and mature fruits) from S. muricatum and S. caripense, generating almost 111,000,000 reads among the two species. A high quality de novo transcriptome was assembled from S. muricatum clean reads resulting in 75,832 unigenes with an average length of 704 bp. These unigenes were functionally annotated based on similarity of public databases. We used Blast2GO, to conduct an exhaustive study of the gene ontology, including GO terms, EC numbers and KEGG pathways. Pepino unigenes were compared to both potato and tomato genomes in order to determine their estimated relative position, and to infer gene prediction models. Candidate genes related to traits of interest in other Solanaceae were evaluated by presence or absence and compared with S. caripense transcripts. In addition, by studying five genes, the phylogeny of pepino and five other members of the family, Solanaceae, were studied. The comparison of S. caripense reads against S. muricatum assembled transcripts resulted in thousands of intra- and interspecific nucleotide-level variants. In addition, more than 1000 SSRs were identified in the pepino transcriptome. 


Conclusions

This study represents the first genomic resource for the pepino. We suggest that the data will be useful not only for improvement of the pepino, but also for potato and tomato breeding and gene transfer. The high quality of the transcriptome presented here also facilitates comparative studies in the genus Solanum. The accurate transcript annotation will enable us to figure out the gene function of particular traits of interest. The high number of markers (SSR and nucleotide-level variants) obtained will be useful for breeding programs, as well as studies of synteny, diversity evolution, and phylogeny.

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