Plant Gene Seeker -PGS
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Plant Gene Seeker -PGS
Absolutely Fascinated for plant & genomes
Curated by Andres Zurita
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Interactions between cytokinin signalling and abiotic stress responses

Interactions between cytokinin signalling and abiotic stress responses | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Plants have evolved elaborate mechanisms for sensing and responding to sub-optimal environmental conditions. Abiotic stresses caused by these conditions trigger a wide range of local and long-distance signals which must be co-ordinated and integrated into whole-plant processes, such as development, in order for the plant to respond properly and survive. Several hormones function as key regulators of stress tolerance, connecting local stimuli to systemic responses. Cytokinin is a hormone well known for its role in numerous aspects of growth and development, although abundant evidence also indicates that cytokinin functions in stress responses as well. At present, a full understanding of the effects of cytokinin on plant resistance to stress is lacking, possibly as a result of the complex interactions between cytokinin and stress signalling. Current knowledge of the physiological relationship between cytokinin and abiotic stress, based on measurements of cytokinin levels under stress conditions and the effects of cytokinin treatment on stress tolerance, has been examined here. A pattern of transcriptional regulation of stress-related genes by cytokinin in different plant species has also been identified. In addition, research regarding the role of specific cytokinin signalling components in a variety of stress responses is presented. We discuss what this body of research collectively implies with regard to cross-talk between cytokinin and abiotic stress tolerance.

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First evidence of farming in Mideast 23,000 years ago

First evidence of farming in Mideast 23,000 years ago | Plant Gene Seeker -PGS | Scoop.it
Until now, researchers believed farming was 'invented' some 12,000 years ago in an area that was home to some of the earliest known human civilizations. A new discovery offers the first evidence that trial plant cultivation began far earlier -- some 23,000 years ago.

Via Ed Rybicki, Saclay Plant Sciences
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Ed Rybicki's curator insight, July 23, 2015 5:27 AM

So, basically, we've had GMOs for over 20 000 years? B-)

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Prepare farms for the future

Scientists must work closely with farmers to ensure that agriculture can stand up to the ravages of climate change.

Via Saclay Plant Sciences
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Global Transcriptome Analysis Reveals Acclimation-Primed Processes Involved in the Acquisition of Desiccation Tolerance in Boea hygrometrica

Global Transcriptome Analysis Reveals Acclimation-Primed Processes Involved in the Acquisition of Desiccation Tolerance in Boea hygrometrica | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Boea hygrometrica resurrection plants require a period of acclimation by slow soil-drying in order to survive a subsequent period of rapid desiccation. The molecular basis of this observation was investigated by comparing gene expression profiles under different degrees of water deprivation. Transcripts were clustered according to the expression profiles in plants that were air-dried (rapid desiccation), soil-dried (gradual desiccation), rehydrated (acclimated) and air-dried after acclimation. Although phenotypically indistinguishable, it was shown by principal component analysis that the gene expression profiles in rehydrated, acclimated plants resemble those of desiccated plants more closely than those of hydrated acclimated plants. Enrichment analysis based on gene ontology was performed to deconvolute the processes that accompanied desiccation tolerance. Transcripts associated with autophagy and α-tocopherol accumulation were found to be activated in both air-dried, acclimated plants and soil-dried non-acclimated plants. Furthermore, transcripts associated with biosynthesis of ascorbic acid, cell wall catabolism, chaperone-assisted protein folding, respiration and macromolecule catabolism were activated and maintained during soil-drying and rehydration. Based on these findings, we hypothesize that activation of these processes leads to the establishment of an optimal physiological and cellular state that enables tolerance during rapid air-drying. Our study provides a novel insight into the transcriptional regulation of critical priming responses to enable survival following rapid dehydration in B. hygrometrica.

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Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis

Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Integrating carbon (C), nitrogen (N), and sulfur (S) metabolism is essential for the growth and development of living organisms. MicroRNAs (miRNAs) play key roles in regulating nutrient metabolism in plants. However, how plant miRNAs mediate crosstalk between different nutrient metabolic pathways is unclear. In this study, deep sequencing of Arabidopsis thaliana small RNAs was used to reveal miRNAs that were differentially expressed in response to C, N, or S deficiency. Comparative analysis revealed that the targets of the differentially expressed miRNAs are involved in different cellular responses and metabolic processes, including transcriptional regulation, auxin signal transduction, nutrient homeostasis, and regulation of development. C, N, and S deficiency specifically induced miR169b/c, miR826 and miR395, respectively. In contrast, miR167, miR172, miR397, miR398, miR399, miR408, miR775, miR827, miR841, miR857, and miR2111 are commonly suppressed by C, N, and S deficiency. In particular, the miRNAs that are induced specifically by a certain nutrient deficiency are often suppressed by other nutrient deficiencies. Further investigation indicated that the modulation of nutrient-responsive miRNA abundance affects the adaptation of plants to nutrient starvation conditions. This study revealed that miRNAs function as important regulatory nodes of different nutrient metabolic pathways.

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Fatal attraction: the intuitive appeal of GMO opposition

Fatal attraction: the intuitive appeal of GMO opposition | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Public opposition to genetically modified organisms (GMOs) remains strong. By contrast, studies demonstrate again and again that GM crops make a valuable contribution to the development of a sustainable type of agriculture. The discrepancy between public opinion and the scientific evidence requires an explanation. We argue that intuitive expectations about the world render the human mind vulnerable to particular misrepresentations of GMOs. We explain how the involvement of particular intuitions accounts for the popularity, persistence, and typical features of GM opposition and tackle possible objections to our approach. To conclude, we discuss the implications for science education, science communication, and the environmental movement.

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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, 2015 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.
Andres Zurita's insight:

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

Andres Zurita's insight:
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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Sequencing, assembly, annotation, and gene expression: novel insights into the hormonal control of carrot root development revealed by a high-throughput transcriptome

Sequencing, assembly, annotation, and gene expression: novel insights into the hormonal control of carrot root development revealed by a high-throughput transcriptome | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Previous studies have indicated that hormonal control is essential for plant root growth. The root of the carrot is an edible vegetable with a high nutritional value. However, molecular mechanisms underlying hormone-mediated root growth of carrot have not been illustrated. Therefore, the present study collected carrot root samples from four developmental stages, and performed transcriptome sequencing to understand the molecular functions of plant hormones in carrot root growth. A total of 160,227 transcripts were generated from our transcriptome, which were assembled into 32,716 unigenes with an average length of 1,453 bp. A total of 4,818 unigenes were found to be differentially expressed between the four developmental stages. In total, 87 hormone-related differentially expressed genes were identified, and the roles of the hormones are extensively discussed. Our results suggest that plant hormones may regulate carrot root growth in a phase-dependent manner, and these findings will provide valuable resources for future research on carrot root development.

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Quest for climate-proof farms

Quest for climate-proof farms | Plant Gene Seeker -PGS | Scoop.it
Climate change is a major threat to food production, so researchers are working with farmers to make agriculture more resilient.

Via Mary Williams
Andres Zurita's insight:

Good strategy is to promote resilient crops.

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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.

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Editorial: Emerging Technologies for the Study of Plant Environmental Sensing

Editorial: Emerging Technologies for the Study of Plant Environmental Sensing | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

It is the plant’s autotrophic photosynthetic abilities that allow it to survive in its original location without the need to move its whole life, but it is continuously exposed to changes in environmental conditions, which at times can be very severe. To tackle the many environmental challenges directly, plants have evolved several environmental sensing systems and physiological mechanisms of adaptation (Taiz et al. 2015). Such environmental factors include light, temperature, gravity, water, nutrients, heavy metals, salt, herbivore insects and animals, and pathogens. In nature, plants may face any of those multiple factors at the same one time.

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Characterizing visible and invisible cell wall mutant phenotypes

Characterizing visible and invisible cell wall mutant phenotypes | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

About 10% of a plant’s genome is devoted to generating the protein machinery to synthesize, remodel, and deconstruct the cell wall. High-throughput genome sequencing technologies have enabled a reasonably complete inventory of wall-related genes that can be assembled into families of common evolutionary origin. Assigning function to each gene family member has been aided immensely by identification of mutants with visible phenotypes or by chemical and spectroscopic analysis of mutants with ‘invisible’ phenotypes of modified cell wall composition and architecture that do not otherwise affect plant growth or development. This review connects the inference of gene function on the basis of deviation from the wild type in genetic functional analyses to insights provided by modern analytical techniques that have brought us ever closer to elucidating the sequence structures of the major polysaccharide components of the plant cell wall.

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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
Andres Zurita's insight:
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

Andres Zurita's insight:

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

Andres Zurita's insight:

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
Andres Zurita's insight:
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

Andres Zurita's insight:

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
Andres Zurita's insight:
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

Andres Zurita's insight:

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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