Plant genetics
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Plant genetics
plant genetics
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ScienceDirect.com - Plant Science - “And yet it moves”: Cell-to-cell and long-distance signaling by plant microRNAs

ScienceDirect.com - Plant Science - “And yet it moves”: Cell-to-cell and long-distance signaling by plant microRNAs | Plant genetics | Scoop.it

MicroRNAs (miRNAs) are key regulators of numerous genes in many eukaryotes. Some plant miRNAs are involved in developmental and physiological processes that require intercellular or inter-organ signaling. Movement of other small RNAs within plants has been established. Recent findings also demonstrate intercellular signaling by miRNAs and strongly support that a subset of these regulatory molecules move from one cell to another or over long distances. Phloem exudates contain diverse miRNAs and at least two of them, involved in responses to nutrient availability, are transmitted through grafts, indicating long-distance movement. Two miRNAs that regulate developmental processes are present in cells outside their domains of expression. Several results strongly support that one of them moves from cell to cell. Research on a mutant affected in plasmodesmata trafficking indicates that these intercellular channels are required for transmission of miRNA activity to adjacent cells. Moreover, ARGONAUTE proteins might be involved in the regulation of miRNA trafficking. Hypothesis on the features and mechanisms that may determine miRNA mobility are presented. Future challenges include identifying other mobile miRNAs; demonstrating that miRNA movement is required for non-cell autonomous action; and characterizing the mechanisms of translocation and genetic pathways that regulate miRNA movement.

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MPMI: A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research (2012)

MPMI: A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research (2012) | Plant genetics | Scoop.it

Nicotiana benthamiana is a widely used model plant species for the study of fundamental questions in molecular plant-microbe interactions and other areas of plant biology. This popularity derives from its well-characterized susceptibility to diverse pathogens and especially its amenability to virus-induced gene silencing (VIGS) and transient protein expression methods. Here we report the generation of a 63-fold coverage draft genome sequence of N. benthamiana and its availability on the Sol Genomics Network (http://solgenomics.net/) for both BLAST searches and for downloading to local servers. The estimated genome size of N. benthamiana is ~3 gigabases (Gb). The current assembly consists of ~141,000 scaffolds, spanning 2.6 Gb of which >50% are longer than 89 kilobases. Of the ~16,000 N. benthamiana unigenes available in GenBank, >90% are represented in the assembly. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1 and MAP kinases. The sequence will also be useful for comparative genomics in the Solanaceae as shown here by the discovery of microsynteny between N. benthamiana and tomato in the region encompassing the Pto/Prf genes.


Via Kamoun Lab @ TSL
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ScienceDirect.com - Current Opinion in Plant Biology - Mapping the genetic basis of ecologically and evolutionarily relevant traits in Arabidopsis thaliana

ScienceDirect.com - Current Opinion in Plant Biology - Mapping the genetic basis of ecologically and evolutionarily relevant traits in Arabidopsis thaliana | Plant genetics | Scoop.it

There has been a long standing interest in the relationship between genetic and phenotypic variation in natural populations, in order to understand the genetic basis of adaptation and to discover natural alleles to improve crops. Here we review recent developments in mapping approaches that have significantly improved our ability to identify causal polymorphism explaining natural variation in ecological and evolutionarily relevant traits. However, challenges in interpreting these discoveries remain. In particular, we need more detailed transcriptomic, epigenomic, and gene network data to help understand the mechanisms behind identified associations. Also, more studies need to be performed under field conditions or using experimental evolution to determine whether polymorphisms identified in the lab are relevant for adaptation and improvement under natural conditions.

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Identification of a dicer homologue gene (DCL2) in Nicotiana tabacum - Udriste - 2012 - Plant Biology - Wiley Online Library

Identification of a dicer homologue gene (DCL2) in Nicotiana tabacum - Udriste - 2012 - Plant Biology - Wiley Online Library | Plant genetics | Scoop.it

Eukaryotes possess a mechanism that generates small interfering RNA (siRNA) and microRNA (miRNA) and use these to regulate gene expression at the transcriptional or post-transcriptional level. These small RNAs (21–24nt) are processed from long double-stranded RNA precursors by type III RNase enzymes, referred to as DICER or DICER-LIKE proteins (DCLs). In Arabidopsis, there are four DCL genes and their role in small RNA biogenesis and silencing has been the subject of intense study. DCL2 is less well studied than the other DCL proteins although it is known to play a role in formation of natural antisense siRNA and may be involved in transitive silencing of transgene transcripts. This study provides basic genomic information on DCL2 in the Nicotiana tabacum (NtDCL2) gene family and its probable roles in plant growth and development.

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Identification of new microRNA-regulated genes by conserved targeting in plant species

MicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. They recognize their targets by sequence complementarity and guide them to cleavage or translational arrest. It is generally accepted that plant miRNAs have extensive complementarity to their targets and their prediction usually relies on the use of empirical parameters deduced from known miRNA–target interactions. Here, we developed a strategy to identify miRNA targets which is mainly based on the conservation of the potential regulation in different species. We applied the approach to expressed sequence tags datasets from angiosperms. Using this strategy, we predicted many new interactions and experimentally validated previously unknown miRNA targets in Arabidopsis thaliana. Newly identified targets that are broadly conserved include auxin regulators, transcription factors and transporters. Some of them might participate in the same pathways as the targets known before, suggesting that some miRNAs might control different aspects of a biological process. Furthermore, this approach can be used to identify targets present in a specific group of species, and, as a proof of principle, we analyzed Solanaceae-specific targets. The presented strategy can be used alone or in combination with other approaches to find miRNA targets in plants.

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Trends in Plant Science - Alternative splicing in plants – coming of age

Trends in Plant Science - Alternative splicing in plants – coming of age | Plant genetics | Scoop.it

More than 60% of intron-containing genes undergo alternativesplicing (AS) in plants. This number will increase when AS in different tissues, developmental stages, and environmental conditions are explored. Although the functional impact of AS on protein complexity is still understudied in plants, recent examples demonstrate its importance in regulating plant processes. AS also regulates transcript levels and the link with nonsense-mediated decay and generation of unproductive mRNAs illustrate the need for both transcriptional and AS data in gene expression analyses. AS has influenced the evolution of the complex networks of regulation of gene expression and variation in AS contributed to adaptation of plants to their environment and therefore will impact strategies for improving plant and crop phenotypes.

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A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

Active DNA demethylation is an important part of epigenetic regulation in plants and animals. How active DNA demethylation is regulated and its relationship with histone modification patterns are unclear. Here, we report the discovery of IDM1, a regulator of DNA demethylation in Arabidopsis. IDM1 is required for preventing DNA hypermethylation of highly homologous multicopy genes and other repetitive sequences that are normally targeted for active DNA demethylation by Repressor of Silencing 1 and related 5-methylcytosine DNA glycosylases. IDM1 binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and acetylates H3 to create a chromatin environment permissible for 5-methylcytosine DNA glycosylases to function. Our study reveals how some genes are indicated by multiple epigenetic marks for active DNA demethylation and protection from silencing.

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ScienceDirect.com - Trends in Plant Science - Exploring the evolutionary path of plant MAPK networks

ScienceDirect.com - Trends in Plant Science - Exploring the evolutionary path of plant MAPK networks | Plant genetics | Scoop.it

The evolutionarily conserved mitogen-activated protein kinase (MAPK) signaling network comprises connected protein kinases arranged in MAPK modules. In this Opinion article, we analyze MAPK signaling components in evolutionarily representative species of the plant lineage and in Naegleria gruberi, a member of an early diverging eukaryotic clade. In Naegleria, there are two closely related MAPK kinases (MKKs) and a single conventional MAPK, whereas in several species of algae, there are two distinct MKKs and multiple MAPKs belonging to different groups. This suggests that the formation of multiple MAPK modules began early during plant evolution. The expansion of MAPK signaling components through gene duplications and the evolution of interaction motifs could have contributed to the highly connected complex MAPK signaling network that we know in Arabidopsis.

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PLoS Genetics: Dynamics of Brassinosteroid Response Modulated by Negative Regulator LIC in Rice

PLoS Genetics: Dynamics of Brassinosteroid Response Modulated by Negative Regulator LIC in Rice | Plant genetics | Scoop.it
Brassinosteroids (BRs) are phytohormones mediating multiple biological processes, such as development and stress response. They have been used in crops to produce high yield. In rice, the ideal plant architecture for high yield includes effective tillers, as well as height and leaf angle, which is modulated by BRs. Activation of BRI1–mediated BR signaling is well understood, but much less is known about its inactivating mechanism. Here, we found a gain-of-function mutant lic-1 with the phenotype of the ideal rice plant architecture. The C3H-type transcription factor LIC antagonizes BZR1 to repress BR signaling in rice. We used BR to induce the negative regulator LIC and found that it functioned at high BR level, which may restrain plant development. LIC was phosphorylated by GSK3–like kinases. Phosphorylated LIC mainly localized in cytoplasm, whereas dephosphorylated LIC was in nucleus, which was regulated by BR treatment. LIC regulated transcription patterns of the downstream genes in an opposite direction to BZR1. BZR1 activated BR signaling, but the brake module of LIC repressed BR cascade amplification. LIC and BZR1 may balance BR signaling to control growth and development in rice.
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PLoS Genetics: IDN2 and Its Paralogs Form a Complex Required for RNA–Directed DNA Methylation

PLoS Genetics: IDN2 and Its Paralogs Form a Complex Required for RNA–Directed DNA Methylation | Plant genetics | Scoop.it

In eukaryotes, transposable elements and other DNA repeats are important parts
of genomes. Suppression of these sequences is required for genome stability and
integrity. DNA methylation is an important chromatin modification that prevents
the expression and movement of these repeat sequences. Small interfering RNAs
initiate DNA methylation and transcriptional gene silencing of the sequences. In
the plant model organism Arabidopsis thaliana, DNA methylation is
mediated by an RNA–directed DNA methylation (RdDM) pathway. Here we report that
the double-stranded RNA-binding protein IDN2 and it paralogs IDP1 and IDP2 (IDN2
PARALOG 1 and 2) cooperate and form a novel complex that is required for
RNA–directed DNA methylation. Unlike IDN2, IDP1 and IDP2 have no double-stranded
RNA binding ability. We propose that the IDN2-IDP1/2 is a complex that functions
at a downstream step of the RdDM pathway. The findings significantly increase
our understanding of the plant RdDM pathway as well as of the RNA–mediated
chromatin changes in yeast and animals.

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Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template-Dependent, Nonvascular, Cell-to-Cell Movement

Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template-Dependent, Nonvascular, Cell-to-Cell Movement | Plant genetics | Scoop.it

Upward long-distance mobile silencing has been shown to be phloem mediated in several different solanaceous species. We show that the Arabidopsis (Arabidopsis thaliana) seedling grafting system and a counterpart inducible system generate upwardly spreading long-distance silencing that travels not in the phloem but by template-dependent reiterated short-distance cell-to-cell spread through the cells of the central stele. Examining the movement of the silencing front revealed a largely unrecognized zone of tissue, below the apical meristem, that is resistant to the silencing signal and that may provide a gating or protective barrier against small RNA signals. Using a range of auxin and actin transport inhibitors revealed that, in this zone, alteration of vesicular transport together with cytoskeleton dynamics prevented or retarded the spread of the silencing signal. This suggests that small RNAs are transported from cell to cell via plasmodesmata rather than diffusing from their source in the phloem.

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ScienceDirect.com - Current Opinion in Plant Biology - Towards understanding how molecular networks evolve in plants

ScienceDirect.com - Current Opinion in Plant Biology - Towards understanding how molecular networks evolve in plants | Plant genetics | Scoop.it

Residing beneath the phenotypic landscape of a plant are intricate and dynamic networks of genes and proteins. As evolution operates on phenotypes, we expect its forces to shape somehow these underlying molecular networks. In this review, we discuss progress being made to elucidate the nature of these forces and their impact on the composition and structure of molecular networks. We also outline current limitations and open questions facing the broader field of plant network analysis.

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ScienceDirect.com - Current Opinion in Plant Biology - Next-generation education in crop genetics

ScienceDirect.com - Current Opinion in Plant Biology - Next-generation education in crop genetics | Plant genetics | Scoop.it

Today, plant breeders are being met with new opportunities to develop superior varieties. Fruitful genetic research into populations with novel diversity using genotyping by sequencing combined with genotype-to-phenotype bioinformatics has generated much knowledge that is directly relevant to crop improvement. These advances can assist the breeders in associating genetic makeup with traits of commercial value. The greatest challenge now is to find ways to attract the best young people to work in plant breeding for its innovation, open field experience and ability to support food security. We discuss the need, opportunities and conflicts associated with revamping plant breeding teaching programs to bridge the art and science of this profession with a rapidly expanding job market.

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Trends in Cell Biology - New insights into Rho signaling from plant ROP/Rac GTPases

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PLoS Genetics: The Role of Rice HEI10 in the Formation of Meiotic Crossovers

PLoS Genetics: The Role of Rice HEI10 in the Formation of Meiotic Crossovers | Plant genetics | Scoop.it

Meiosis is a specialized cell division that is essential for sexual reproduction. Errors in meiosis are the leading cause of both infertility and birth defects. Most meiotic genes and their functions seem to be highly conserved among different species. HEI10 was first identified to regulate cell cycle and cell invasion in human somatic cells. Studies in mice revealed that the mutation of HEI10 led to the absence of chiasmata and a final sterile phenotype. However, the exact function of HEI10 in meiotic recombination remains unresolved. In this study, we characterize the rice HEI10 homolog and demonstrate that HEI10 is required for normal crossover formation, but not for synapsis. HEI10 protein initially appears as distinct foci. Thereafter, the signals elongate along the SC and finally restrict to prominent foci that correspond to future chiasma sites. In addition, we also show a close relationship of HEI10 with two other characterized ZMM proteins, ZEP1 and MER3. We propose that the HEI10 exerts its effects in the recombination process through modification of diverse meiotic components.

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A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

Active DNA demethylation is an important part of epigenetic regulation in plants and animals. How active DNA demethylation is regulated and its relationship with histone modification patterns are unclear. Here, we report the discovery of IDM1, a regulator of DNA demethylation in Arabidopsis. IDM1 is required for preventing DNA hypermethylation of highly homologous multicopy genes and other repetitive sequences that are normally targeted for active DNA demethylation by Repressor of Silencing 1 and related 5-methylcytosine DNA glycosylases. IDM1 binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and acetylates H3 to create a chromatin environment permissible for 5-methylcytosine DNA glycosylases to function. Our study reveals how some genes are indicated by multiple epigenetic marks for active DNA demethylation and protection from silencing.

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A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis

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TIME FOR COFFEE Represses Accumulation of the MYC2 Transcription Factor to Provide Time-of-Day Regulation of Jasmonate Signaling in Arabidopsis

TIME FOR COFFEE Represses Accumulation of the MYC2 Transcription Factor to Provide Time-of-Day Regulation of Jasmonate Signaling in Arabidopsis | Plant genetics | Scoop.it

Plants are confronted with predictable daily biotic and abiotic stresses that result from the day–night cycle. The circadian clock provides an anticipation mechanism to respond to these daily stress signals to increase fitness. Jasmonate (JA) is a phytohormone that mediates various growth and stress responses. Here, we found that the circadian-clock component TIME FOR COFFEE (TIC) acts as a negative factor in the JA-signaling pathway. We showed that the tic mutant is hypersensitive to growth-repressive effects of JA and displays altered JA-regulated gene expression. TIC was found to interact with MYC2, a key transcription factor of JA signaling. From this, we discovered that the circadian clock rhythmically regulates JA signaling. TIC is a key determinant in this circadian-gated process, and as a result, the tic mutant is defective in rhythmic JA responses to pathogen infection. TIC acts here by inhibiting MYC2 protein accumulation and by controlling the transcriptional repression of CORONATINE INSENSITIVE1 in an evening-phase–specific manner. Taken together, we propose that TIC acts as an output component of the circadian oscillator to influence JA signaling directly.

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Loss of Cellulose Synthase-Like F6 Function Affects Mixed-Linkage Glucan Deposition, Cell Wall Mechanical Properties, and Defense Responses in Vegetative Tissues of Rice

Loss of Cellulose Synthase-Like F6 Function Affects Mixed-Linkage Glucan Deposition, Cell Wall Mechanical Properties, and Defense Responses in Vegetative Tissues of Rice | Plant genetics | Scoop.it

Mixed-linkage glucan (MLG) is a cell wall polysaccharide containing a backbone of unbranched (1,3)- and (1,4)-linked β-glucosyl residues. Based on its occurrence in plants and chemical characteristics, MLG has primarily been associated with the regulation of cell wall expansion due to its high and transient accumulation in young, expanding tissues. The Cellulose synthase-like F (CslF) subfamily of glycosyltransferases has previously been implicated in mediating the biosynthesis of this polymer. We confirmed that the rice (Oryza sativa) CslF6 gene mediates the biosynthesis of MLG by overexpressing it in Nicotiana benthamiana. Rice cslf6 knockout mutants show a slight decrease in height and stem diameter but otherwise grew normally during vegetative development. However, cslf6 mutants display a drastic decrease in MLG content (97% reduction in coleoptiles and virtually undetectable in other tissues). Immunodetection with an anti-MLG monoclonal antibody revealed that the coleoptiles and leaves retain trace amounts of MLG only in specific cell types such as sclerenchyma fibers. These results correlate with the absence of endogenous MLG synthase activity in mutant seedlings and 4-week-old sheaths. Mutant cell walls are weaker in mature stems but not seedlings, and more brittle in both stems and seedlings, compared to wild type. Mutants also display lesion mimic phenotypes in leaves, which correlates with enhanced defense-related gene expression and enhanced disease resistance. Taken together, our results underline a weaker role of MLG in cell expansion than previously thought, and highlight a structural role for MLG in nonexpanding, mature stem tissues in rice.


Via Nicolas Denancé
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PLoS Genetics: Deep Sequencing of Plant and Animal DNA Contained within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns

PLoS Genetics: Deep Sequencing of Plant and Animal DNA Contained within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns | Plant genetics | Scoop.it

Chemicals derived from plants and animals are widely used in traditional Chinese medicine (TCM), and it is commonplace for remedies to contain a complex list of ingredients. Due to their heterogeneous origins, and subsequent processing into pills and powders, it can be difficult for the biological origin of ingredients within each remedy to be reliably determined. In this study, we have, for the first time, used a second-generation DNA sequencing method to analyse TCM remedies and determine their animal and plant composition. Using this deep-sequencing approach we identified plant species that are known to contain toxic chemicals and identified animal DNA from species that are currently endangered and protected by international laws. Consumers need to be made aware of legal and health safety issues that surround TCMs before adopting them as a treatment option. More widespread testing of complementary medicines using the DNA methods developed herein represents an efficient and cost-effective way to audit their composition.

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