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Rescooped by Guogen Yang from Plants and Microbes
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Nature Genetics: Oomycete pathogens encode RNA silencing suppressors (2013)

Nature Genetics: Oomycete pathogens encode RNA silencing suppressors (2013) | Plant-Microbe Interaction | Scoop.it

Effectors are essential virulence proteins produced by a broad range of parasites, including viruses, bacteria, fungi, oomycetes, protozoa, insects and nematodes. Upon entry into host cells, pathogen effectors manipulate specific physiological processes or signaling pathways to subvert host immunity. Most effectors, especially those of eukaryotic pathogens, remain functionally uncharacterized. Here, we show that two effectors from the oomycete plant pathogen Phytophthora sojae suppress RNA silencing in plants by inhibiting the biogenesis of small RNAs. Ectopic expression of thesePhytophthora suppressors of RNA silencing enhances plant susceptibility to both a virus and Phytophthora, showing that some eukaryotic pathogens have evolved virulence proteins that target host RNA silencing processes to promote infection. These findings identify RNA silencing suppression as a common strategy used by pathogens across kingdoms to cause disease and are consistent with RNA silencing having key roles in host defense.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana | Plant-Microbe Interaction | Scoop.it

Nice combination of QTL mapping and gene expression analysis to identify new genes involved in drought response. From this approach, the authors "produced ranked lists of candidate genes for several drought-associated traits, including water use efficiency, growth, abscisic acid concentration (ABA), and proline concentration."


Via Mary Williams
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Salicylic Acid Inhibits the Replication of Tomato bushy stunt virus by Directly Targeting a Host Component in the Replication Complex

Salicylic Acid Inhibits the Replication of Tomato bushy stunt virus by Directly Targeting a Host Component in the Replication Complex | Plant-Microbe Interaction | Scoop.it

Although the plant hormone salicylic acid (SA) plays a central role in signaling resistance to viral infection, the underlying mechanisms are only partially understood. Identification and characterization of SA’s direct targets have been shown to be an effective strategy for dissecting the complex SA-mediated defense signaling network. In search of additional SA targets, we previously developed two sensitive approaches that utilize SA analogs in conjunction with either a photoaffinity labeling technique or surface plasmon resonance-based technology to identify and evaluate candidate SA-binding proteins (SABPs) from Arabidopsis. Using these approaches, we have now identified several members of the Arabidopsis glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein family, including two chloroplast-localized and two cytosolic isoforms, as SABPs. Cytosolic GAPDH is a well-known glycolytic enzyme; it also is an important host factor involved in the replication of Tomato bushy stunt virus (TBSV), a single-stranded RNA virus. Using a yeast cell-free extract, an in vivo yeast replication system, and plant protoplasts, we demonstrate that SA inhibits TBSV replication. SA does so by inhibiting the binding of cytosolic GAPDH to the negative (−)RNA strand of TBSV. Thus, this study reveals a novel molecular mechanism through which SA regulates virus replication.


Via Christophe Jacquet
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Rescooped by Guogen Yang from Plants and Microbes
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eLife: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness (2015)

eLife: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness (2015) | Plant-Microbe Interaction | Scoop.it

Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Laccaria bicolor Aquaporin LbAQP1 is required for Hartig Net Development in Trembling Aspen (Populus tremuloides)

Laccaria bicolor Aquaporin LbAQP1 is required for Hartig Net Development in Trembling Aspen (Populus tremuloides) | Plant-Microbe Interaction | Scoop.it

The development of ectomycorrhizal associations is crucial for growth of many forest trees. However, the signals that are exchanged between the fungus and the host plant during the colonization process are still poorly understood. In this study, we have identified the relationship between expression patterns of Laccaria bicolor aquaporin LbAQP1 and the development of ectomycorrhizal structures in trembling aspen (Populus tremuloides) seedlings. The peak expression of LbAQP1 was 700-fold higher in the hyphae within the root than in the free-living mycelium after 24 h of direct interaction with the roots. Moreover, in LbAQP1 knock-down strains, a non-mycorrhizal phenotype was developed without the Hartig net and the expression of the mycorrhizal effector protein MiSSP7 quickly declined after an initial peak on day 5 of interaction of the fungal hyphae with the roots. The increase in the expression of LbAQP1 required a direct contact of the fungus with the root and it modulated the expression of MiSSP7. We have also determined that LbAQP1 facilitated NO, H2O2 and CO2 transport when heterologously expressed in yeast. The report demonstrates that the Laccaria bicolor aquaporin LbAQP1 acts as a molecular signaling channel, which is fundamental for the development of Hartig net in root tips of Populus tremuloides.


Via Kevin Garcia, Jean-Michel Ané
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Full Establishment of Arbuscular Mycorrhizal Symbiosis in Rice Occurs Independently of Enzymatic Jasmonate Biosynthesis

Full Establishment of Arbuscular Mycorrhizal Symbiosis in Rice Occurs Independently of Enzymatic Jasmonate Biosynthesis | Plant-Microbe Interaction | Scoop.it
Development of the mutualistic arbuscular mycorrhiza (AM) symbiosis between most land plants and fungi of the Glomeromycota is regulated by phytohormones. The role of jasmonate (JA) in AM colonization has been investigated in the dicotyledons Medicago truncatula, tomato and Nicotiana attenuata and contradicting results have been obtained with respect to a neutral, promotive or inhibitory effect of JA on AM colonization. Furthermore, it is currently unknown whether JA plays a role in AM colonization of monocotyledonous roots. Therefore we examined whether JA biosynthesis is required for AM colonization of the monocot rice. To this end we employed the rice mutant constitutive photomorphogenesis 2 (cpm2), which is deficient in JA biosynthesis. Through a time course experiment the amount and morphology of fungal colonization did not differ between wild-type and cpm2 roots. Furthermore, no significant difference in the expression of AM marker genes was detected between wild type and cpm2. However, treatment of wild-type roots with 50 μM JA lead to a decrease of AM colonization and this was correlated with induction of the defense gene PR4. These results indicate that JA is not required for AM colonization of rice but high levels of JA in the roots suppress AM development likely through the induction of defense.

Via Jean-Michel Ané, Francis Martin
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Jean-Michel Ané's curator insight, April 12, 11:22 AM

I am so glad that PLoS ONE allows to publish such "negative results" because they are very important too. I am not sure that this could have been published in more conventional journals.

Rescooped by Guogen Yang from WU_Phyto-Publications
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MPP (2015): A conserved proline residue in Dothideomycete Avr4 effector proteins is required to trigger a Cf-4-dependent hypersensitive response

MPP (2015): A conserved proline residue in Dothideomycete Avr4 effector proteins is required to trigger a Cf-4-dependent hypersensitive response | Plant-Microbe Interaction | Scoop.it
CfAvr4, a chitin-binding effector protein produced by the Dothideomycete tomato pathogen Cladosporium fulvum, protects the cell wall of this fungus against hydrolysis by secreted host chitinases during infection. However, in the presence of the Cf-4 immune receptor of tomato, CfAvr4 triggers a hypersensitive response (HR), which renders the pathogen avirulent. Recently, several orthologs of CfAvr4 were identified from phylogenetically closely related species of Dothideomycete fungi. Of these, DsAvr4 from Dothistroma septosporum also triggers a Cf-4–dependent HR, but CaAvr4 and CbAvr4 from Cercospora apii and Cercospora beticola, respectively, do not. All, however, bind chitin. To identify the region(s) and specific amino acid residue(s) of CfAvr4 and DsAvr4 required to trigger a Cf-4–dependent HR, chimeric and mutant proteins, in which specific protein regions or single amino acid residues, respectively, had been exchanged between CfAvr4 and CaAvr4 or DsAvr4 and CbAvr4, were tested for their ability to trigger an HR in Nicotiana benthamiana plants transgenic for the Cf-4 immune receptor gene. Based on this approach, a single region common to CfAvr4 and DsAvr4 was determined to carry a conserved proline residue necessary for the elicitation of this HR. In support of this result, a Cf-4–dependent HR was triggered by mutant CaAvr4 and CbAvr4 proteins carrying an arginine-to-proline substitution at this position. This study provides the first step in deciphering how Avr4 orthologs from different Dothideomycete fungi trigger a Cf-4–dependent HR.

Via WU_Phyto
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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A microcosm of microbes underfoot

A microcosm of microbes underfoot | Plant-Microbe Interaction | Scoop.it
This past week, as I harvested the last of my fall green beans and pulled up the vines (and put them in the compost), I saw something that made me think about the great big web of life that we rarely see and hardly think about.

There’s a huge microcosm of life underfoot, namely fungi and bacteria that have evolved over millions of years to live symbiotically with plants.

My bean roots had tiny little nodules on them, which are home to bacteria that perform a very important function. These bacteria, along with fungi, are so important to plant health that nearly all plants have an association with a bacteria or fungus.

Bumps on the bean roots

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant-microbe interaction
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ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis

ALD1 Regulates Basal Immune Components and Early Inducible Defense Responses in Arabidopsis | Plant-Microbe Interaction | Scoop.it

Robust immunity requires basal defense machinery to mediate timely responses and feedback cycles to amplify defenses against potentially spreading infections. AGD2-LIKE DEFENSE RESPONSE PROTEIN 1 (ALD1) is needed for the accumulation of the plant defense signal salicylic acid (SA) during the first hours after infection with the pathogen Pseudomonas syringae and is also upregulated by infection and SA. ALD1 is an aminotransferase with multiple substrates and products in vitro. Pipecolic acid (Pip) is an ALD1-dependent bioactive product induced by P. syringae. Here, we addressed roles of ALD1 in mediating defense amplification as well as the levels and responses of basal defense machinery. ALD1 needs immune components PAD4 and ICS1 (an SA synthesis enzyme) to confer disease resistance, possibly through a transcriptional amplification loop between them. Furthermore, ALD1 affects basal defense by controlling microbial-associated molecular pattern (MAMP) receptor levels and responsiveness. Vascular exudates from uninfected ALD1-overexpressing plants confer local immunity to the wild type and ald1 mutants yet are not enriched for Pip. We infer that, in addition to affecting Pip accumulation, ALD1 produces non-Pip metabolites that play roles in immunity. Thus, distinct metabolite signals controlled by the same enzyme affect basal and early defenses versus later defense responses, respectively.


Via Christophe Jacquet, Suayib Üstün
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Transcriptional networks in plant immunity

Transcriptional networks in plant immunity | Plant-Microbe Interaction | Scoop.it
Next to numerous abiotic stresses, plants are constantly exposed to a variety of pathogens within their environment. Thus, their ability to survive and prosper during the course of evolution was strongly dependent on adapting efficient strategies to perceive and to respond to such potential threats. It is therefore not surprising that modern plants have a highly sophisticated immune repertoire consisting of diverse signal perception and intracellular signaling pathways. This signaling network is intricate and deeply interconnected, probably reflecting the diverse lifestyles and infection strategies used by the multitude of invading phytopathogens. Moreover it allows signal communication between developmental and defense programs thereby ensuring that plant growth and fitness are not significantly retarded. How plants integrate and prioritize the incoming signals and how this information is transduced to enable appropriate immune responses is currently a major research area. An important finding has been that pathogen-triggered cellular responses involve massive transcriptional reprogramming within the host. Additional key observations emerging from such studies are that transcription factors (TFs) are often sites of signal convergence and that signal-regulated TFs act in concert with other context-specific TFs and transcriptional co-regulators to establish sensory transcription regulatory networks required for plant immunity.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant Pathogenomics
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Molecular Genetics and Genomics: Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat (2014)

Molecular Genetics and Genomics: Full-genome identification and characterization of NBS-encoding disease resistance genes in wheat (2014) | Plant-Microbe Interaction | Scoop.it

Host resistance is the most economical, effective and ecologically sustainable method of controlling diseases in crop plants. In bread wheat, despite the high number of resistance loci that have been cataloged to date, only few have been cloned, underlying the need for genomics-guided investigations capable of providing a prompt and acute knowledge on the identity of effective resistance genes that can be used in breeding programs. Proteins with a nucleotide-binding site (NBS) encoded by the major plant disease resistance (R) genes play an important role in the responses of plants to various pathogens. In this study, a comprehensive analysis of NBS-encoding genes within the whole wheat genome was performed, and the genome scale characterization of this gene family was established. From the recently published wheat genome sequence, we used a data mining and automatic prediction pipeline to identify 580 complete ORF candidate NBS-encoding genes and 1,099 partial-ORF ones. Among complete gene models, 464 were longer than 200 aa, among them 436 had less than 70 % of sequence identity to each other. This gene models set was deeply characterized. (1) First, we have analyzed domain architecture and identified, in addition to typical domain combinations, the presence of particular domains like signal peptides, zinc fingers, kinases, heavy-metal-associated and WRKY DNA-binding domains. (2) Functional and expression annotation via homology searches in protein and transcript databases, based on sufficient criteria, enabled identifying similar proteins for 60 % of the studied gene models and expression evidence for 13 % of them. (3) Shared orthologous groups were defined using NBS-domain proteins of rice and Brachypodium distachyon. (4) Finally, alignment of the 436 NBS-containing gene models to the full set of scaffolds from the IWGSC’s wheat chromosome survey sequence enabled high-stringence anchoring to chromosome arms. The distribution of the R genes was found balanced on the three wheat sub-genomes. In contrast, at chromosome scale, 50 % of members of this gene family were localized on 6 of the 21 wheat chromosomes and ~22 % of them were localized on homeologous group 7. The results of this study provide a detailed analysis of the largest family of plant disease resistance genes in allohexaploid wheat. Some structural traits reported had not been previously identified and the genome-derived data were confronted with those stored in databases outlining the functional specialization of members of this family. The large reservoir of NBS-type genes presented and discussed will, firstly, form an important framework for marker-assisted improvement of resistance in wheat, and, secondly, open up new perspectives for a better understanding of the evolution dynamics of this gene family in grass species and in polyploid systems.


Via Christophe Jacquet, Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi

A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi | Plant-Microbe Interaction | Scoop.it
The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant Immunity And Microbial Effectors
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Transcriptional Dynamics of Phytophthora infestans During Sequential Stages of Hemibiotrophic Infection of Tomato

Transcriptional Dynamics of Phytophthora infestans During Sequential Stages of Hemibiotrophic Infection of Tomato | Plant-Microbe Interaction | Scoop.it

Hemibiotrophic plant pathogens, such as the oomycete Phytophthora infestans, employ a biphasic infection strategy, initially behaving as biotrophs where minimal symptoms are exhibited by the plant, and subsequently as necrotrophs, feeding on dead plant tissue. The regulation of this transition and the breadth of molecular mechanisms that modulate plant defenses are not well understood, although effector proteins secreted by the pathogen are thought to play a key role. We examined the transcriptional dynamics of P. infestans in a compatible interaction with its host tomato (Solanum lycopersicum), at three infection stages: biotrophy; the transition from biotrophy to necrotrophy; and necrotrophy. The expression data suggested a tight temporal regulation of many pathways associated with suppression of plant defense mechanisms and pathogenicity, including the induction of putative cytoplasmic and apoplastic effectors. Twelve of these were experimentally evaluated to determine their ability to suppress necrosis caused by the P. infestans necrosis-inducing protein PiNPP1.1 in Nicotiana benthamiana. Four effectors suppressed necrosis, suggesting that they might prolong the biotrophic phase. This study suggests that a complex regulation of effector expression modulates the outcome of the interaction.


Via IPM Lab
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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ENHANCED DISEASE RESISTANCE4 Associates with CLATHRIN HEAVY CHAIN2 and Modulates Plant Immunity by Regulating Relocation of EDR1 in Arabidopsis

ENHANCED DISEASE RESISTANCE4 Associates with CLATHRIN HEAVY CHAIN2 and Modulates Plant Immunity by Regulating Relocation of EDR1 in Arabidopsis | Plant-Microbe Interaction | Scoop.it
Obligate biotrophs, such as the powdery mildew pathogens, deliver effectors to the host cell and obtain nutrients from the infection site. The interface between the plant host and the biotrophic pathogen thus represents a major battleground for plant-pathogen interactions. Increasing evidence shows that cellular trafficking plays an important role in plant immunity. Here, we report that Arabidopsis thaliana ENHANCED DISEASE RESISTANCE4 (EDR4) plays a negative role in resistance to powdery mildew and that the enhanced disease resistance in edr4 mutants requires salicylic acid signaling. EDR4 mainly localizes to the plasma membrane and endosomal compartments. Genetic analyses show that EDR4 and EDR1 function in the same genetic pathway. EDR1 and EDR4 accumulate at the penetration site of powdery mildew infection, and EDR4 physically interacts with EDR1, recruiting EDR1 to the fungal penetration site. In addition, EDR4 interacts with CLATHRIN HEAVY CHAIN2 (CHC2), and edr4 mutants show reduced endocytosis rates. Taken together, our data indicate that EDR4 associates with CHC2 and modulates plant immunity by regulating the relocation of EDR1 in Arabidopsis.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Loci and candidate gene identification for resistance to Sclerotinia sclerotiorum in soybean (Glycine max L. Merr.) via association and linkage maps

Loci and candidate gene identification for resistance to Sclerotinia sclerotiorum in soybean (Glycine max L. Merr.) via association and linkage maps | Plant-Microbe Interaction | Scoop.it
Soybean white mold (SWM), caused by Sclerotinia sclerotiorum ((Lib.) W. Phillips), is currently considered to be the second most important cause of soybean yield loss due to disease. Research is needed to identify SWM-resistant germplasm and gain a better understanding of the genetic and molecular basis of SWM resistance in soybean. Stem pigmentation after treatment with oxaloacetic acid is an effective indicator of resistance to SWM. A total of 128 recombinant inbred lines (RILs) derived from a cross of ‘Maple Arrow’ (partial resistant to SWM) and ‘Hefeng 25’ (susceptible) and 330 diverse soybean cultivars were screened for the soluble pigment concentration of their stems, which were treated with oxalic acid. Four quantitative trait loci (QTLs) underlying soluble pigment concentration were detected by linkage mapping of the RILs. Three hundred and thirty soybean cultivars were sequenced using the whole-genome encompassing approach and 25 179 single-nucleotide polymorphisms (SNPs) were detected for the fine mapping of SWM resistance genes by genome-wide association studies. Three out of five SNP markers representing a linkage disequilibrium (LD) block and a single locus on chromosome 13 (Gm13) were significantly associated with the soluble pigment content of stems. Three more SNPs that represented three minor QTLs for the soluble pigment content of stems were identified on another three chromosomes by association mapping. A major locus with the largest effect on Gm13 was found both by linkage and association mapping. Four potential candidate genes involved in disease response or the anthocyanin biosynthesis pathway were identified at the locus near the significant SNPs (<60 kbp). The beneficial allele and candidate genes should be useful in soybean breeding for improving resistance to SWM.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plants and Microbes
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New Phytologist: The tomato I-3 gene: a novel gene for resistance to Fusarium wilt disease - Catanzariti (2015)

New Phytologist: The tomato I-3 gene: a novel gene for resistance to Fusarium wilt disease - Catanzariti (2015) | Plant-Microbe Interaction | Scoop.it
Plant resistance proteins provide race-specific immunity through the recognition of pathogen effectors. The resistance genes I, I-2 and I-3 have been incorporated into cultivated tomato (Solanum lycopersicum) from wild tomato species to confer resistance against Fusarium oxysporum f. sp. lycopersici (Fol) races 1, 2 and 3, respectively. Although the Fol effectors corresponding to these resistance genes have all been identified, only the I-2 resistance gene has been isolated from tomato.To isolate the I-3 resistance gene, we employed a map-based cloning approach and used transgenic complementation to test candidate genes for resistance to Fol race 3.Here, we describe the fine mapping and sequencing of genes at the I-3 locus, which revealed a family of S-receptor-like kinase (SRLK) genes. Transgenic tomato lines were generated with three of these SRLK genes and one was found to confer Avr3-dependent resistance to Fol race 3, confirming it to be I-3.The finding that I-3 encodes an SRLK reveals a new pathway for Fol resistance and a new class of resistance genes, of which Pi-d2from rice is also a member. The identification of I-3 also allows the investigation of the complex effector–resistance protein interaction involving Avr1-mediated suppression of I-2- and I-3-dependent resistance in tomato.
Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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A symbiosis toolkit: Genetic analysis of mycorrhiza evolution

A symbiosis toolkit: Genetic analysis of mycorrhiza evolution | Plant-Microbe Interaction | Scoop.it
I wanted to write a bit more about my PhD and what I have been up to. However, I broke my knee 5 weeks ago playing rugby: rupturing two cruciate ligaments and fracturing my tibia… So I have been away from the lab. During an extended procrastination break I did however get chance to write this brief post, simplified to my level of understanding, about a recent Nature Genetics paper on the phylogenies of mycorrhizal fungi. 

Mycorrhizal fungi form key association with plants. They effectively extend the surface area of their hosts roots - the fungi supply the plant with nutrients such as nitrogen and phosphorus, in return, the plant supplies the fungi with carbon fixed by photosynthesis. This association is ubiquitous in higher plant species, where more than 80% have fungal partners. Thus exploring this relationship is crucial to understanding many ecological and evolutionary questions. 

Kohler et al.’s (2015) large scale study extended our knowledge of this plant-fungal association by delving into the evolution of mycorrhizal fungi. They compared fugal phylogenies of biotrophic (obtain carbon from plant hosts) and saprotrophic (carbon from degrading complex organic substrates) fungal genomes. This included studying 49 genomes of saprotrophs, ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species. Their comparison of these fungal genomes provides deeper understanding on how the plant-fungal association evolved and how this association aids the plant in adapting to its environment.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Nuclear processes associated with plant immunity and pathogen susceptibility

Nuclear processes associated with plant immunity and pathogen susceptibility | Plant-Microbe Interaction | Scoop.it
Plants are sessile organisms that have evolved exquisite and sophisticated mechanisms to adapt to their biotic and abiotic environment. Plants deploy receptors and vast signalling networks to detect, transmit and respond to a given biotic threat by inducing properly dosed defence responses. Genetic analyses and, more recently, next-generation -omics approaches have allowed unprecedented insights into the mechanisms that drive immunity. Similarly, functional genomics and the emergence of pathogen genomes have allowed reciprocal studies on the mechanisms governing pathogen virulence and host susceptibility, collectively allowing more comprehensive views on the processes that govern disease and resistance. Among others, the identification of secreted pathogen molecules (effectors) that modify immunity-associated processes has changed the plant–microbe interactions conceptual landscape. Effectors are now considered both important factors facilitating disease and novel probes, suited to study immunity in plants. In this review, we will describe the various mechanisms and processes that take place in the nucleus and help regulate immune responses in plants. Based on the premise that any process required for immunity could be targeted by pathogen effectors, we highlight and describe a number of functional assays that should help determine effector functions and their impact on immune-related processes. The identification of new effector functions that modify nuclear processes will help dissect nuclear signalling further and assist us in our bid to bolster immunity in crop plants.

Via Christophe Jacquet
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Jennifer Mach's curator insight, April 13, 8:34 AM

The abstract opens with the classic "plants are sessile organisms" gambit...

Rescooped by Guogen Yang from Rice Blast
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Pseudo-backcrossing design for rapidly pyramiding multiple traits into a preferential rice variety

Four resistance donors with five target genes (Sub1A-C, xa5, Xa21, TPS and SSIIa) and three QTLs (qBph3, qBL1 and qBL11) were backcrossed individually using markers into the pseudo-recurrent parent ‘PinK3’ via one cycle of backcrossing followed by two cycles of pseudo-backcrossing and three selfings with rigorous foreground marker-assisted selection. In total, 29 pseudo-backcross inbred lines (BILs) were developed. Genome composition was surveyed using 61 simple sequence repeats (SSRs), 35 of which were located on six carrier chromosomes, with the remainder located on six non-carrier chromosomes. The recurrent genome content (%RGC) and donor genome content (%DGC), which were based on the physical positions of BC1F2, ranged from 69.99 to 88.98% and 11.02 to 30.01%, respectively. For the pseudo-BC3F3BILs, the %RGC and %DGC ranged from 74.50 to 81.30% and 18.70 to 25.50%, respectively. These results indicated that without direct background selection, no further increases in %RGC were obtained during pseudo-backcrossing, whereas rigorous foreground marker-assisted selection tended to reduce linkage drag during pseudo-backcrossing. The evaluation of new traits in selected pseudo-BC3F3BILs indicated significant improvements in resistance to BB, BL, BPH and Sub compared with PinK3, as well as significant improvements in grain yield (21-68%) over the donors, although yield was 7-26% lower than in ‘PinK3’. All pyramided lines were aromatic and exhibited improved starch profiles, rendering them suitable for industrial food applications.

Via Elsa Ballini
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Rescooped by Guogen Yang from Rice Blast
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RiceVarMap: a comprehensive database of rice genomic variations

RiceVarMap: a comprehensive database of rice genomic variations | Plant-Microbe Interaction | Scoop.it
Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.

Via Elsa Ballini
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Impact of water regimes on an experimental community of four desert arbuscular mycorrhizal fungal (AMF) species, as affected by the introduction of a non-native AMF species

Impact of water regimes on an experimental community of four desert arbuscular mycorrhizal fungal (AMF) species, as affected by the introduction of a non-native AMF species | Plant-Microbe Interaction | Scoop.it
Field studies have revealed the impact of changing water regimes on the structure of arbuscular mycorrhizal fungal (AMF) communities, but it is not known what happens to the abundance of individual AMF species within the community when the water conditions in the rhizosphere change. The behavior of four AMF species isolated from the Arabian desert (Diversispora aurantia, Diversispora omaniana, Septoglomus africanum, and an undescribed Paraglomus species) was investigated when assembled in microcosms containing Sorghum bicolor as host plant, and treated with various water regimes. Furthermore, the impact of invasion of these assemblages by Rhizophagus irregularis, an AMF species widely used in commercial inocula, was studied. The abundance of each AMF species in sorghum roots was measured by determining the transcript numbers of their large ribosomal subunit (rLSU) by real-time PCR, using cDNA and species-specific primers. Plant biomass and length of AMF extraradical hyphae were also measured. The abundance of each AMF species within the sorghum roots was influenced by both the water regime and the introduction of R. irregularis. Under dry conditions, the introduction of R. irregularis reduced the total abundance of all native AMF species in roots and also led to a reduction in the amount of extraradical mycelium, as well as to a partial decrease in plant biomass. The results indicate that both water regime and the introduction of an invasive AMF species can strongly alter the structure of an AMF native assemblage with a consequent impact on the entire symbiotic mycorrhizal relationship.

Via Christophe Jacquet, Jean-Michel Ané
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Frontiers | Signal regulators of systemic acquired resistance | Plant-Microbe Interaction

Frontiers | Signal regulators of systemic acquired resistance | Plant-Microbe Interaction | Plant-Microbe Interaction | Scoop.it
Salicylic acid (SA) is an important phytohormone that plays a vital role in a number of physiological responses, including plant defense. The last two decades have witnessed a number of breakthroughs related to biosynthesis, transport, perception and signaling mediated by SA. These findings demonstrate that SA plays a crictical role in both local and systemic defense responses. Systemic acquired resistance (SAR) is one such SA-dependent response. SAR is a long distance signaling mechanism that provides broad spectrum and long-lasting resistance to secondary infections throughout the plant. This unique feature makes SAR a highly desirable trait in crop production. This review summarizes the recent advances in the role of SA in SAR and discusses its relationship to other SAR inducers.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Secondary metabolites in plant innate immunity

Secondary metabolites in plant innate immunity | Plant-Microbe Interaction | Scoop.it
Plant secondary metabolites carry out numerous functions in interactions between plants and a broad range of other organisms. Experimental evidence strongly supports the indispensable contribution of many constitutive and pathogen-inducible phytochemicals to plant innate immunity. Extensive studies on model plant species, particularly Arabidopsis thaliana, have brought significant advances in our understanding of the molecular mechanisms underpinning pathogen-triggered biosynthesis and activation of defensive secondary metabolites. However, despite the proven significance of secondary metabolites in plant response to pathogenic microorganisms, little is known about the precise mechanisms underlying their contribution to plant immunity. This insufficiency concerns information on the dynamics of cellular and subcellular localization of defensive phytochemicals during the encounters with microbial pathogens and precise knowledge on their mode of action. As many secondary metabolites are characterized by their in vitro antimicrobial activity, these compounds were commonly considered to function in plant defense as in planta antibiotics. Strikingly, recent experimental evidence suggests that at least some of these compounds alternatively may be involved in controlling several immune responses that are evolutionarily conserved in the plant kingdom, including callose deposition and programmed cell death.

Via Christophe Jacquet, Mary Williams
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline

Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline | Plant-Microbe Interaction | Scoop.it
Plants are continuously monitoring the presence of microorganisms to establish an adapted response. Plants commonly use pattern recognition receptors (PRRs) to perceive microbe- or pathogen-associated molecular patterns (MAMPs/PAMPs) which are microorganism molecular signatures. Located at the plant plasma membrane, the PRRs are generally receptor-like kinases (RLKs) or receptor-like proteins (RLPs). MAMP detection will lead to the establishment of a plant defense program called MAMP-triggered immunity (MTI). In this review, we overview the RLKs and RLPs that assure early recognition and control of pathogenic or beneficial bacteria. We also highlight the crucial function of PRRs during plant-microbe interactions, with a special emphasis on the receptors of the bacterial flagellin and peptidoglycan. In addition, we discuss the multiple strategies used by bacteria to evade PRR-mediated recognition.

Via Jean-Michel Ané
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Jean-Michel Ané's curator insight, April 14, 12:53 PM

Another nice review

Rescooped by Guogen Yang from Virology and Bioinformatics from Virology.ca
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Genomics, Medicine, and Pseudoscience: How disruptive are MOOCs? Hopkins launches new genomic data science series.

Genomics, Medicine, and Pseudoscience: How disruptive are MOOCs? Hopkins launches new genomic data science series. | Plant-Microbe Interaction | Scoop.it

Via Chris Upton + helpers
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Frontiers | Biodiversity of genes encoding anti-microbial traits within plant associated microbes | Plant Genetics and Genomics

Frontiers | Biodiversity of genes encoding anti-microbial traits within plant associated microbes | Plant Genetics and Genomics | Plant-Microbe Interaction | Scoop.it
The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.

Via Christophe Jacquet
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