Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis

Tillage shapes the soil and rhizosphere microbiome of barley-but not its susceptibility towards Blumeria graminis f. sp. hordei

Long-term agricultural practices are assumed to shape the rhizosphere microbiome of crops with implications for plant health. In a long-term field experiment, we investigated the effect of different tillage and fertilization practices on soil and barley rhizosphere microbial communities by means of amplicon sequencing of 16S rRNA gene fragments from total community DNA. Differences in the microbial community composition depending on the tillage practice, but not the fertilization intensity were revealed. To examine whether these soil and rhizosphere microbiome differences influence the plant defense response, barley (cultivar Golden Promise) was grown in field or standard potting soil under greenhouse conditions and challenged with Blumeria graminis f. sp. hordei (Bgh). Amplicon sequence analysis showed that preceding tillage practice, but also aboveground Bgh challenge significantly influenced the microbial community composition. Expression of plant defense-related genes PR1b and PR17b was higher in challenged compared to unchallenged plants. The Bgh infection rates were strikingly lower for barley grown in field soil compared to potting soil. Although previous agricultural management shaped the rhizosphere microbiome, no differences in plant health were observed. We propose therefore that the management-independent higher microbial diversity of field soils compared to potting soils contributed to the low infection rates of barley.

Analysis of expressed sequence tags from cDNA library of Fusarium culmorum infected barley (Hordeum vulgare L.) roots

Fusarium culmorum is one of the most common and globally important causal agent of root and crown rot diseases of cereals. These diseases cause grain yield loss and reduced grain quality in barley. In this study, we have analyzed an expressed sequence tag (EST) database derived from F. culmorum infected barley root tissues available at the National Center for Biotechnology Information (NCBI). The 2294 sequences were assembled into 1619 non-redundant sequences consisting of 359 contigs and 1260 singletons using the program CAP3. BLASTX analysis for these sequences was conducted in order to find similar sequences in all databases. Gene Ontology search, enzyme search, KEGG mapping and InterProScan search were done using Blast2GO 3.0.7 tool. By BLASTX analysis, 41.7%, 7.7%, 3.2% and 47.4% of ESTs were categorized as annotated, unannotated, not mapping and without blast hits, respectively. BLASTX analysis revealed that the majority of top hits were barley proteins (43.5%). Based on Gene Ontology classification, 38.3%, 31.3%, and 16% of ESTs were assigned to molecular function, biological process, and cellular component GO terms, respectively. Most abundant GO terms were as follows: 157 sequences were related to response to stress (biological process), 207 sequences were related to ion binding (molecular function), and 160 sequences were related to plastid (cellular component). Furthermore, based on KEGG mapping, 369 sequences could be assigned to 264 enzymes and 83 different KEGG pathways. According to Enzyme Commission (EC) distribution; 94 sequences were transferases (EC2) while 70 sequences were hydrolases (EC3).

Alternative cell death mechanisms determine epidermal resistance in incompatible barley-Ustilago interactions

Programmed cell death is a key feature of epidermal plant immunity, which is particularly effective against biotrophic microbes that depend on living host tissue. The covered smut fungus Ustilago hordei establishes a compatible biotrophic interaction with its host plant barley. The maize smut U. maydis triggers a nonhost response in barley, which results in epidermal cell death. Similarly, Ustilago mutants being deleted for pep1, a gene encoding a secreted effector, are blocked upon host penetration. We studied the epidermal responses of barley to incompatible Ustilago strains. Molecular and cellular analyses were used to test the impact of Bax inhibitor-1 (BI-1), a suppressor of programmed cell death, on the barley nonhost resistance to U. maydis as well as Ustilago Δpep1 mutants. Overexpression of BI-1 resulted in partial break of barley nonhost resistance to U. maydis. By contrast, the epidermal cell death response triggered by pep1 deletion mutants was not impaired by BI-1. Hypersensitive-response-like cell death caused by U. maydis wild-type infection showed features of necrotic cell death, while Δpep1 mutant-induced host responses involved hallmarks of autophagy. Therefore, we propose that the mechanisms of epidermal cell death in response to different types of incompatible pathogens depend on spatial and temporal appearance of cell-death-triggering stimuli.

Transgenic barley: a prospective tool for biotechnology and agriculture

Barley (Hordeum vulgare L.) is one of the founder crops of agriculture, and today it is the fourth most important cereal grain worldwide. Barley is used as malt in brewing and distilling industry, as an additive for animal feed, and as a component of various food and bread for human consumption. Progress in stable genetic transformation of barley ensures a potential for improvement of its agronomic performance or use of barley in various biotechnological and industrial applications. Recently, barley grain has been successfully used in molecular farming as a promising bioreactor adapted for production of human therapeutic proteins or animal vaccines. In addition to development of reliable transformation technologies, an extensive amount of various barley genetic resources and tools such as sequence data, microarrays, genetic maps, and databases has been generated. Current status on barley transformation technologies including gene transfer techniques, targets, and progeny stabilization, recent trials for improvement of agricultural traits and performance of barley, especially in relation to increased biotic and abiotic stress tolerance, and potential use of barley grain as a protein production platform have been reviewed in this study. Overall, barley represents a promising tool for both agricultural and biotechnological transgenic approaches, and is considered an ancient but rediscovered crop as a model industrial platform for molecular farming.

The conserved oligomeric Golgi complex is involved in penetration resistance of barley to the barley powdery mildew fungus

Membrane trafficking is vital to plant development and adaptation to the environment. It is suggested that post-Golgi vesicles and multivesicular bodies are essential for plant defence against directly penetrating fungal parasites at the cell wall. However, the actual plant proteins involved in membrane transport for defence are largely unidentified. We applied a candidate gene approach and single cell transient-induced gene silencing for the identification of membrane trafficking proteins of barley involved in the response to the fungal pathogen Blumeria graminis f.sp. hordei. This revealed potential components of vesicle tethering complexes [putative exocyst subunit HvEXO70F-like and subunits of the conserved oligomeric Golgi (COG) complex] and Golgi membrane trafficking (COPIγ coatomer and HvYPT1-like RAB GTPase) as essential for resistance to fungal penetration into the host cell.

Warriors at the gate that never sleep: non-host resistance in plants

The native resistance of most plant species against a wide variety of pathogens is known as non-host resistance (NHR), which confers durable protection to plant species. Only a few pathogens or parasites can successfully cause diseases. NHR is polygenic and appears to be linked with basal plant resistance, a form of elicited protection. Sensing of pathogens by plants is brought about through the recognition of invariant pathogen-associated molecular patterns (PAMPs) that trigger downstream defense signaling pathways. Race-specific resistance, (R)-gene mediated resistance, has been extensively studied and reviewed, while our knowledge of NHR has advanced only recently due to the improved access to excellent model systems. The continuum of the cell wall (CW) and the CW-plasma membrane (PM)-cytoskeleton plays a crucial role in perceiving external cues and activating defense signaling cascades during NHR. Based on the type of hypersensitive reaction (HR) triggered, NHR was classified into two types, namely type-I and type-II. Genetic analysis of Arabidopsis mutants has revealed important roles for a number of specific molecules in NHR, including the role of SNARE-complex mediated exocytosis, lipid rafts and vesicle trafficking. As might be expected, R-gene mediated resistance is found to overlap with NHR, but the extent to which the genes/pathways are common between these two forms of disease resistance is unknown. The present review focuses on the various components involved in the known mechanisms of NHR in plants with special reference to the role of CW-PM components.

Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions

Barley Mildew resistance locus a (Mla) is a major determinant of immunity to the powdery mildew pathogen, Blumeria graminis f. sp. hordei. Alleles of Mla encode cytoplasmic- and membrane-localized coiled-coil, nucleotide binding site, leucine-rich repeat proteins that mediate resistance when complementary avirulence effectors (AVR(a)) are present in the pathogen. Presence of an appropriate AVR(a) protein triggers nuclear relocalization of MLA, in which MLA binds repressing host transcription factors. Timecourse expression profiles of plants harboring Mla1, Mla6, and Mla12 wild-type alleles versus paired loss-of-function mutants were compared to discover conserved transcriptional targets of MLA and downstream signaling cascades. Pathogen-dependent gene expression was equivalent or stronger in susceptible plants at 20 h after inoculation (HAI) and was attenuated at later timepoints, whereas resistant plants exhibited a time-dependent strengthening of the transcriptional response, increasing in both fold change and the number of genes differentially expressed. Deregulation at 20 HAI implicated 16 HAI as a crucial point in determining the future trajectory of this interaction and was interrogated by quantitative analysis. In total, 28 potential transcriptional targets of the MLA regulon were identified. These candidate targets possess a diverse set of predicted functions, suggesting that multiple pathways are required to mediate the hypersensitive reaction.

Barley stripe mosaic virus-induced gene silencing (BSMV-IGS) as a tool for functional analysis of barley genes potentially involved in nonhost resistance

Barley is an alternative host for the rice blast fungus Magnaporthe oryzae but is resistant to Magnaporthe species associated with the grass genera Pennisetum and Digitaria. The latter cases are examples for nonhost resistance which confers effective and durable protection to plants against a broad spectrum of pathogens. Comparative transcript profiling of host and nonhost interaction revealed an early and pronounced change in gene expression in epidermal tissue of barley infected with a Magnaporthe nonhost isolate. Interestingly, this set of genes did not overlap considerably with the transcriptional response of barley against nonhost rust or powdery mildew isolates. For a functional testing of candidate genes a combined approach of virus-induced gene silencing (VIGS) and subsequent pathogen challenge was established. As anticipated, VIGS-mediated down-regulation of Mlo-transcripts led to higher resistance against Blumeria graminis f.sp. hordei and enhanced susceptibility against M. oryzae.

Pathogenesis-associated transcriptional patterns in Triticeae

The Triticeae tribe of the plant Poaceae family contains some of the most important cereal crop plants for nutrition of humans and livestock such as wheat and barley. Despite the agronomical relevance of plant immunity, knowledge on mechanisms of disease or resistance in Triticeae is limited. It is hardly understood what actually stops a microbial invader when restricted by the plant and in how far a susceptible host plant contributes to pathogenesis. Transcriptional reprogramming of the host plant may be involved in both immunity and disease. This paper gives an overview about recent analyses of global pathogenesis-related transcriptional patterns in response of Triticeae to biotrophic or non-biotrophic fungal pathogens and their toxins. It highlights enriched biological functions in association with successful plant defence or disease as well as experiments that successfully translated gene expression data into analysis of gene functions.

BAX INHIBITOR-1 is required for full susceptibility of barley to powdery mildew

BAX INHIBITOR-1 (BI-1) is one of the few proteins known to have cross-kingdom conserved functions in negative control of programmed cell death. Additionally, barley BI-1 (HvBI-1) suppresses defense responses and basal resistance to the powdery mildew fungus Blumeria graminis f. sp. hordei and enhances resistance to cell death-provoking fungi when overexpressed in barley. Downregulation of HvBI-1 by transient-induced gene silencing or virus-induced gene silencing limited susceptibility to B. graminis f. sp. hordei, suggesting that HvBI-1 is a susceptibility factor toward powdery mildew. Transient silencing of BI-1 did not limit supersusceptibility induced by overexpression of MLO. Transgenic barley plants harboring an HvBI-1 RNA interference (RNAi) construct displayed lower levels of HvBI-1 transcripts and were less susceptible to powdery mildew than wild-type plants. At the cellular level, HvBI-1 RNAi plants had enhanced resistance to penetration by B. graminis f. sp. hordei. These data support a function of BI-1 in modulating cell-wall-associated defense and in establishing full compatibility of B. graminis f. sp. hordei with barley.

Expression analysis of defense-related genes in Zingiber (Zingiberaceae) species with different levels of compatibility to the soft rot pathogen Pythium aphanidermatum

Ginger (Zingiber officinale Roscoe) cultivars are susceptible to soft rot disease caused by Pythium aphanidermatum. We analyzed changes in transcript levels of 41 genes in the highly susceptible ginger cultivar varada, a less susceptible wild accession (wild ginger), and a Pythium aphanidermatum-resistant relative, Z. zerumbet, following treatment with Pythium aphanidermatum or one of three signaling molecules: salicylic acid (SA), jasmonic acid (JA), or ethylene (ET). The 41 studied genes were chosen because they are known to be involved in the hypersensitive response (HR), cell signaling, or host defense. Expression of most genes peaked within 24 h of Pythium aphanidermatum infection. Interestingly, the level of induction was typically manyfold higher in Z. zerumbet than in wild ginger. However, several HR genes that were significantly induced in wild ginger were not induced in Z. zerumbet. Most of the genes, including those involved in signaling, did not respond to any of the three signaling molecules in Z. zerumbet while several genes responded to all the three signaling molecules in varada. In wild ginger, a large proportion of the genes responded to ET, but not to SA or JA. These results suggest that different mechanisms govern the three pathosystems. Resistance in Z. zerumbet seems to be independent of HR and the tested signaling molecules, whereas both mechanisms appear to be activated in the tolerance reaction of wild ginger. This work revealed potential defense components of this understudied tropical taxa, and will contribute to the design of strategies for transgenic improvement of ginger.

Efficient generation of transgenic barley: the way forward to modulate plant-microbe interactions

Stable genetic transformation represents the gold standard approach to the detailed elucidation of plant gene functions. This is particularly relevant in barley, an important experimental model widely employed in applied molecular, genetic and cell biological research, and biotechnology. Presented are details of the establishment of a protocol for Agrobacterium-mediated gene transfer to immature embryos, which enables the highly efficient generation of transgenic barley. Advancements were achieved through comparative experiments on the influence of various explant treatments and co-cultivation conditions. The analysis of representative numbers of transgenic lines revealed that the obtained T-DNA copy numbers are typically low, the generative transmission of the recombinant DNA is in accordance with the Mendelian rules and the vast majority of the primary transgenics produce progeny that expresses the respective transgene product. Moreover, the newly established protocol turned out to be useful to transform not only the highly amenable cultivar (cv.) 'Golden Promise' but also other spring and winter barley genotypes, albeit with substantially lower efficiency. As a major result of this study, a very useful tool is now available for future functional gene analyses as well as genetic engineering approaches. With the aim to modify the expression of barley genes putatively involved in plant-fungus interactions, numerous transgenic plants have been generated using diverse expression cassettes. These plants represent an example of how transformation technology may contribute to further our understanding of important biological processes.

Systemic and local modulation of plant responses by Piriformospora indica and related Sebacinales species

Piriformospora indica is a fungus of the order Sebacinales (Basidiomycota) infesting roots of mono- and dicotyledonous plants. Endophytic fungal colonization leads to enhanced plant growth while host cell death is required for proliferation in differentiated root tissue to form a mutualistic interaction. Colonization of barley roots by P. indica and related Sebacina vermifera strains also leads to systemic resistance against the leaf pathogenic fungus Blumeria graminis f.sp. hordei due to a yet unknown mechanism of induced resistance. In order to elucidate plant response pathways governed by these root endophytes, we analyzed gene expression in barley plants exhibiting an established symbiosis with P. indica 3 weeks after inoculation. P. indica-colonized roots showed no induction of defence-related genes, while other genes showed a differential regulation pattern indicating a faster P. indica-dependent root development. Gene expression analysis of leaves detected only few systemically induced mRNAs. Among differentially regulated transcripts, we characterized the pathogenesis-related gene HvPr17b and the molecular chaperone HvHsp70 in more detail. HvPr17b shows similarity with TaWCI5, a wheat gene inducible by chemical resistance inducers and salicylate, and was previously proven to exhibit antifungal activity against B. graminis. HvHsp70 is the first gene found to systemically indicate root colonization with endophytic fungi of the order Sebacinales. Both genes are discussed as markers for endophytic colonization and resulting systemic responses.

Accommodation of powdery mildew fungi in intact plant cells

Parasitic powdery mildew fungi have to overcome basic resistance and manipulate host cells to establish a haustorium as a functional feeding organ in a host epidermal cell. Currently, it is of central interest how plant factors negatively regulate basal defense or whether they even support fungal development in compatible interactions. Additionally, creation of a metabolic sink in infected cells may involve host activity. Here, we review the current progress in understanding potential fungal targets for host reprogramming and nutrient acquisition.

Fungal transcriptomics

We have now entered in the post-genomic era, where we have knowledge of plethora of fungal genomes and cutting edge technology is available to study global mRNA, protein and metabolite profiles. These so-called 'omic' technologies (transcriptomics, proteomics and metabolomics) provide the possibility to characterize plant-pathogen interactions and pathogenesis at molecular level. This article provides an overview of transcriptomics and its applications in fungal plant pathology.

Transcript profiling in host-pathogen interactions

Using genomic technologies, it is now possible to address research hypotheses in the context of entire developmental or biochemical pathways, gene networks, and chromosomal location of relevant genes and their inferred evolutionary history. Through a range of platforms, researchers can survey an entire transcriptome under a variety of experimental and field conditions. Interpretation of such data has led to new insights and revealed previously undescribed phenomena. In the area of plant-pathogen interactions, transcript profiling has provided unparalleled perception into the mechanisms underlying gene-for-gene resistance and basal defense, host vs nonhost resistance, biotrophy vs necrotrophy, and pathogenicity of vascular vs nonvascular pathogens, among many others. In this way, genomic technologies have facilitated a system-wide approach to unifying themes and unique features in the interactions of hosts and pathogens.