Gene Expression In Barley Research Articles

Genome-Wide Identification and Hormone Response Analysis of the COBL Gene Family in Barley.

Barley (Hordeum vulgare L.), a diverse cereal crop, exhibits remarkable versatility in its applications, ranging from food and fodder to industrial uses. The content of cellulose in barley is significantly influenced by the COBRA genes, which encode the plant glycosylphosphatidylinositol (GPI)-anchored protein (GAP) that plays a pivotal role in the deposition of cellulose within the cell wall. The COBL (COBRA-Like) gene family has been discovered across numerous species, yet the specific members of this family in barley remain undetermined. In this study, we discovered 13 COBL genes within the barley genome using bioinformatics methods, subcellular localization, and protein structure analysis, finding that most of the barley COBL proteins have a signal peptide structure and are localized on the plasma membrane. Simultaneously, we constructed a phylogenetic tree and undertook a comprehensive analysis of the evolutionary relationships. Other characteristics of HvCOBL family members, including intraspecific collinearity, gene structure, conserved motifs, and cis-acting elements, were thoroughly characterized in detail. The assessment of HvCOBL gene expression in barley under various hormone treatments was conducted through qRT-PCR analysis, revealing jasmonic acid (JA) as the predominant hormonal regulator of HvCOBL gene expression. In summary, this study comprehensively identified and analyzed the barley COBL gene family, aiming to provide basic information for exploring the members of the HvCOBL gene family and to propose directions for further research.

Investigation of morpho-physiolgical traits and gene expression in barley under nitrogen deficiency

Nitrogen (N) is an essential element for plant growth, and its deficiency influences plants at several physiological and gene expression levels. Barley (Hordeum vulgare) is one of the most important food grains from the Poaceae family and one of the most important staple food crops. However, the seed yield is limited by a number of stresses, the most important of which is the insufficient use of N. Thus, there is a need to develop N-use effective cultivars. In this study, comparative physiological and molecular analyses were performed using leaf and root tissues from 10 locally grown barley cultivars. The expression levels of nitrate transporters, HvNRT2 genes, were analyzed in the leaf and root tissues of N-deficient (ND) treatments of barley cultivars after 7 and 14 days following ND treatment as compared to the normal condition. Based on the correlation between the traits, root length (RL) had a positive and highly significant correlation with fresh leaf weight (FLW) and ascorbate peroxidase (APX) concentration in roots, indicating a direct root and leaf relationship with the plant development under ND. From the physiological aspects, ND enhanced carotenoids, chlorophylls a/b (Chla/b), total chlorophyll (TCH), leaf antioxidant enzymes such as ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT), and root antioxidant enzymes (APX and POD) in the Sahra cultivar. The expression levels of HvNRT2.1, HvNRT2.2, and HvNRT2.4 genes were up-regulated under ND conditions. For the morphological traits, ND maintained root dry weight among the cultivars, except for Sahra. Among the studied cultivars, Sahra responded well to ND stress, making it a suitable candidate for barely improvement programs. These findings may help to better understand the mechanism of ND tolerance and thus lead to the development of cultivars with improved nitrogen use efficiency (NUE) in barley.

Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes.

Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.

WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications.

WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications.

Effect of zinc deficiency and excess on catalase activity and HvCAT2 gene expression in barley

Effect of zinc deficiency and excess on catalase activity and HvCAT2 gene expression in barley

Phenotype, Physiology, and Gene Expression of Barley Seedlings in Response to Nano Zinc Oxide Stress

In recent years, zinc oxide nanoparticles (ZnO NPs) have been widely used as zinc fertilizers and pesticides. The use of ZnO NPs in this way can provide benefits to humans, but also has potential risks. ZnO NPs inevitably enter the environment during their production and use, which affects the ecological environment and crop growth. In order to investigate the phenotype, physiology, and gene expression of barley (Hordeum vulgare L.) seedlings under ZnO NPs stress, the barely cultivars ZJU3 (P21), Golden Promise (GP) and L23 were chosen for study. Different ZnO NPs concentrations were applied to compare the physiological and biochemical indexes of the barley seedlings and the responses of six stress-related genes, when seedlings were cultured to the two-leaf stage through hydroponics. The results showed that the density of brown spots on the leaf surface increased with increasing ZnO NPs concentration. ZnO NPs stress inhibited the root growth of barley seedlings, and P21 was the most sensitive. Furthermore, ZnO NPs stress could stimulate plants to produce a large number of reactive oxygen species (ROS), resulting in an imbalance between the production and removal of ROS and membrane lipid peroxidation in plants. This imbalance inhibited the growth and development of the barley seedlings. With increasing ZnO NPs concentration, the activity of superoxide dismutase was gradually increased, the activity of catalase was progressively decreased, and the contents of malondialdehyde and proline were increased. Compared with the control, among six stress-related genes, the expression levels of five genes were downregulated and one gene was upregulated in the experimental group. This study preliminarily revealed the toxic effect of ZnO NPs on seedlings and the effect on the expression of stress-related resistance genes in different barley varieties.

A heat-shock inducible system for flexible gene expression in cereals

BackgroundFunctional characterisation of genes using transgenic methods is increasingly common in cereal crops. Yet standard methods of gene over-expression can lead to undesirable developmental phenotypes, or even embryo lethality, due to ectopic gene expression. Inducible expression systems allow the study of such genes by preventing their expression until treatment with the specific inducer. When combined with the Cre-Lox recombination system, inducible promoters can be used to initiate constitutive expression of a gene of interest. Yet while these systems are well established in dicot model plants, like Arabidopsis thaliana, they have not yet been implemented in grasses.ResultsHere we present an irreversible heat-shock inducible system developed using Golden Gate-compatible components which utilises Cre recombinase to drive constitutive gene expression in barley and wheat. We show that a heat shock treatment of 38 °C is sufficient to activate the construct and drive expression of the gene of interest. Modulating the duration of heat shock controls the density of induced cells. Short durations of heat shock cause activation of the construct in isolated single cells, while longer durations lead to global construct activation. The system can be successfully activated in multiple tissues and at multiple developmental stages and shows no activation at standard growth temperatures (~ 20 °C).ConclusionsThis system provides an adaptable framework for use in gene functional characterisation in cereal crops. The developed vectors can be easily adapted for specific genes of interest within the Golden Gate cloning system. By using an environmental signal to induce activation of the construct, the system avoids pitfalls associated with consistent and complete application of chemical inducers. As with any inducible system, care must be taken to ensure that the expected construct activation has indeed taken place.

Identification of transcription factors that bind to the 5'-UTR of the barley PHO2 gene.

In barley and other higher plants, phosphate homeostasis is maintained by a regulatory network involving the PHO2 (PHOSPHATE2)encoding ubiquitin-conjugating (UBC) E2 enzyme, the PHR1 (PHOSPHATE STARVATION RESPONSE 1) transcription factor (TF), IPS1 (INDUCED BYPHOSPHATESTARVATION1) RNA, and miR399. During phosphate ion (Pi) deprivation, PHR1 positively regulates MIR399 expression, after transcription and processing mature miR399 guides the Ago protein to the 5'-UTR of PHO2 transcripts. Non-coding IPS1 RNA is highly expressed during Pi starvation, and the sequestration of miR399 molecules protects PHO2 mRNA from complete degradation. Here, we reveal new cis- and trans-regulatory elements that are crucial for efficient PHO2 gene expression in barley. We found that the 5'-UTR of PHO2 contains two PHR1 binding sites (P1BSs) and one Pi-responsive PHO element. Using a yeast one-hybrid (Y1H) assay, we identified two candidate proteins that might mediate this transcriptional regulation: a barley PHR1 ortholog and a TF containing an uncharacterized MYB domain. Additional results classified this new potential TF as belonging to the APL (ALTERED PHLOEM DEVELOPMENT) protein family, and we observed its nuclear localization in barley protoplasts. Pi starvation induced the accumulation of barley APL transcripts in both the shoots and roots. Interestingly, the deletion of the P1BS motif from the first intron of the barley 5'-UTR led to a significant increase in the transcription of a downstream β-glucuronidase (GUS) reporter gene in tobacco leaves. Our work extends the current knowledge about putative cis- and trans-regulatory elements that may affect the expression of the barley PHO2 gene.

Alleviation of arsenic toxicity by phosphate is associated with its regulation of detoxification, defense, and transport gene expression in barley

Arsenic (As) contamination in soils has posed a severe threat to safe crop production. The previous studies showed the antagonism between phosphorus (P) and As in plant growth and As uptake, while the mechanisms of alleviating As toxicity by P is not completely clear. Due to the limiting P condition, it is imperative to understand how low P addition can be used to suppress arsenate As (V) uptake and the subsequent mechanisms involved. Thus in this study we investigated the effect of P addition on As uptake, anti-oxidative enzyme activity, and anti-oxidant content, and the relative expression of transport, defense, and detoxification genes using two barley genotypes differing in As toxicity tolerance. P addition significantly reduced As concentration in plant tissues, and caused the great changes in activities of catalase and superoxide dismutase, glutathione content, and the relative expression of examined genes when the plants of the two barley genotypes were exposed to 100 μmol L−1 As, with ZDB160 (As-tolerant) being much more affected than ZDB475 (As-sensitive). The current results show that P addition can alleviate As toxicity by regulating the expression of As transport, defense, and detoxification genes to a greater extent in As tolerance of barley, suggesting the possibility of controlling As uptake and toxicity by applying low amount of P fertilizers in the As-contaminated soils.

Root and cell hydraulic conductivity, apoplastic barriers and aquaporin gene expression in barley (Hordeum vulgare L.) grown with low supply of potassium.

Limited supply of mineral nutrients often reduces plant growth and transpirational water flow while increasing the ratio of water-absorbing root to water-losing shoot surface. This could potentially lead to an imbalance between water uptake (too much) and water loss (too little). The aim of the present study was to test whether, as a countermeasure, the hydraulic properties (hydraulic conductivity, Lp) of roots decrease at organ and cell level and whether any decreases in Lp are accompanied by decreases in the gene expression level of aquaporins (AQPs) or increases in apoplastic barriers to radial water movement. Barley plants were grown hydroponically on complete nutrient solution, containing 2 mm K+ (100 %), or on low-K solution (0.05 mm K+; 2.5 %), and analysed when they were 15-18 d old. Transpiration, fresh weight, surface area, shoot water potential (ψ), K and Ca concentrations, root (exudation) and cortex cell Lp (cell pressure probe), root anatomy (cross-sections) and AQP gene expression (qPCR) were analysed. The surface area ratio of root to shoot increased significantly in response to low K. This was accompanied by a small decrease in the rate of water loss per unit shoot surface area, but a large (~50 %) and significant decrease in Lp at root and cortex cell levels. Aquaporin gene expression in roots did not change significantly, due to some considerable batch-to-batch variation in expression response, though HvPIP2;5 expression decreased on average by almost 50 %. Apoplastic barriers in the endodermis did not increase in response to low K. Barley plants that are exposed to low K adjust to an increased ratio of root (water uptake) to shoot (water loss) surface primarily through a decrease in root and cell Lp. Reduced gene expression of HvPIP2;5 may contribute to the decrease in Lp.

Identification of Suitable Reference Genes for Barley Gene Expression Under Abiotic Stresses and Hormonal Treatments

Barley (Hordeum vulgare L.) is an important cereal crop and also can be considered as a model plant for the Triticeae family. Quantitative real-time PCR (qRT-PCR) has emerged as a more practical technique to study barley gene expression, and the data normalization with reference genes is essential for accurate and reliable results. In this study, 17 candidate reference genes were evaluated from two distinct plant tissues (roots and leaves) at the barley seedling stage under different abiotic stresses (osmotic, salt, and heat) and hormonal treatments (gibberellin A3 (GA3) and methyl jasmonate (JA)). Our qRT-PCR data were analyzed with three commonly used software packages: geNorm, NormFider, and BestKeeper. In combination with the analysis of these three packages, four to five candidate genes were selected as suitable reference genes in each experimental set. These results confirmed that expression stability of reference genes depends on the experimental conditions. This study is the systematic analysis for the selection of superior reference genes for qRT-PCR in barley under different abiotic and hormonal treatments and will benefit further studies on gene expression in barley and other species of Triticeae family.

Transcriptome analysis of barley identifies heat shock and HD-Zip I transcription factors up-regulated in response to multiple abiotic stresses

Analyzing barley gene expression profiles in response to abiotic stress is critical to understanding how barley manages stress, and provides vital information to improve environmental stress tolerance for stable crop production. We developed an Agilent 60-mer oligo DNA microarray with 42,491 probe sets based on the sequences of 36,632 barley (Hordeum vulgare L.) full-length cDNA clones and conducted global expression profiling on barley seedlings subjected to desiccation, salt, cold and abscisic acid (ABA). We identified 281 genes that were differentially expressed in response to desiccation, salt, and cold stresses and ABA treatment. Among them, a class C heat shock transcription factor (HvHsfC1) and a homeodomain leucine zipper (HD-Zip) family I transcription factor (HvHox22) showed more than tenfold and fourfold higher expression, respectively, in response to the stimuli. Heat shock and HD-Zip transcription factors function as important regulators in stress responses in rice (Oryza sativa) and Arabidopsis thaliana; our results suggest these two transcription factors also play important roles in abiotic stress responses in barley. We mapped HvHox22 to the long arm of chromosome 2H and HvHsfC1 to the long arm of 4H, where drought resistance quantitative trait loci were previously detected. Our microarray data and identification of these stress response genes provide key information for dissection of the mechanism of abiotic stress tolerance in barley.

The choice of reference gene set for assessing gene expression in barley (Hordeum vulgare L.) under low temperature and drought stress

Drought and low temperature are the two most significant causes of abiotic stress in agricultural crops and, therefore, they pose considerable challenges in plant science. Hence, it is crucial to study response mechanisms and to select genes for identification signaling pathways that lead from stimulus to response. The assessment of gene expression is often attempted using real-time RT-PCR (qRT-PCR), a technique which requires a careful choice of reference gene(s) for normalization purpose. Here, we report a comparison of 13 potential reference genes for studying gene expression in the leaf and crown of barley seedlings subjected to low temperature or drought stress. All three currently available software packages designed to identify reference genes from qRT-PCR data (GeNorm, NormFinder and BestKeeper) were used to identify informative sets of up to three reference genes. Interestingly, the data obtained from the separate treatment of leaf and crown have led to the recommendations that HSP70 and S-AMD (and possibly HSP90) to be used as the reference genes for low-temperature stressed leaves, HSP90 and EF1α for low-temperature stressed crowns, cyclophilin and ADP-RF (and possibly ACT) for drought-stressed leaves, and EF1α and S-AMD for drought-stressed crowns. Our results have demonstrated that the gene expression can be highly tissue- or organ-specific in barley and have confirmed that reference gene choice is essential in qRT-PCR. The findings can also serve as guidelines for the selection of reference genes under different stress conditions and lay foundation for more accurate and widespread use of qRT-PCR in barley gene analysis.

Bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes

Barley (Hordeum vulgare) is one of the world’s most important cereal crops. Although its large and complex genome has held back barley genomics for quite a while, the whole genome sequence was released in 2012 by the International Barley Genome Sequencing Consortium (IBSC). Moreover, more than 30,000 barley full-length cDNAs (FLcDNAs) are now available in the public domain. Here we present the Barley Gene Expression Database (bex-db: http://barleyflc.dna.affrc.go.jp/bexdb/index.html) as a repository of transcriptome data including the sequences and the expression profiles of barley genes resulting from microarray analysis. In addition to FLcDNA sequences, bex-db also contains partial sequences of more than 309,000 novel expressed sequence tags (ESTs). Users can browse the data via keyword, sequence homology and expression profile search options. A genome browser was also developed to display the chromosomal locations of barley FLcDNAs and wheat (Triticum aestivum) transcripts as well as Aegilops tauschii gene models on the IBSC genome sequence for future comparative analysis of orthologs among Triticeae species. The bex-db should provide a useful resource for further genomics studies and development of genome-based tools to enhance the progress of the genetic improvement of cereal crops.

Isolating Barley (Hordeum vulgare L.) B1 Hordein Gene Promoter and Using Sequencing Analaysis For The Identification of Conserved Regulatory Elements By Bioinformatic Tools

Gene expression is a complex multi-step process. For the efficient expression of foreign genes in plants, it is essential to optimize every step of the process for the plant machinery, which includes choosing suitable promoters. Promoters play the most important role in determining the temporal and spatial expression pattern and transcript level of a gene. Some strong constitutive promoters, such as cauliflower mosaic virus 35s promoter, are widely used in plant genetic engineering research. However, the expression levels of the foreign genes in all tissues are often unsatisfied, but some of such problems can be may solved by using a strong seed-specific promoter to restrict gene expression to the seed only. The aim of this article was to characterize a B1 hordein-specific promoter. The promoter region of B1 hordein gene was isolated from the genomic DNA of Walfajre and Alger barley by polymerase chain reaction. Sequence analysis showed that the cloned fragment B hordein promoter (BHP) - contained motifs like TATA box, (CA)n box, ACGT motif, AAAG motif, GCN4-like motif and Ebox, which constituted the seed-specific promoter activity. It was therefore concluded that B1 hordein promoters can be used to engineer and subsequently study stable seed specific gene expression in barley, and potentially to modify barley seeds through genetic engineering. Keywords: Barley, Seed Specific Promoter, Motif, Hordein African Journal of Biotechnology Vol. 11(29), pp. 7378-7387, 10 April, 2012

Tissue‐dependent limited pleiotropy affects gene expression in barley

Non-synonymous coding mutations in a gene change the resulting protein, no matter where it is expressed, but the effects of cis-regulatory mutations could be spatially or temporally limited - a phenomenon termed limited pleiotropy. Here, we report the genome-wide occurrence of limited pleiotropy of cis-regulatory mutations in barley (Hordeum vulgare L.) using Affymetrix analysis of 22,840 genes in a population of 139 doubled haploid lines derived from a cross between the cultivars Steptoe (St) and Morex (Mx). We identified robust cis-acting expression regulators that segregate as major genes in two successive ontogenetic stages: germinating embryo tissues and seedling leaves from the embryonic axis. We show that these polymorphisms may be consistent in both tissues or may cause a dramatic change in transcript abundance in one tissue but not in another. We also show that the parental allele that increases expression can vary with the tissue, suggesting nucleotide polymorphism in enhancer sequences. Because of the limited pleiotropy of cis-regulating mutations, the number of cis expression quantitative trait loci (cis-eQTLs) discovered by 'genetical genomics' is strongly affected by the particular tissue or developmental stage studied. Given that limited pleiotropy is a common feature of cis-regulatory mutations in barley, we predict that the phenomenon would be relevant to developmental and/or tissue-specific interactions across wide taxonomic boundaries in both plants and animals.

Genevestigator Transcriptome Meta-Analysis and Biomarker Search using Rice and Barley Gene Expression Databases

The wide-spread use of microarray technologies to study plant transcriptomes has led to important discoveries and to an accumulation of profiling data covering a wide range of different tissues, developmental stages, perturbations, and genotypes. Querying a large number of microarray experiments can provide insights that cannot be gained by analyzing single experiments. However, such a meta-analysis poses significant challenges with respect to data comparability and normalization, systematic sample annotation, and analysis tools. Genevestigator addresses these issues using a large curated expression database and a set of specifically developed analysis tools that are accessible over the internet. This combination has already proven to be useful in the area of plant research based on a large set of Arabidopsis data (Grennan, 2006). Here, we present the release of the Genevestigator rice and barley gene expression databases that contain quality-controlled and well annotated microarray experiments using ontologies. The databases currently comprise experiments from pathology, plant nutrition, abiotic stress, hormone treatment, genotype, and spatial or temporal analysis, but are expected to cover a broad variety of research areas as more experimental data become available. The transcriptome meta-analysis of the model species rice and barley is expected to deliver results that can be used for functional genomics and biotechnological applications in cereals.

How can we exploit functional genomics approaches for understanding the nature of plant defences? Barley as a case study

The concept ‘functional genomics’ refers to the methods used for the functional characterisation of genomes. The methods utilised provide new opportunities for studying the nature and role of defence mechanisms in plants. Unlike Arabidopsis, poplar and rice, the full genomic sequence of barley is not available. In this case, the analysis of barley gene expression data plays a pivotal role for obtaining insight into the functional characterisation of individual gene products. Many genes are activated transcriptionally following attack by pathogens and these often contribute to the defence mechanisms which underlie disease resistance. The use of large-scale complementary DNA library constructions and genome-wide transcript profiles of plants exposed to biotic stress provide the data required to drive hypotheses concerning the function of newly identified genes. In this paper, we illustrate how publicly available gene expression data has proved valid for studies of plant defence responses; enabling a cost-effective workflow starting from isolated gene transcripts to elucidation of biological function upon biotic stress.

Transcriptome Analysis of Trichothecene-Induced Gene Expression in Barley

Fusarium head blight, caused primarily by Fusarium graminearum, is a major disease problem on barley (Hordeum vulgare L.). Trichothecene mycotoxins produced by the fungus during infection increase the aggressiveness of the fungus and promote infection in wheat (Triticum aestivum L.). Loss-of-function mutations in the TRI5 gene in F. graminearum result in the inability to synthesize trichothecenes and in reduced virulence on wheat. We examined the impact of pathogen-derived trichothecenes on virulence and the transcriptional differences in barley spikes infected with a trichothecene-producing wild-type strain and a loss-of-function tri5 trichothecene nonproducing mutant. Disease severity, fungal biomass, and floret necrosis and bleaching were reduced in spikes inoculated with the tri5 mutant strain compared with the wild-type strain, indicating that the inability to synthesize trichothecenes results in reduced virulence in barley. We detected 63 transcripts that were induced during trichothecene accumulation, including genes encoding putative trichothecene detoxification and transport proteins, ubiquitination-related proteins, programmed cell death-related proteins, transcription factors, and cytochrome P450s. We also detected 414 gene transcripts that were designated as basal defense response genes largely independent of trichothecene accumulation. Our results show that barley exhibits a specific response to trichothecene accumulation that can be separated from the basal defense response. We propose that barley responds to trichothecene accumulation by inducing at least two general responses. One response is the induction of genes encoding trichothecene detoxification and transport activities that may reduce the impact of trichothecenes. The other response is to induce genes encoding proteins associated with ubiquitination and cell death which may promote successful establishment of the disease.

An atlas of gene expression from seed to seed through barley development

Assaying relative and absolute levels of gene expression in a diverse series of tissues is a central step in the process of characterizing gene function and a necessary component of almost all publications describing individual genes or gene family members. However, throughout the literature, such studies lack consistency in genotype, tissues analyzed, and growth conditions applied, and, as a result, the body of information that is currently assembled is fragmented and difficult to compare between different studies. The development of a comprehensive platform for assaying gene expression that is available to the entire research community provides a major opportunity to assess whole biological systems in a single experiment. It also integrates detailed knowledge and information on individual genes into a unified framework that provides both context and resource to explore their contributions in a broader biological system. We have established a data set that describes the expression of 21,439 barley genes in 15 tissues sampled throughout the development of the barley cv. Morex grown under highly controlled conditions. Rather than attempting to address a specific biological question, our experiment was designed to provide a reference gene expression data set for barley researchers; a gene expression atlas and a comparative data set for those investigating genes or regulatory networks in other plant species. In this paper we describe the tissues sampled and their transcriptomes, and provide summary information on genes that are either specifically expressed in certain tissues or show correlated expression patterns across all 15 tissue samples. Using specific examples and an online tutorial, we describe how the data set can be interrogated for patterns and levels of barley gene expression and how the resulting information can be used to generate and/or test specific biological hypotheses.