Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis

BACKGROUND

Barley is known to be recalcitrant to tissue culture, which hinders genetic transformation and its biotechnological application. To date, the ideal explant for transformation remains limited to immature embryos; the mechanism underlying embryonic callus formation is elusive.

RESULTS

This study aimed to uncover the different transcription regulation pathways between calli formed from immature (IME) and mature (ME) embryos through transcriptome sequencing. We showed that incubation of embryos in an auxin-rich medium caused dramatic changes in gene expression profiles within 48 h. Overall, 9330 and 11,318 differentially expressed genes (DEGs) were found in the IME and ME systems, respectively. 3880 DEGs were found to be specific to IME_0h/IME_48h, and protein phosphorylation, regulation of transcription, and oxidative-reduction processes were the most common gene ontology categories of this group. Twenty-three IAA, fourteen ARF, eight SAUR, three YUC, and four PIN genes were found to be differentially expressed during callus formation. The effect of callus-inducing medium (CIM) on IAA genes was broader in the IME system than in the ME system, indicating that auxin response participates in regulating cell reprogramming during callus formation. BBM, LEC1, and PLT2 exhibited a significant increase in expression levels in the IME system but were not activated in the ME system. WUS showed a more substantial growth trend in the IME system than in the ME system, suggesting that these embryonic, shoot, and root meristem genes play crucial roles in determining the acquisition of competency. Moreover, epigenetic regulators, including SUVH3A, SUVH2A, and HDA19B/703, exhibited differential expression patterns between the two induction systems, indicating that epigenetic reprogramming might contribute to gene expression activation/suppression in this process. Furthermore, we examined the effect of ectopic expression of HvBBM and HvWUS on Agrobacterium-mediated barley transformation. The transformation efficiency in the group expressing the PLTPpro:HvBBM + Axig1pro:HvWUS construct was increased by three times that in the control (empty vector) because of enhanced plant regeneration capacity.

CONCLUSIONS

We identified some regulatory factors that might contribute to the differential responses of the two explants to callus induction and provide a promising strategy to improve transformation efficiency in barley.

Site-Directed Mutagenesis in Barley Using RNA-Guided Cas Endonucleases During Microspore-Derived Generation of Doubled Haploids

In plant research and breeding, haploid technology is employed upon crossing, induced mutagenesis or genetic engineering to generate populations of meiotic recombinants that are themselves genetically fixed. Thanks to the speed and efficiency in producing true-breeding lines, haploid technology has become a major driver of modern crop improvement. In the present study, we used embryogenic pollen cultures of winter barley ( Hordeum vulgare ) for Cas9 endonuclease-mediated targeted mutagenesis in haploid cells, which facilitates the generation of homozygous primary mutant plants. To this end, microspores were extracted from immature anthers, induced to undergo cell proliferation and embryogenic development in vitro, and were then inoculated with Agrobacterium for the delivery of T-DNAs comprising expression units for Cas9 endonuclease and target gene-specific guide RNAs (gRNAs). Amongst the regenerated plantlets, mutants were identified by PCR amplification of the target regions followed by sequencing of the amplicons. This approach also enabled us to discriminate between homozygous and heterozygous or chimeric mutants. The heritability of induced mutations and their homozygous state were experimentally confirmed by progeny analyses. The major advantage of the method lies in the preferential production of genetically fixed primary mutants, which facilitates immediate phenotypic analyses and, relying on that, a particularly efficient preselection of valuable lines for detailed investigations using their progenies.

Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora

In barley, it is possible to induce embryogenesis in the haploid and uninucleate microspore to obtain a diploid plant that is perfectly homozygous. To change developmental fates in this fashion, microspores need to engage in cellular de-differentiation, interrupting the pollen formation, and restore totipotency prior to engaging in embryogenesis. In this work, we used the barley cultivar Gobernadora to characterize the transcriptome of microspores prior to (day 0) and immediately after (days 2 and 5) the application of a stress pretreatment. A deep RNA-seq analysis revealed that microspores at these three time points exhibit a transcriptome of ∼14k genes, ∼90% of which were shared. An expression analysis identified a total of 3,382 differentially expressed genes (DEGs); of these, 2,155 and 2,281 DEGs were respectively identified when contrasting expression at days 0 and 2 and at days 2 and 5. These define 8 expression profiles in which DEGs share a common up- or down-regulation at these time points. Up-regulation of numerous glutathione S-transferase and heat shock protein genes as well as down-regulation of ribosomal subunit protein genes was observed between days 0 and 2. The transition from microspores to developing embryos (days 2 vs. 5) was marked by the induction of transcription factor genes known to play important roles in early embryogenesis, numerous genes involved in hormone biosynthesis and plant hormonal signal transduction in addition to genes involved in secondary metabolism. This work sheds light on transcriptional changes accompanying an important developmental shift and provides candidate biomarkers for embryogenesis in barley.

Method for hull-less barley transformation and manipulation of grain mixed-linkage beta-glucan

Hull-less barley is increasingly offering scope for breeding grains with improved characteristics for human nutrition; however, recalcitrance of hull-less cultivars to transformation has limited the use of these varieties. To overcome this limitation, we sought to develop an effective transformation system for hull-less barley using the cultivar Torrens. Torrens yielded a transformation efficiency of 1.8%, using a modified Agrobacterium transformation method. This method was used to over-express genes encoding synthases for the important dietary fiber component, (1,3;1,4)-β-glucan (mixed-linkage glucan), primarily present in starchy endosperm cell walls. Over-expression of the HvCslF6 gene, driven by an endosperm-specific promoter, produced lines where mixed-linkage glucan content increased on average by 45%, peaking at 70% in some lines, with smaller increases in transgenic HvCslH1 grain. Transgenic HvCslF6 lines displayed alterations where grain had a darker color, were more easily crushed than wild type and were smaller. This was associated with an enlarged cavity in the central endosperm and changes in cell morphology, including aleurone and sub-aleurone cells. This work provides proof-of-concept evidence that mixed-linkage glucan content in hull-less barley grain can be increased by over-expression of the HvCslF6 gene, but also indicates that hull-less cultivars may be more sensitive to attempts to modify cell wall composition.

Dynamics of post-translationally modified histones during barley pollen embryogenesis in the presence or absence of the epi-drug trichostatin A

Improving pollen embryogenesis. Despite the agro-economic importance of pollen embryogenesis, the mechanisms underlying this process are still poorly understood. We describe the dynamics of chromatin modifications (histones H3K4me2, H3K9ac, H3K9me2, and H3K27me3) and chromatin marks (RNA polymerase II CDC phospho-Ser5, and CENH3) during barley pollen embryogenesis. Immunolabeling results show that, in reaction to stress, immature pollen rapidly starts reorganizing several important chromatin modifications indicative of a change in cell fate. This new chromatin modification pattern was accomplished within 24 h from whereon it remained unaltered during subsequent mitotic activity. This indicates that cell fate transition, the central element of pollen embryogenesis, is completed early on during the induction process. Application of the histone deacetylase inhibitor trichostatin A stimulated pollen embryogenesis when used on pollen with a gametophytic style chromatin pattern. However, when this drug was administered to embryogenic pollen, the chromatin markers reversed toward a gametophytic profile, embryogenesis was halted and all pollen invariably died.

phenoSeeder - A Robot System for Automated Handling and Phenotyping of Individual Seeds

The enormous diversity of seed traits is an intriguing feature and critical for the overwhelming success of higher plants. In particular, seed mass is generally regarded to be key for seedling development but is mostly approximated by using scanning methods delivering only two-dimensional data, often termed seed size. However, three-dimensional traits, such as the volume or mass of single seeds, are very rarely determined in routine measurements. Here, we introduce a device named phenoSeeder, which enables the handling and phenotyping of individual seeds of very different sizes. The system consists of a pick-and-place robot and a modular setup of sensors that can be versatilely extended. Basic biometric traits detected for individual seeds are two-dimensional data from projections, three-dimensional data from volumetric measures, and mass, from which seed density is also calculated. Each seed is tracked by an identifier and, after phenotyping, can be planted, sorted, or individually stored for further evaluation or processing (e.g. in routine seed-to-plant tracking pipelines). By investigating seeds of Arabidopsis (Arabidopsis thaliana), rapeseed (Brassica napus), and barley (Hordeum vulgare), we observed that, even for apparently round-shaped seeds of rapeseed, correlations between the projected area and the mass of seeds were much weaker than between volume and mass. This indicates that simple projections may not deliver good proxies for seed mass. Although throughput is limited, we expect that automated seed phenotyping on a single-seed basis can contribute valuable information for applications in a wide range of wild or crop species, including seed classification, seed sorting, and assessment of seed quality.

Transcriptome analysis reveals translational regulation in barley microspore-derived embryogenic callus under salt stress

Transcriptome analysis of barley embryogenic callus from isolated microspore culture under salt stress uncovered a role of translation inhibition and selective activation of stress-specific proteins in cellular defense. Soil salinity is one of the major abiotic stresses which constrains the plant growth and reduces the productivity of field crops. In this study, it was observed that the salt stress in barley isolated microspore culture impacted not only on the quantity of embryogenic callus but also on the quality for later differentiation. The barley microspore-derived embryogenic callus, a transient intermediate form linked cells and plants, was employed for a global transcriptome analysis by RNA sequencing to provide new insights into the cellular adaptation or acclimation to stress. A total of 596 differentially expressed genes (DEGs) were identified, in which 123 DEGs were up-regulated and 473 DEGs were down-regulated in the embryogenic callus produced from microspore culture under salt stress as compared to the control conditions. KEGG pathway analysis identified 'translation' (27 DEGs; 12.56 %) as the largest group and followed by 'folding, sorting and degradation' (25 DEGs; 11.63 %) in 215 mapped metabolic pathways. The results of RNA-Seq data and quantitative real-time polymerase chain reaction validation showed that the genes related to translation regulation (such as eIF1A, RPLP0, RPLP2, VARS) were down-regulated to control general protein synthesis, and the genes related to endoplasmic reticulum stress response (such as small heat shock protein genes) were selectively up-regulated against protein denaturing during microspore embryogenesis under continuous salt stress. These transcriptional remodeling might affect the essential protein synthesis for the cell development to fulfill totipotency under salt stress.

The Dynamics of Transcript Abundance during Cellularization of Developing Barley Endosperm

Within the cereal grain, the endosperm and its nutrient reserves are critical for successful germination and in the context of grain utilization. The identification of molecular determinants of early endosperm development, particularly regulators of cell division and cell wall deposition, would help predict end-use properties such as yield, quality, and nutritional value. Custom microarray data have been generated using RNA isolated from developing barley grain endosperm 3 d to 8 d after pollination (DAP). Comparisons of transcript abundance over time revealed 47 gene expression modules that can be clustered into 10 broad groups. Superimposing these modules upon cytological data allowed patterns of transcript abundance to be linked with key stages of early grain development. Here, attention was focused on how the datasets could be mined to explore and define the processes of cell wall biosynthesis, remodeling, and degradation. Using a combination of spatial molecular network and gene ontology enrichment analyses, it is shown that genes involved in cell wall metabolism are found in multiple modules, but cluster into two main groups that exhibit peak expression at 3 DAP to 4 DAP and 5 DAP to 8 DAP. The presence of transcription factor genes in these modules allowed candidate genes for the control of wall metabolism during early barley grain development to be identified. The data are publicly available through a dedicated web interface (https://ics.hutton.ac.uk/barseed/), where they can be used to interrogate co- and differential expression for any other genes, groups of genes, or transcription factors expressed during early endosperm development.

Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos

Barley (Hordeum vulgare L.) seed germination initiates many important biological processes such as DNA, membrane and mitochondrial repairs. However, little is known on cell wall modifications in germinating embryos. We have investigated cell wall polysaccharide composition change, gene transcription and alternative splicing events in four barley varieties at 24h and 48 h germination. Cell wall components in germinating barley embryos changed rapidly, with increases in cellulose and (1,3)(1,4)-β-D-glucan (20-100%) within 24h, but decreases in heteroxylan and arabinan (3-50%). There were also significant changes in the levels of type I arabinogalactans and heteromannans. Alternative splicing played very important roles in cell wall modifications. At least 22 cell wall transcripts were detected to undergo either alternative 3' splicing, alternative 5' splicing or intron retention type of alternative splicing. These genes coded enzymes catalyzing synthesis and degradation of cellulose, heteroxylan, (1,3)(1,4)-β-D-glucan and other cell wall polymers. Furthermore, transcriptional regulation also played very important roles in cell wall modifications. Transcript levels of primary wall cellulase synthase, heteroxylan synthesizing and nucleotide sugar inter-conversion genes were very high in germinating embryos. At least 50 cell wall genes changed transcript levels significantly. Expression patterns of many cell wall genes coincided with changes in polysaccharide composition. Our data showed that cell wall polysaccharide metabolism was very active in germinating barley embryos, which was regulated at both transcriptional and post-transcriptional levels.

Cell layer-specific distribution of transiently expressed barley ESCRT-III component HvVPS60 in developing barley endosperm

The significance of the endosomal sorting complexes required for transport (ESCRT)-III in cereal endosperm has been shown by the identification of the recessive mutant supernumerary aleurone layer1 (SAL1) in maize. ESCRT-III is indispensable in the final membrane fission step during biogenesis of multivesicular bodies (MVBs), responsible for protein sorting to vacuoles and to the cell surface. Here, we annotated barley ESCRT-III members in the (model) crop Hordeum vulgare and show that all identified members are expressed in developing barley endosperm. We used fluorescently tagged core ESCRT-III members HvSNF7a/CHMP4 and HvVPS24/CHMP3 and the associated ESCRT-III component HvVPS60a/CHMP5 for transient localization studies in barley endosperm. In vivo confocal microscopic analyses show that the localization of recombinantly expressed HvSNF7a, HvVPS24 and HvVPS60a differs within barley endosperm. Whereas HvSNF7a induces large agglomerations, HvVPS24 shows mainly cytosolic localization in aleurone and subaleurone. In contrast, HvVPS60a localizes strongly at the plasma membrane in aleurone. In subaleurone, HvVPS60a was found to a lesser extent at the plasma membrane and at vacuolar membranes. These results indicate that the steady-state association of ESCRT-III may be influenced by cell layer-specific protein deposition or trafficking and remodelling of the endomembrane system in endosperm. We show that sorting of an artificially mono-ubiquitinated Arabidopsis plasma membrane protein is inhibited by HvVPS60a in aleurone. The involvement of HvVPS60a in different cell layer-specific trafficking pathways, reflected by localization of HvVPS60a at the plasma membrane in aleurone and at the PSV membrane in subaleurone, is discussed.

Light Inhibition of Shoot Regeneration Is Regulated by Endogenous Abscisic Acid Level in Calli Derived from Immature Barley Embryos

Shoot regeneration in calli derived from immature barley embryos is regulated by light conditions during the callus-induction period. Barley cultivars Kanto Nijo-5 (KN5) and K-3 (K3) showed lower efficiency of shoot regeneration in a 16-h photoperiod during callus-induction than those in continuous darkness, whereas shoot regeneration was enhanced in cultures under a 16-h photoperiod in Golden Promise (GP) and Lenins (LN). These cultivars were classified as photo-inhibition type (KN5 and K3) or photo-induction type (GP and LN) according to their response to light. Contents of endogenous plant hormones were determined in calli cultured under a 16-h photoperiod and continuous darkness. In photo-inhibition type, higher accumulation of abscisic acid (ABA) was detected in calli cultured under a 16-h photoperiod, whereas calli showed lower levels of endogenous ABA in continuous darkness. However, cultivars of photo-induction type showed lower levels of ABA in calli cultured under both light conditions, similarly to photo-inhibition type in continuous darkness. Exogenous ABA inhibited the callus growth and shoot regeneration independent of light conditions in all cultivars. In photo-inhibition type, lower levels of endogenous ABA induced by ABA biosynthesis inhibitor, fluridone, reduced the photo-inhibition of shoot regeneration. Expression of ABA biosynthesis gene, HvNCED1, in calli was regulated by the light conditions. Higher expression was observed in calli cultured under a 16-h photoperiod. These results indicate that ABA biosynthesis could be activated through the higher expression of HvNCED1 in a 16-h photoperiod and that the higher accumulations of ABA inhibit shoot regeneration in the photo-inhibition type cultivars.

A Role for Reactive Oxygen Species Produced by NADPH Oxidases in the Embryo and Aleurone Cells in Barley Seed Germination

Reactive oxygen species (ROS) promote the germination of several seeds, and antioxidants suppress it. However, questions remain regarding the role and production mechanism of ROS in seed germination. Here, we focused on NADPH oxidases, which produce ROS. After imbibition, NADPH oxidase mRNAs were expressed in the embryo and in aleurone cells of barley seed; these expression sites were consistent with the sites of ROS production in the seed after imbibition. To clarify the role of NADPH oxidases in barley seed germination, we examined gibberellic acid (GA) / abscisic acid (ABA) metabolism and signaling in barley seeds treated with diphenylene iodonium chloride (DPI), an NADPH oxidase inhibitor. DPI significantly suppressed germination, and suppressed GA biosynthesis and ABA catabolism in embryos. GA, but not ABA, induced NADPH oxidase activity in aleurone cells. Additionally, DPI suppressed the early induction of α-amylase by GA in aleurone cells. These results suggest that ROS produced by NADPH oxidases promote GA biosynthesis in embryos, that GA induces and activates NADPH oxidases in aleurone cells, and that ROS produced by NADPH oxidases induce α-amylase in aleurone cells. We conclude that the ROS generated by NADPH oxidases regulate barley seed germination through GA / ABA metabolism and signaling in embryo and aleurone cells.

Carotenoids of aleurone, germ, and endosperm fractions of barley, corn and wheat differentially inhibit oxidative stress

The antioxidant potential of carotenoids from aleurone, germ, and endosperm fractions of barley, corn, and wheat has been evaluated. HPLC analysis confirmed the presence of lutein and zeaxanthin carotenoids (nd-15139 μg/kg) in extracts of cereal grain fractions. The antioxidant properties using 2,2-diphenyl-1-picrylhydrazyl, oxygen radical absorbance capacity, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) assays revealed significantly higher (P<0.001) antioxidant activity in the germ than in the aleurone and endosperm fractions. Using 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) assay, 2,2'azobis (2-amidinopropane)dihydrochloride (AAPH)-induced cell loss was effectively reduced by preincubating Caco-2, HT-29, and FHs 74 Int cells with carotenoid extracts. Moreover, carotenoid extracts reduced (P<0.001) AAPH-induced intracellular oxidation in the cell lines, suggesting antioxidant activity. Of the 84 antioxidant pathway genes included in microarray array analysis (HT-29 cells), the expressions of 28 genes were enhanced (P<0.05). Our findings suggest that carotenoids of germ, aleurone, and endosperm fractions improved antioxidant capacity and thus have the potential to mitigate oxidative stress.

High-frequency generation and characterization of intergeneric hybrids and haploids from new wheat-barley crosses

Hybrid plants and a high frequency of maternal haploids were obtained using an efficient wheat-barley hybridization system (with new genotype combinations) and confirmed by several cytological and molecular tools. An efficient hybridization system between wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) is presented on the basis of three new genotype combinations. A particularly high, 14% frequency of plant regeneration per florets was achieved in the wheat-barley genotype combination of 'Sichuan' × 'Morex'. The genome composition in 42 of the 95 plants regenerated by embryo rescue was determined using ploidy analysis, genomic in situ hybridization and the application of chromosome arm-specific molecular markers (SSR and STS). A high overall frequency (76%) of maternal (wheat) haploids was observed in all the tests for all three cross combinations. A major implication of this observation is that this new hybridization system represents a useful tool to study the mechanism of uniparental chromosome elimination in cereals.

Improving the efficiency of isolated microspore culture in six-row spring barley: II-exploring novel growth regulators to maximize embryogenesis and reduce albinism

Two alternative cytokinins, thidiazuron and meta-topoline, were tested in isolated microspore culture on recalcitrant barley genotypes (six-row, spring), and green plant regeneration was improved substantially. Doubled-haploid (DH) plants are coveted in plant breeding and in genetic studies, since they are rapidly obtained and perfectly homozygous. In barley, DHs are produced mainly via androgenesis, and isolated microspore culture (IMC) constitutes the method offering the greatest potential efficiency. However, IMC can often be challenging in some genotypes because of low yield of microspores, low regeneration and high incidence of albinism. Six-row spring-type barleys, the predominant type grown in Eastern Canada, are considered recalcitrant in this regard. Our general objective was to optimize an IMC protocol for DH production in six-row spring barley. In particular, we explored the use of alternative hormones in the induction medium (thidiazuron and dicamba), and in the regeneration medium (meta-topoline). This optimization was performed on two typical six-row spring (ACCA and Léger), a two-row spring (Gobernadora) and a two-row winter (Igri) barley cultivar. When 6-benzyl-aminopurine (BAP) was replaced by a combination of thidiazuron and dicamba in the induction medium, a 5.1-fold increase (P < 0.01) in the production of green plants resulted. This increase was mainly achieved by a reduction of albinism. Moreover, a 2.9-fold increase (P < 0.01) in embryo differentiation into green plants was obtained using meta-topoline instead of BAP in the regeneration medium. Together, these innovations allowed us to achieve a substantial improvement in the efficiency of IMC in this recalcitrant type of barley. These results were later successfully validated using sets of F1s from a six-row spring barley breeding program.

Improving the efficiency of isolated microspore culture in six-row spring barley: I-optimization of key physical factors

An improved isolated microspore culture protocol alleviating the recalcitrance typically observed in six-row spring barley was developed by optimizing four key physical factors to increase embryogenesis and reduce albinism. Doubled haploid (DH) plants are completely homozygous individuals that can be generated in just a few months via androgenesis in vitro. DHs are useful tools in genetic research and in plant breeding. Isolated microspore culture (IMC) is the most efficient way to produce DHs, but a strong genotype dependency imposes limitations to its wide application. Six-row, spring barley genotypes are considered as particularly recalcitrant due to a low frequency of embryogenesis and a high rate of albinism. Seeking to develop an efficient IMC protocol for this type of barley, we explored four important factors: (1) the harvest stage of immature spikes, (2) the type of pretreatment applied, (3) the osmotic potential in the induction medium, and (4) the plating density of microspores. This work was first performed using four barley genotypes: two typical six-row spring cultivars (ACCA and Léger), a two-row spring (Gobernadora) and a two-row winter (Igri) cultivar. First, by optimizing the harvest stage for each genotype we obtained a twofold to fourfold increase in the yield of embryogenic microspores. Second, two pretreatments (0.3 M mannitol for 2 days, or a combination of cold and heat over 15 days) both performed significantly better than the commonly used cold pretreatment (28 days at 4 °C). Third, an induction medium-containing mannitol (32 g/l) doubled green plant regeneration. Fourth, a plating density of 10(6) microspores/ml yielded the highest number of green regenerated plants. Our most important findings were then confirmed using sets of F1s from a six-row, spring-type breeding program.

Distribution of carotenoids in endosperm, germ, and aleurone fractions of cereal grain kernels

To compare the distribution of carotenoids across the grain, non-corn and corn cereals were hand dissected into endosperm, germ and aleurone fractions. Total carotenoid content (TCC) and carotenoid composition were analysed using spectrophotometry and HPLC. Cereal carotenoid composition was similar; however, concentrations varied significantly (p<0.05). Endosperm fractions had TCC ranging from 0.88 to 2.27 and 14.17 to 31.35 mg/kg in non-corn cereals and corn, respectively. TCC, lutein and zeaxanthin in germ fractions were higher in non-corn cereals than in corn. Lutein and zeaxanthin contents were lower in non-corn cereal endosperms. The aleurone layer had zeaxanthin levels 2- to 5-fold higher than lutein among the cereals. Positive significant correlations (p<0.05) were found between TCC, carotenoids analysed by HPLC and DPPH results. This study is the first to report on carotenoid composition of the aleurone layer. Our findings suggest that the aleurone of wheat, oat, corn and germ of barley have significantly enhanced carotenoid levels.

Time-lapse imaging of the initiation of pollen embryogenesis in barley (Hordeum vulgare L.)

Pollen embryogenesis provides exciting opportunities in the areas of breeding and biotechnology as well as representing a convenient model for studying the process of plant cell proliferation in general and embryogenesis in particular. A cell culture system was devised in which immature barley pollen could be cultured as a monolayer trapped between the bottom glass-cover slip of a live-cell chamber and a diaphanous PTFE membrane within a liquid medium over a period of up to 28 d, allowing the process of embryogenesis to be tracked in individual pollen. Z-stacks of images were automatically captured every 3min, starting from the unicellular pollen stage up to the development of multicellular, embryogenic structures. The method should prove useful for the elucidation of ultrastructural features and molecular processes associated with pollen embryogenesis.

Crosstalk between reactive oxygen species and hormonal signalling pathways regulates grain dormancy in barley

Seed dormancy, defined as the inability to germinate under favourable conditions, is controlled by abscisic acid (ABA) and gibberellins (GAs). Phytohormone signalling interacts with reactive oxygen species (ROS) signalling regarding diverse aspects of plant physiology and is assumed to be important in dormancy alleviation. Using dormant barley grains that do not germinate at 30 °C in darkness, we analysed ROS content and ROS-processing systems, ABA content and metabolism, GA-responsive genes and genes involved in GA metabolism in response to hydrogen peroxide (H₂O₂) treatment. During after-ripening, the ROS content in the embryo was not affected, while the antioxidant glutathione (GSH) was gradually converted to glutathione disulphide (GSSG). ABA treatment up-regulated catalase activity through transcriptional activation of HvCAT2. Exogenous H₂O₂ partially alleviated dormancy although it was associated with a small increase in embryonic ABA content related to a slight induction of HvNCED transcripts. H₂O₂ treatment did not affect ABA sensitivity but up-regulated the expression of HvExpA11 (GA-induced gene), inhibited the expression of HvGA2ox3 involved in GA catabolism and enhanced the expression of HvGA20ox1 implicated in GA synthesis. In barley, H₂O₂ could be implicated in dormancy alleviation through activation of GA signalling and synthesis rather than repression of ABA signalling.

Genotypic differences in callus induction and plant regeneration from mature embryos of barley (Hordeum vulgare L.)

An efficient induction system and regeneration protocol based on mature barley embryos were developed. Embryos isolated from mature seeds, dehusked by hand and inoculated with longitudinally bisected sections, showed low contamination and high primary callus-forming capability. The influences of nine culture media on primary callus induction and germination from the mature embryos of barley cultivars Golden Promise and Zaoshu 3 were analyzed. The results showed that the two cultivars had much higher values of primary callus induction in the B16M6D medium as compared to the other eight medium formulations, with a frequency of 74.3% and 78.4% for Golden Promise and Zaoshu 3, respectively. Furthermore, Zaoshu 3 demonstrated particularly high stability in callus induction over the different media, indicating its potential utilization in callus induction and regeneration for its good agronomic traits and wide adaption. There were significant differences amongst 11 barley genotypes in terms of primary callus induction in the optimum medium, with percentages of callus induction and germination response ranging from 17.9% to 78.4% and 2.8% to 47.4%, respectively. Green plantlets of Dong 17, Golden Promise, and Zaoshu 3 were successfully developed from primary calli through embryogenesis, with green plant differentiation frequencies ranging from 9.7% to 21.0% across genotypes.

Megapixel imaging of (micro)nutrients in mature barley grains

Understanding the accumulation and distribution of essential nutrients in cereals is of primary importance for improving the nutritional quality of this staple food. While recent studies have improved the understanding of micronutrient loading into the barley grain, a detailed characterization of the distribution of micronutrients within the grain is still lacking. High-definition synchrotron X-ray fluorescence was used to investigate the distribution and association of essential elements in barley grain at the micro scale. Micronutrient distribution within the scutellum and the embryo was shown to be highly variable between elements in relation to various morphological features. In the rest of the grain, the distribution of some elements such as Cu and Zn was not limited to the aleurone layer but extended into the endosperm. This pattern of distribution was less marked in the case of Fe and, in particular, Mn. A significant difference in element distribution was also found between the ventral and dorsal part of the grains. The correlation between the elements was not consistent between and within tissues, indicating that the transport and storage of elements is highly regulated. The complexity of the spatial distribution and associations has important implications for improving the nutritional content of cereal crops such as barley.

Agrobacterium tumefaciens-mediated genetic transformation of cereals using immature embryos

A critical step in the development of a robust Agrobacterium tumefaciens-mediated transformation -system for cereal crop plants is the establishment of optimal conditions for efficient T-DNA delivery into target tissue, from which plants can be regenerated. Although, Agrobacterium-mediated transformation of cereals is an important method that has been widely used by many laboratories around the world, routine protocols have been established only in specific cultivars within a species and with specific tissues of high regeneration potential. Cocultivation of highly embryogenic callus tissue or healthy immature embryos with A. tumefaciens is considered one of the critical factors in successful genetic transformation of crop plants. Immature embryos collected only from vigorously growing healthy and green plants grown in the field or in the well-conditioned greenhouse are the ideal target for genetic transformation of recalcitrant crop species. Here, we describe an Agrobacterium-mediated transformation method that uses immature embryos as the starting material for inoculation with Agrobacterium. The aim of this chapter is to provide the key steps/components involved in Agrobacterium-mediated transformation of cereal crops. However, these steps or components often vary between protocols and from laboratory to laboratory, and can be optimized or modified based on the requirement of a specific cultivar or species.

Chromosomal loci associated with endosperm hardness in a malting barley cross

A breeding objective for the malting barley industry is to produce lines with softer, plumper grain containing moderate protein content (9-12%) as they are more likely to imbibe water readily and contain more starch per grain, which in turn produces higher levels of malt extract. In a malting barley mapping population, 'Arapiles' × 'Franklin', the most significant and robust quantitative trait locus (QTL) for endosperm hardness was observed on the short arm of chromosome 1H, across three environments over two growing seasons. This accounted for 22.6% (Horsham 2000), 26.8% (Esperance 2001), and 12.0% (Tarranyurk 2001) of the genetic variance and significantly increased endosperm hardness by 2.06-3.03 SKCS hardness units. Interestingly, Arapiles and Franklin do not vary in Ha locus alleles. Therefore, this region, near the centromere on chromosome 1H, may be of great importance when aiming to manipulate endosperm hardness and malting quality. Interestingly, this region, close to the centromere on chromosome 1H, in our study, aligns with the region of the genome that includes the HvCslF9 and the HvGlb1 genes. Potentially, one or both of these genes could be considered to be candidate genes that influence endosperm hardness in the barley grain. Additional QTLs for endosperm hardness were detected on chromosomes 2H, 3H, 6H and 7H, confirming that the hardness trait in barley is complex and multigenic, similar to many malting quality traits of interest.

Proteomic and activity profiles of ascorbate-glutathione cycle enzymes in germinating barley embryo

Enzymes involved in redox control are important during seed germination and seedling growth. Ascorbate-glutathione cycle enzymes in barley embryo extracts were monitored both by 2D-gel electrophoresis and activity measurements from 4 to 144 h post imbibition (PI). Strikingly different activity profiles were observed. No ascorbate peroxidase (APX) activity was present in mature seeds but activity was detected after 24 h PI and increased 14-fold up to 144 h PI. In contrast, dehydroascorbate reductase (DHAR) activity was present at 4h PI and first decreased by 9-fold until 72 h PI followed by a 5-fold increase at 144 h PI. Glutathione reductase and monodehydroascorbate reductase activities were also detected at 4 h PI, and showed modest increases of 1.8- and 2.7-fold, respectively, by 144 h PI. The combination of functional analysis with the proteomics approach enabled correlation of the activity profiles and protein abundance. While gel spots containing APX showed intensity changes consistent with the activity profile from 0 to 72 h PI, DHAR spot intensities indicated that post-translational regulation may be responsible for the observed changes in activity. Transcript profiling, 2D-western blotting and mass spectrometric characterization of multiple APX spots demonstrated the presence of APX1 and minor amounts of APX2.

DNA polymorphisms and haplotype patterns of transcription factors involved in barley endosperm development are associated with key agronomic traits

BACKGROUND

Association mapping is receiving considerable attention in plant genetics for its potential to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest. In the present study association mapping in barley (Hordeum vulgare L.) is investigated by associating DNA polymorphisms with variation in grain quality traits, plant height, and flowering time to gain further understanding of gene functions involved in the control of these traits. We focused on the four loci BLZ1, BLZ2, BPBF and HvGAMYB that play a role in the regulation of B-hordein expression, the major fraction of the barley storage protein. The association was tested in a collection of 224 spring barley accessions using a two-stage mixed model approach.

RESULTS

Within the sequenced fragments of four candidate genes we observed different levels of nucleotide diversity. The effect of selection on the candidate genes was tested by Tajima's D which revealed significant values for BLZ1, BLZ2, and BPBF in the subset of two-rowed barleys. Pair-wise LD estimates between the detected SNPs within each candidate gene revealed different intra-genic linkage patterns. On the basis of a more extensive examination of genomic regions surrounding the four candidate genes we found a sharp decrease of LD (r2<0.2 within 1 cM) in all but one flanking regions.Significant marker-trait associations between SNP sites within BLZ1 and flowering time, BPBF and crude protein content and BPBF and starch content were detected. Most haplotypes occurred at frequencies <0.05 and therefore were rejected from the association analysis. Based on haplotype information, BPBF was associated to crude protein content and starch content, BLZ2 showed association to thousand-grain weight and BLZ1 was found to be associated with flowering time and plant height.

CONCLUSIONS

Differences in nucleotide diversity and LD pattern within the candidate genes BLZ1, BLZ2, BPBF, and HvGAMYB reflect the impact of selection on the nucleotide sequence of the four candidate loci.Despite significant associations, the analysed candidate genes only explained a minor part of the total genetic variation although they are known to be important factors influencing the expression of seed quality traits. Therefore, we assume that grain quality as well as plant height and flowering time are influenced by many factors each contributing a small part to the expression of the phenotype. A genome-wide association analysis could provide a more comprehensive picture of loci involved in the regulation of grain quality, thousand grain weight and the other agronomic traits that were analyzed in this study. However, despite available high-throughput genotyping arrays the marker density along the barely genome is still insufficient to cover all associations in a whole genome scan. Therefore, the candidate gene-based approach will further play an important role in barley association studies.

Microspore embryogenesis and programmed cell death in barley: effects of copper on albinism in recalcitrant cultivars

Albinism remains a major problem in cereal improvement programs that rely on doubled haploid (DH) technology, and the factors controlling the phenomenon are not well understood. Here we report on the positive influence of copper on the production of DH plants obtained through microspore embryogenesis (ME) in recalcitrant cultivars of barley (Hordeum vulgare L.). The presence of copper sulphate in the anther pre-treatment medium improved green DH plant regeneration from cultivars known to produce exclusively albino plants using classical procedures. In plastids, the effect of copper was characterized by a decrease in starch and a parallel increase in internal membranes. The addition of copper sulphate in the ME pre-treatment medium should enable breeders to exploit the genetic diversity of recalcitrant cultivars through DH technology. We examined programmed cell death (PCD) during microspore development to determine whether PCD may interfere with the induction of ME and/or the occurrence of albinism. By examining the fate of nuclei in various anther cell layers, we demonstrated that the kinetics of PCD in anthers differed between the barley cultivars Igri and Cork that show a low and a high rate of albinism, respectively. However, no direct correlation between PCD in the anther cell layers and the rate of albinism was observed and copper had no influence on the PCD kinetic in these cultivars. It was concluded that albinism following ME was not due to PCD in anthers, but rather to another unknown phenomenon that appears to specifically affect plastids during microspore/pollen development.

Regeneration capacity of mature embryo-derived callus in barley ( Hordeum vulgare L.)

In this study, induction of regenerable callus from mature embryos in eight Turkish barley varieties was analysed by using different plant growth regulators (PGRs). Varying concentrations (0.5-4 mg l -1 ) of 2,4-dichlorophenoxyacetic acid (2,4-D) and dicamba (3,6-dichloro-o-anisic acid) were tested for callus induction from mature embryos. Highest percent of callus induction was observed in Bornova 92 variety (98.3%) on MS medium supplemented with 4 mg l -1 dicamba. Calli were transferred to regeneration media with 0.5 mg l -1 dicamba, 0.5 mg l -1 zeatin riboside (ZR) and 2 mg l -1 thidiazuron (TDZ). Low concentrations of dicamba induced multiple shoots during callus regeneration. When the effect of precultivation with 2,4-D or dicamba on the shoot induction were evaluated, lower concentrations (< 4 mg l -1 ) of auxins have been found optimal. On the regeneration medium with 0.5 mg l -1 dicamba, shoots were able to elongate up to 20 cm and shoot numbers were between 1-23 per callus. The use of ZR led to formation of short shoot buds and somatic embryos in 2 weeks period. The effect of TDZ was different from other PGRs by inducing green solid sectors on calli surfaces (Total 51 sectors/20 callus/Akhisar variety). Five plantlets have been grown from these solid cell clumps and transferred to specific media for root formation. As a result, five varieties (Süleyman Bey, Bornova 92, Vamyk Hoca, Kaya and Akhisar) tested in our study showed the potential to produce regenerable callus by using low amounts of dicamba or TDZ. The optimization process starts from culturing embryos to plantlet formation took nearly 4 weeks.

Microspore embryogenesis: assignment of genes to embryo formation and green vs. albino plant production

Plant microspores can be reprogrammed from their normal pollen development to an embryogenic route in a process termed microspore embryogenesis or androgenesis. Stress treatment has a critical role in this process, inducing the dedifferentiation of microspores and conditioning the following androgenic response. In this study, we have used three barley doubled haploid lines with similar genetic background but different androgenic response. The Barley1 GeneChip was used for transcriptome comparison of these lines after mannitol stress treatment, allowing the identification of 213 differentially expressed genes. Most of these genes belong to the functional categories "cell rescue, defense, and virulence"; "metabolism"; "transcription"; and "transport". These genes were grouped into clusters according to their expression profiles among lines. A principal component analysis allowed us to associate specific gene expression clusters to phenotypic variables. Genes associated with the ability of microspores to divide and form embryos were mainly involved in changes in the structure and function of membranes, efficient use of available energy sources, and cell fate. Genes related to stress response, transcription and translation regulation, and degradation of pollen-specific proteins were associated with green plant production, while expression of genes related to plastid development was associated with albino plant regeneration.

[Estimation of the efficiency of callus formation and regeneration in barley spring varieties zoned in Ukraine]

The data on in vitro culture establishment and on estimation of callus formation and plant regeneration for eight barley Hordeum vulgare varieties (Getman, Tabora, Adagio, Galactic, Europrestige, Korona, Nevada and Stalker) zoned in Ukraine is represented. Mature embryos of these genotypes were used to study the callus induction and plant regeneration. Using of this approach can rather simplify and intensify the work. Medium, that consists of MS salts supplemented with caseine hydrolysate (1 g/L), L-proline (690 mg/L), thiamine-HCl (1 mg/L), maltose (30 g/L), 2,4-D (2 mg/L), CuSO4 (12.5 mg/L), myoinositol (250 mg/l), gerlite (3.5 g/L) pH 5.6-5.8 was used for both callus formation and plant regeneration. Formation of callus from mature embryos was observed in all studied varieties and showed high frequency (from 65 +/- 3.4% to 100%). It was found that cultivars Korona (88 +/- 2.8%), Europrestige (89 +/- 6.5%), Tabora (93 +/- 3.4%), Getman (99 +/- 0.8%) and Nevada (100%) had the highest regeneration potential. Organogenesis and somatic embryogenesis were the two ways of plant regeneration from callus tissues in barley. The highest general regeneration potential of cultivar Getman (50 +/- 5%) was observed. This cultivar was selected for the further work for development of effective genetic transformation protocol.

HvPG1 and ECA1: two genes activated transcriptionally in the transition of barley microspores from the gametophytic to the embryogenic pathway

Microspores genetically programmed to produce male gametes can be switched to the embryogenic pathway to give rise to haploid embryos. Microspore embryogenesis is usually induced in barley by stress pre-treatment applied to vacuolated microspores. We studied the expression of two genes during the early stages of microspore embryogenesis to gain further insight into the microspore transition from the gametophytic to the embryogenic pathway. RT-PCR together with in situ hybridization on sections (ISH) and whole-mount in situ hybridization (WISH) were used to analyse the expression of the early-culture abundant gene (ECA1), which is expressed in barley during microspore embryogenesis, and a polygalacturonase gene (HvPG1), a late pollen gene expressed during gametogenesis only after microspore division. Both ECA1 and HvPG1 genes were transcriptionally active after stress pre-treatment in the same populations of microspore-derived structures, representing the sporophytically induced ones. ECA1 transcripts were also detected after 3 days' culture. Our results point to the possibility of using ECA1 gene expression as a marker for the induction of microspore embryogenesis and the earliest stages of this process. Finally, we demonstrate that WISH is a suitable technique for studying gene expression in embryogenic microspore populations and, because different structures can be examined individually, is an appropriate complement to transcriptomic profile analyses in the study of early microspore embryogenesis.

DNA-Bound peptides control the mRNA transcription through CDK7

The degradation of intracytosolic proteins has been well described. However, the degradation pathway and physiological functions of the DNA-Bound peptides, which are free of degradation by peptidase of the post-ubiquitin-proteasome pathway, are still unclear. In this study, the DNA-Bound peptides were isolated from barley germ and two main fractions of about 25 different peptides were obtained. The DNA-Bound peptides were found to inhibit the proliferation of HeLa cells in a series of experiments. The DNA-Bound peptides also significantly inhibited in vitro and in vivo DNA transcription activity by regulating the expression and the corresponding functions of CDK7. Furthermore, signaling issues involving NFkappaB and ERK1/2 were observed. Such data suggests that DNA transcription could be inhibited by the DNA-Bound peptides via the CDK7 pathway. Thus we concluded that some of the post-proteasomal peptides were involved in the regulation of eukaryotic mRNA transcription.

Microspore embryogenesis in barley: anther pre-treatment stimulates plant defence gene expression

Microspore embryogenesis (ME) is a process in which the gametophytic pollen programme of the microspore is reoriented towards a new embryo sporophytic programme. This process requires a stress treatment, usually performed in the anther or isolated microspores for several days. Despite the universal use of stress to induce ME, very few studies have addressed the physiological processes that occur in the anther during this step. To further understand the processes triggered by stress treatment, we followed the response of anthers by measuring the expression of stress-related genes in two barley (Hordeum vulgare L.) cultivars differing in their ME response. Genes encoding enzymes involved in oxidative stress (glutathione-S-transferase, GST; oxalate oxidase, OxO), in the synthesis of jasmonic acid (13-lipoxygenase, Lox; allene oxide cyclase, AOC; allene oxide synthase, AOS) and in the phenylpropanoid pathway (phenylalanine ammonia lyase, PAL), as well as those encoding PR proteins (Barwin, chitinase 2b, Chit 2b; glucanase, Gluc; basic pathogenesis-related protein 1, PR1; pathogenesis-related protein 10, PR10) were up-regulated in whole anthers upon stress treatment, indicating that anther perceives stress and reacts by triggering general plant defence mechanisms. In particular, both OxO and Chit 2b genes are good markers of anther reactivity owing to their high level of induction during the stress treatment. The effect of copper sulphate appeared to limit the expression of defence-related genes, which may be correlated with its positive effect on the yield of microspore embryos.

A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling

Nutrients destined for the developing cereal grain encounter several restricting barriers on their path towards their final storage sites in the grain. In order to identify transporters and chelating agents that may be involved in transport and deposition of zinc in the barley grain, expression profiles have been generated of four different tissue types: the transfer cells, the aleurone layer, the endosperm, and the embryo. Cells from these tissues were isolated with the 'laser capture microdissection' technology and the extracted RNA was subjected to three rounds of T7-based amplification. The amplified RNA was subsequently hybridized to Affymetrix 22K Barley GeneChips. Due to the short average length of the amplified transcripts and the positioning of numerous probe sets at locations more than 400 base pairs (bp) from the poly(A)-tail, a normalization approach was used where the probe positions were taken into account. On the basis of the expression levels of a number of metal homeostasis genes, a working model is proposed for the translocation of zinc from the phloem to the storage sites in the developing grain.

Effects of hyperbaric oxygenation on cultured barley embryos

Changes in relative water content (RWC), lipid peroxidation, proline and antioxidant system in relation to the tolerance to oxidative stress enzymes mediated high pressure were investigated in Hordeum vulgare L. cv. Tokak. For this purpose, mature embryos cultured on MS media were treated in a hyperbaric oxygenation chamber (approx. 59.06 feets, 2 kp/cm2) with pure oxygen for 60 minutes/day for a growth period of ten days in a plant growth chamber. Constitutive activities of SOD, APOX, GR and POX were higher in hyperbaric oxygenated (HBO) explants, being 96.07%, 28.57%, 77.77% and 54.14% for the 5th days; 95.78%, 40%, 37.5%, and 94.98% for the 10th days of culture, respectively, than in the control plants. Increase in SOD activity was also shown on polyacrilamide gel electrophoresis on the 10th day of application. Proline accumulation was increased in HBO-treated explants both on the 5th days (85.71%) and 10th days (37.14%) of treatment. MDA content was found to be higher in HBO treated explants both on the 5th (53.84%) and 10th (59.83%) days of culture.

Transformation of different barley (Hordeum vulgare L.) cultivars by Agrobacterium tumefaciens infection of in vitro cultured ovules

Most cultivars of higher plants display poor regeneration capacity of explants due to yet unknown genotypic determined mechanisms. This implies that technologies such as transformation often are restricted to model cultivars with good tissue characteristics. In the present paper, we add further evidence to our previous hypothesis that regeneration from young barley embryos derived from in vitro-cultured ovules is genotype independent. We investigated the ovule culture ability of four cultivars Femina, Salome, Corniche and Alexis, known to have poor response in other types of tissue culture, and compared that to the data for the model cultivar, Golden Promise. Subsequently, we analyzed the transformation efficiencies of the four cultivars using the protocol for Agrobacterium infection of ovules, previously developed for Golden Promise. Agrobacterium tumefaciens strain AGL0, carrying the binary vector pVec8-GFP harboring a hygromycin resistance gene and the green fluorescence protein (GFP) gene, was used for transformation. The results strongly indicate that the tissue culture response level in ovule culture is genotype independent. However, we did observe differences between cultivars with respect to frequencies of GFP-expressing embryos and frequencies of regeneration from the GFP-expressing embryos under hygromycin selection. The final frequencies of transformed plants per ovule were lower for the four cultivars than that for Golden Promise but the differences were not statistically significant. We conclude that ovule culture transformation can be used successfully to transform cultivars other than Golden Promise. Similar to that observed for Golden Promise, the ovule culture technique allows for the rapid and direct generation of high quality transgenic plants.

Farmers' seed management and innovation in varietal selection: implications for barley breeding in Tigray, northern Ethiopia

Farmers' innovation and selection of barley varieties were studied in the Tigray Region in northern Ethiopia. Two districts each in the central and southern zones and three districts in the eastern zone of Tigray were randomly selected for this study, which sought to understand the current status of local barley varieties and to measure their relative preference by farmers. Household surveys were conducted covering 240 households to elicit farmers' views on the values, constraints, and opportunities of growing local varieties of barley. This was supported by focus-group and informal discussions with elders, key informants, and women's groups. Case studies were made of local farmers whom the community recognized as barley breeders. Twenty-four barley varieties and their major descriptors were recorded. Seed and varietal-selection criteria depended on the environmental and varietal characteristics. Investigation of intrahousehold decision making indicated that, while men tended to decide on the type of variety to grow, seed storage and processing were exclusively the responsibility of women. Farmers undertook preharvest and postharvest selection, giving emphasis mainly to earliness and spike characteristics. The distinct varietal-selection and seed-renewal procedures revealed their potential for use in further plant breeding. The case-study analysis of farmer-developed varieties provided knowledge that, if combined with scientists' knowledge, could lead to identification and development of valuable cultivars with a wide potential for use in semiarid areas of Tigray and other parts of Ethiopia.

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.

A novel late embryogenesis abundant protein and peroxidase associated with black point in barley grains

Black point of barley grain is a disorder characterised by a brown-black discolouration at the embryo end of the grain. Black point is undesirable to the malting industry and results in significant economic loss annually. To identify proteins associated with barley black point we utilised a proteomic approach with 2-DE to compare proteins from whole grain samples of black pointed and healthy grain. From this comparison two condition-specific proteins were identified: a novel 75 kDa late embryogenesis abundant (LEA) protein and a barley grain peroxidase 1 (BP1) that were specifically more abundant in healthy grain and black pointed grain, respectively. Although LEA protein was less abundant in black pointed grain, LEA gene expression was greater suggesting protein degradation had possibly occurred in black pointed grain. Similarly, the increase in BP1 in black pointed grain could not be explained by gene expression. Western blot analysis also revealed that the identified LEA protein is biotinylated in vivo. The role that each of these proteins might have in black point development is discussed.

Spatio-temporal changes in germination and radical elongation of barley seeds tracked by proteome analysis of dissected embryo, aleurone layer, and endosperm tissues

Germination of barley is accompanied by changes in water-soluble seed proteins. 2-DE was used to describe spatio-temporal proteome differences in dissected seed tissues associated with germination and the subsequent radicle elongation. Protein identification by MS enabled assignment of proteins and functions to the seed embryo, aleurone, and endosperm. Abundance in 2-DE patterns was monitored for 48 different proteins appearing in 79 gel spots at 8 time-points up to 72 h post imbibition (PI). In embryo, a beta-type proteasome subunit and a heat shock protein 70 fragment were among the earliest proteins to appear (at 4 h PI). Other early changes were observed that affected spots containing desiccation stress-associated late embryogenesis abundant and abscisic acid (ABA)-induced proteins. From 12 h PI proteins characteristic for desiccation stress disappeared rapidly, as did a putative embryonic protein and an ABA-induced protein, suggesting that these proteins are also involved in desiccation stress. Several redox-related proteins differed in spatio-temporal patterns at the end of germination and onset of radicle elongation. Notably, ascorbate peroxidase that was observed only in the embryo, increased in abundance at 36 h PI. The surprisingly early changes seen in the protein profiles already 4 h after imbibition indicate that germination is programmed during seed maturation.

Detection of seed dormancy QTL in multiple mapping populations derived from crosses involving novel barley germplasm

Seed dormancy is one of the most important traits in germination process to control malting and pre-harvest sprouting in barley (Hordeum vulgare L.). EST based linkage maps were constructed on seven recombinant inbred (RI) and one doubled haploid (DH) populations derived from crosses including eleven cultivated and one wild barley strains showing the wide range of seed dormancy levels. Seed dormancy of each RI and DH line was estimated from the germination percentage at 5 and 10 weeks post-harvest after-ripening periods in 2003 and 2005. Quantitative trait loci (QTLs) controlling seed dormancy were detected by the composite interval mapping procedure on the RI and DH populations. A total of 38 QTLs clustered around 11 regions were identified on the barley chromosomes except 2H among the eight populations. Several QTL regions detected in the present study were reported on similar positions in the previous QTL studies. The QTL on at the centromeric region of long arm of chromosome 5H was identified in all the RI and DH populations with the different degrees of dormancy depth and period. The responsible gene of the QTL might possess a large allelic variation among the cross combinations, or can be multiple genes located on the same region. The various loci and their different effects in dormancy found in the barley germplasm in the present study enable us to control the practical level of seed dormancy in barley breeding programs.

[Effect of rye Secale cereale L. chromosomes 1R and 3R on polyembryony expression in hybrid combinations between (Hordeum vulgare L.)-Triticum aestivum L. alloplasmic recombinant lines and wheat T. aestivum L.-rye S. cereale L. substitution lines]

The effect of rye chromosomes on polyembryony was studied for reciprocal hybrid combinations between (Hordeum vulgare L.)-Triticum aestivum L. alloplasmic recombinant lines and five wheat T. aestivum L. (cultivar Saratovskaya 29)-rye Secale cereale L. (cultivar Onokhoiskaya) substitution lines: IR(1D), 2R(2D), 3R(3B), 5R(5A), and 6R(6A), and for direct hybrid combinations between the [H. marinum ssp. gussoneanum (H. geniculatum All.)]-T. aestivum alloplasmic recombinant line and the wheat-rye substitution lines 1R (1A), 1R (1D), and 3R(3B). Chromosomes 1R and 3R of rye cultivar Onokhoiskaya proved to affect the expression of polyembryony in the hybrid combinations that involved the alloplasmic recombinant lines of common wheat as maternal genotypes. Based on this finding, polyembryony was regarded as a phenotypic expression of nuclear-cytoplasmic interactions where an important role is played by rye chromosomes 1R and 3R and the H. vulgare cytoplasm. Consideration is given to the association between the effect of rye chromosomes 1R and 3R on polyembryony in the [(Hordeum)-T. aestivum x wheat-rye substitution lines] hybrid combinations and their stimulating effect on the development on angrogenic embryoids in isolated anther cultures of the wheat-rye substitution lines.

Salicylic acid inhibits gibberellin-induced alpha-amylase expression and seed germination via a pathway involving an abscisic-acid-inducible WRKY gene

It is well known that abscisic acid (ABA) antagonizes gibberellin (GA)-promoted seed germination. Recent circumstantial evidence suggests that salicylic acid (SA) also inhibits seed germination in maize and Arabidopsis. Our study shows that SA blocks barley seed germination in a dosage dependent manner. As an initial effort to addressing the mechanism controlling the crosstalk of SA, GA and ABA signaling in barley, we studied the regulation of alpha-amylases by SA and a WRKY gene whose expression is modulated by these hormones. Assays of alpha-amylase activity reveal that GA-induced alpha-amylase production in aleurone cells is inhibited by bioactive SA, but not its analogs, 3-hydroxybenzoic acid and 4-hydroxybenzoic acid. This inhibitory effect is unlikely due to repressing alpha-amylase secretion or inhibiting alpha-amylase enzyme activities. Northern blot analyses indicate that SA suppresses GA-induced expression of a barley low pI alpha-amylase gene (Amy32b). Because our previous data indicate that ABA-inducible and GA-suppressible WRKY genes inhibit the expression of alpha-amylase genes in rice, we studied the steady state mRNA levels of a barley WRKY gene, HvWRKY38. The expression of HvWRKY38 in barley aleurone cells is down-regulated by GA, but up-regulated by SA and ABA. However, the regulation of HvWRKY38 by SA appears to be different from that of ABA in term of the kinetics and levels of induction. Over-expression of HvWRKY38 in aleurone cells by particle bombardment blocks GA induction of the Amy32b promoter reporter construct (Amy32b-GUS). Therefore, HvWRKY38 might serve as a converging node of SA and ABA signal pathways involved in suppressing GA-induced seed germination.

Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue

BACKGROUND

Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes. Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. For that purpose, high-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0-26 days after flowering).

RESULTS

Temporal expression profiles of 4824 genes at 14 time points are faithfully embedded into two-dimensional displays. Thereby, similar shapes of coexpressed genes get closely grouped by a correlation-based similarity measure. As a main result, by using power transformation of correlation terms, a characteristic cloud of points with bipolar sandglass shape is obtained that is inherently connected to expression patterns of pre-storage, intermediate and storage phase of endosperm development.

CONCLUSION

The new HiT-MDS-2 method helps to create global views of expression patterns and to validate centroids obtained from clustering programs. Furthermore, functional gene annotation for developing endosperm barley tissue is successfully mapped to the visualization, making easy localization of major centroids of enriched functional categories possible.

Identification of transcripts potentially involved in barley seed germination and dormancy using cDNA-AFLP

Freshly harvested barley seeds are considered as dormant since they do not germinate at temperatures above 20 degrees C. This dormancy is broken during dry storage. Molecular regulation of dormancy was investigated using cDNA-AFLP to identify transcripts differentially expressed in dormant and non-dormant embryos. Transcript patterns in embryos from dry dormant and non-dormant seeds and from both seeds imbibed for 5 h at 30 degrees C, a temperature at which dormancy is expressed, were compared. Thirty-nine Transcript-Derived Fragments (TDF) that were reproducibly differentially expressed among treatments were identified, and 25 of these were cloned and sequenced. Among these, eight transcripts were observed to be differentially expressed during after-ripening, seven of which decline, probably due to post-maturation degradation. HV13B, TDF identified as having homology to fructose-6-phosphate-2-kinase/fructose-2,6-biphosphatase, may have a role in the maintenance of dormancy in barley and probably in other cereals. During the first 5 h of imbibition, there was expression of 24 TDF which was apparently independent of dormancy, revealing putative epigenetic regulation. This was typified by HV44A, a SET domain protein. Seven TDF differentially expressed, and especially HV12D, HV42B, and HV32B, in dormant and non-dormant seeds were potential signalling elements. HV12D had homology with an ARIADNE gene which could be implicated in ABA signalling.

Barley (Hordeum vulgare L.)

Crop improvement is limited by the availability of valuable traits in sexually compatible species. Access to new characters using genetic engineering would be of great value. Barley has been transformed using microprojectile bombardment and by direct gene transfer to protoplasts, but neither method has been able to produce fertile transformants in large numbers with simple transgene integration characteristics. Agrobacterium-mediated transformation was first achieved in 1997, and it has become the method of choice. Using immature embryos of the barley variety Golden Promise as the target organ, the binary vector pWBVec8 containing the intron-interrupted hygromycin resistance gene hph as the selectable marker, and selection of transformed cells on hygromycin, the Agrobacterium method is efficient, and the transgene insertion characteristics are superior to other methods. However, the procedure is strongly genotype dependent. In this report, we describe a transformation protocol giving details of plant culture, embryo isolation and preparation, vector details, Agrobacterium culture, infection methods, subsequent procedures for callus generation and plantlet production, and analysis of transgenic plants.

The relationship between induction of embryogenesis and chromosome doubling in microspore cultures

The objective of this paper is to review the relationship between induction of microspore embryogenesis and chromosome doubling. It has been augmented with relative data on chromosome doubling by nuclear fusion. Some of the treatments used for induction of embryogenesis may also lead to doubling of the chromosome number, either through nuclear fusion or endomitosis. High frequencies of spontaneous chromosome doubling in cereal species appear to be induced by treatments that block cell wall formation during the first cell divisions, resulting in coenocytic cells in which the nuclei are able to fuse. The use of mannitol as a pretreatment for induction of embryogenesis in barley, wheat, and maize microspore cultures provides examples of nuclear fusion. The use of antimicrotubule agents for embryo induction via treatments during the first few hours of microspore culture has also resulted in high frequencies of chromosome doubling. Factors such as the doubling agent concentration, temperature during treatment, and duration of treatment may be critical for individual species. Actin filament as well as microtubule assembly studies related to new cell wall formation provide further evidence at the molecular level for the relationship between microspore embryogenesis and chromosome doubling.

Temporal and spatial appearance of wall polysaccharides during cellularization of barley (Hordeum vulgare) endosperm

Barley endosperm begins development as a syncytium where numerous nuclei line the perimeter of a large vacuolated central cell. Between 3 and 6 days after pollination (DAP) the multinucleate syncytium is cellularized by the centripetal synthesis of cell walls at the interfaces of nuclear cytoplasmic domains between individual nuclei. Here we report the temporal and spatial appearance of key polysaccharides in the cell walls of early developing endosperm of barley, prior to aleurone differentiation. Flowering spikes of barley plants grown under controlled glasshouse conditions were hand-pollinated and the developing grains collected from 3 to 8 DAP. Barley endosperm development was followed at the light and electron microscope levels with monoclonal antibodies specific for (1-->3)-beta-D: -glucan (callose), (1-->3,1-->4)-beta-D: -glucan, hetero-(1-->4)-beta-D: -mannans, arabino-(1-->4)-beta-D: -xylans, arabinogalactan-proteins (AGPs) and with the enzyme, cellobiohydrolase II, to detect (1-->4)-beta-D: -glucan (cellulose). Callose and cellulose were present in the first formed cell walls between 3 and 4 DAP. However, the presence of callose in the endosperm walls was transient and at 6 DAP was only detected in collars surrounding plasmodesmata. (1-->3,1-->4)-beta-D: -Glucan was not deposited in the developing cell walls until approximately 5 DAP and hetero-(1-->4)-beta-D: -mannans followed at 6 DAP. Deposition of AGPs and arabinoxylan in the wall began at 7 and 8 DAP, respectively. For arabinoxylans, there is a possibility that they are deposited earlier in a highly substituted form that is inaccessible to the antibody. Arabinoxylan and heteromannan were also detected in Golgi and associated vesicles in the cytoplasm. In contrast, (1-->3,1-->4)-beta-D: -glucan was not detected in the cytoplasm in endosperm cells; similar results were obtained for coleoptile and suspension cultured cells.

Androgenic response to preculture stress in microspore cultures of barley

Various stresses such as starvation and cold or heat shocks have been identified as triggers in the induction of the microspore embryogenesis. This study attempts to quantify the effects of different pretreatment conditions for successful microspore culture of malting barley (cv. Scarlett). While the sporophytic microspore development could be induced from treated and nontreated microspores, abiotic stress was essential for embryo formation and plant regeneration. The type of stress treatment applied affected the numbers and the ratios of albino and green plants regenerated, as well as their fertility. The highest number of green plants was obtained after the treatment of anthers in 0.3 M mannitol at 32 degrees C for 24 h before microspore culture.

Gene expression patterns reveal tissue-specific signaling networks controlling programmed cell death and ABA- regulated maturation in developing barley seeds

Gene expression patterns covering over 10,000 seed-expressed sequences were analyzed by macroarray technology in maternal tissue (mainly pericarp) and filial endosperm and embryo during barley seed development from anthesis until late maturation. Defined sets of genes showing distinct expression patterns characterized both tissue type and major developmental phases. The analysis focused on regulatory networks involved in programmed cell death (PCD) and abscisic acid (ABA)-mediated maturation. These processes were similar in the different tissues, but typically involved the expression of alternative members of a common gene family. The analysis of co-expressed gene sets and the identification of cis regulatory elements in orthologous rice gene 'promoter' regions suggest that PCD in the pericarp is mediated by distinct classes of proteases and is under the hormonal control of both jasmonic acid (JA) and ethylene via ethylene-responsive element binding protein (EREBP) transcription factors (TFs). On the other hand, PCD in endosperm apparently involves only the ethylene pathway, but employs distinct gene family members from those active in the pericarp, and a different set of proteases and TFs. JA biosynthetic genes are hardly activated. Accordingly, JA levels are high in the pericarp but low in the endosperm during middle and late developmental stages. Similarly, genes acting in the deduced ABA biosynthetic pathway and signaling network differ between endosperm and embryo. ABA in the endosperm appears to exert an influence over storage product synthesis via SNF1 kinase. In the embryo, ABA seems to influence the acquisition of desiccation tolerance via ABA response element binding factors, but the data also suggest the existence of an ABA-independent but interactive pathway acting via the dehydration-responsive element binding (DREB) 2A TF.

Distinct developmental defense activations in barley embryos identified by transcriptome profiling

Proper embryo development is crucial for normal growth and development of barley. Numerous related aspects of this process--for example how the embryo establishes and sustains disease resistance for extended periods during dormancy--remain largely unknown. Here we report the results of microarray analyses of >22,000 genes, which together with measurements of jasmonic acid and salicylic acid during embryo development provide new information on the initiation in the developing barley embryo of at least two distinct types of developmental defense activation (DDA). Early DDA is characterized by the up-regulation of a specific set of genes around 20 days after flowering, including co-regulation of those for encoding 9-lipoxygenase and several oxylipin-generating enzymes, possibly leading to the formation of alpha-ketols. The same developmental phase includes an up-regulation of several defense genes, and indications of co-regulation of those for enzymes involved in the generation of phenylpropanoid phytoalexins. Late DDA is initiated prior to grain desiccation, around 37 days after flowering, with up-regulation of several genes encoding proteins with roles in antioxidant responses as well as a simultaneous up-regulation of several PR genes is notable. Throughout barley embryo development, there are no indications of an increased biosynthesis of either jasmonic acid or salicylic acid. Collectively, the results help explain how the proposed DDA enables protection of the developing barley embryo and grain for purposes of disease resistance.