Barley Gene Research Articles

In silico Analysis of OsNRT2.3 Reveals OsAMT1.3, OsZIFL9, OsbZIP27, and OsIRT1 as Potential Drought-related Genes During Nitrogen Use Efficiency in Oryza sativa L.

Nitrate transporter (NRT) is responsible for the molecular mechanism of the root nitrate (NO3-) uptake system for plant development. Although several NRT genes are identified and characterised in plants, knowledge of the NRT2 gene family and its nitrogen use efficiency (NUE) function in drought stress has remained elusive in rice. This study conducted an in silico analysis on 20 NRT2 family genes of rice, wheat, soybean, barley, maize, and papaya. Phylogenetic and motifs analysis clustered genes encoding NRT2 proteins into four monophyletic groups, and the motifs of NRT2 genes were significantly conserved for the specific domain of NO3- transmembrane transporter. Interestingly, co-expression analysis revealed that potential drought-related genes were expressed similarly to the functional NUE gene, OsNRT2.3. Furthermore, half of the co-expressed genes were enriched in nitrogen use efficiency (NUE)-related processes, such as transport, stress, macromolecule metabolic pathways, and transcription regulation. Expression pattern analysis of OsNRT2.3 and its co-expressed genes in tissue-specific and nitrogen (N) response led to the discovery of OsAMT1.3, OsZIFL9, OsbZIP27, and OsIRT1 as four strong candidates to participate in drought stress during NO3- uptake system. The co-expression of iron (Fe) uptake genes, OsZIFL9 and OsIRT1, with OsNRT2.3 also suggested a possible interaction of Fe and nitrogen (N) during an increasing amount of Fe, which led to the acidification of rice apoplasts during water deficiency. Together, this study will provide a valuable resource for potential candidate genes that can further investigate their molecular response to drought during NUE.

The Correlations of Barley Vitality and Storage Reserve Mobilization during Early Germination

The elucidation of the genetic relationship about storage reserve mobilization and enzymatic activity during barley germination is of particular importance for breeding and malt production. In addition to plant hormones such as gibberellic acid (GA) and abscisic acid (ABA), recent research has highlighted the importance of reactive oxygen species (ROS) signaling with hydrolase induction and plant growth. In this study, the correlation of barley vitality and mobilization of storage reserves during early seed germination was investigated. The activity of important hydrolases, as well as ROS-producing NADPH (nicotinamide adenine dinucleotide phosphate) oxidases, was monitored between six different cultivars. Associated gene expression from imbibition to germination was also analyzed by correlation analysis and cluster analysis. During early germination, the activities of α-amylase, limit dextrinase, and β-glucanase had significant positive correlations with each other and affected seed germination. Gene expression analysis showed that RbohB1 and RbohF1 (NADPH oxidases) had strong correlations with AMY1 (α-amylase) and LD (limit dextrinase). The GA synthesis gene GA3ox2 was found to have a significant correlation with protease genes Cys (cysteine protease) and Ser (serine protease), while the ABA synthesis gene NCED1 (nine-cis-epoxycarotenoid dioxygenase) had significant negative correlations with Cys and GA3ox2. Gene expression and enzyme assays indicated that NADPH oxidase, α-amylase, and limit dextrinase correlated well with barley vitality during early germination. The expression of the GA synthesis genes correlated well with glucanase and protease. These results provide information about barley gene regulation by analyzing correlations between genes.

Genome-Wide Identification and Expression Analysis of Kinesin Family in Barley (Hordeum vulgare).

Kinesin, as a member of the molecular motor protein superfamily, plays an essential function in various plants' developmental processes. Especially at the early stages of plant growth, including influences on plants' growth rate, yield, and quality. In this study, we did a genome-wide identification and expression profile analysis of the kinesin family in barley. Forty-two HvKINs were identified and screened from the barley genome, and a generated phylogenetic tree was used to compare the evolutionary relationships between Rice and Arabidopsis. The protein structure prediction, physicochemical properties, and bioinformatics of the HvKINs were also dissected. Our results reveal the important regulatory roles of HvKIN genes in barley growth. We found many cis- elements related to GA3 and ABA in homeopathic elements of the HvKIN gene and verified them by QRT-PCR, indicating their potential role in the barley kinesin family. The current study revealed the biological functions of barley kinesin genes in barley and will aid in further investigating the kinesin in other plant species.

Evolutionary Conservation and Transcriptome Analyses Attribute Perenniality and Flowering to Day-Length Responsive Genes in Bulbous Barley (Hordeum bulbosum).

Rapid population growth and dramatic climatic turnovers are challenging global crop production. These challenges are spurring plant breeders to enhance adaptation and sustainability of major crops. One intriguing approach is to turn annual systems into perennial ones, yet long-term classical breeding efforts to induce perenniality have achieved limited success. Here, we report the results of our investigation of the genetic basis of bulb formation in the nonmodel organism Hordeum bulbosum, a perennial species closely related to barley. To identify candidate genes that regulate bulb formation in H. bulbosum, we applied two complementary approaches. First, we explored the evolutionary conservation of expressed genes among annual Poaceae species. Next, we assembled a reference transcriptome for H. bulbosum and conducted a differential expression (DE) analysis before and after stimulating bulb initiation. Low conservation was identified in genes related to perenniality in H. bulbosum compared with other species, including bulb development and sugar accumulation genes. We also inspected these genes using a DE analysis, which enabled identification of additional genes responsible for bulb initiation and flowering regulation. We propose a molecular model for the regulation of bulb formation involving storage organ development and starch biosynthesis genes. The high conservation observed along a major part of the pathway between H. bulbosum and barley suggests a potential for the application of biotechnological techniques to accelerate breeding toward perenniality in barley.

Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley.

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI.

Compositional variances in cuticular lipids of wild and domesticated barley leaves and their impact on plant-environment interactions

One of the oldest cereal crops, barley is thought to have been domesticated ∼ 8000 years ago, in the Fertile Crescent. In this study, we explored the overlooked contribution of cuticular lipid metabolism to barley domestication by comparatively characterizing wild and domesticated barley variants. We revealed substantial phenotypic variances in plants’ overall morphology and in vegetative and reproductive tissues. Multiple microscopic approaches combined with gas chromatography-mass spectrometry (GC-MS) metabolite profiling indicated that wild barley leaves are more densely covered with epicuticular waxes compared to domesticated leaves with distinct compositions, but both variants contain a similar cuticle ultrastructure. Gene expression assays corroborated these observations showing higher transcript expression of key epicuticular wax biosynthetic genes in wild barley leaves, but similar expression patterns of cutin biosynthetic genes in leaves of both cultivars. Wild barley leaves also transpired water at higher rates apparently due to higher stomata density and conductance. Previous evidence claimed that barley leaf epicuticular waxes shape the interactions with Blumeria graminis f.sp. hordei (Bgh), the causal agent of powdery mildew in barely. However, in-vivo and in-vitro inoculation assays inferred that the disparate wax content and composition in wild and domesticated leaves had no apparent effect on Bgh pre-penetration processes. Altogether, our data provide novel insight into the compositional variances in cuticular lipids of wild and domesticated barley leaves and their impact on plant-environment interactions.

Novel resistance to the Bymovirus BaMMV established by targeted mutagenesis of the PDIL5-1 susceptibility gene in barley.

The Potyviridae are the largest family of plant-pathogenic viruses. Members of this family are the soil-borne bymoviruses barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV), which, upon infection of young winter barley seedlings in autumn, can cause yield losses as high as 50%. Resistance breeding plays a major role in coping with these pathogens. However, some viral strains have overcome the most widely used resistance. Thus, there is a need for novel sources of resistance. In ancient landraces and wild relatives of cultivated barley, alleles of the susceptibility factor PROTEIN DISULFIDE ISOMERASE LIKE 5-1 (PDIL5-1) were identified to confer resistance to all known strains of BaYMV and BaMMV. Although the gene is highly conserved throughout all eukaryotes, barley is thus far the only species for which PDIL5-1-based virus resistance has been reported. Whereas introgression by crossing to the European winter barley breeding pool is tedious, time-consuming and additionally associated with unwanted linkage drag, the present study exemplifies an approach to targeted mutagenesis of two barley cultivars employing CRISPR-associated endonuclease technology to induce site-directed mutations similar to those described for PDIL5-1 alleles that render certain landraces resistant. Homozygous primary mutants were produced in winter barley, and transgene-free homozygous M2 mutants were produced in spring barley. A variety of mutants carrying novel PDIL5-1 alleles were mechanically inoculated with BaMMV, by which all frameshift mutations and certain in-frame mutations were demonstrated to confer resistance to this virus. Under greenhouse conditions, virus-resistant mutants showed no adverse effects in terms of growth and yield.

Genome wide identification of AGC kinase genes and their expression in response to heat and cold stresses in barley

AGC kinases are highly conserved regulators in a variety of cellular processes such as differentiation, proliferation, and growth. They are known to play important roles in stress and hormonal responses, including ROS signaling. AGC kinases are the main class of protein kinases in plants, having central functions in different stages of plant growth. In the present study, the analysis of phylogenetic relationships, gene structures, chromosomal locations, synteny analysis, gene ontology, subcellular localization, and gene expression of AGC kinase identified 28 AGC kinase genes in barley. Phylogenetic tree grouped them into seven subfamilies, as supported by exon-intron organization. Gene duplication and synteny indicated that tandom and block duplication events played an essential role in the expansion of AGC kinase gene families in barley. The Real-time quantitative reverse transcription PCR (qRT-PCR) analysis performed for HvAGC kinase gene were largely expressed in different tissues of roots, stems, and leaves in Azaran and Jolgeh cultivars under heat and cold stresses. The results of chromosomal localization showed that the AGC kinases were located on all chromosomes of barley except chromosome 1. Genome evolution of species was surveyed using identification of orthologous and paralogous genes. Identifying overlaps between orthologous clusters can enable us to study the function and evolution of proteins in different species. To our knowledge, this is the first detailed report of using AGC kinases for bioinformatics analysis in barley. Results revealed a broad understanding of the AGC kinase gene family in barley, which will be valuable for improving barley varieties’ response to heat and cold stresses. Also, HvNDR6.2 gene can utilized as molecular markers under cold stress in the three organs.

BGFD: an integrated multi-omics database of barley gene families

BackgroundA gene family comprises a group of genes with similar functional domains that play various roles in plant growth, development, and responses to environmental stimuli. Barley (Hordeum vulgare L.) is the fourth most cultivated cereal crop worldwide, and it is an important model species for genetic studies. Systematic identification and annotation of gene families are key for studies of molecular function and evolutionary history.ResultsWe constructed a multi-omics database containing 5593 genes of 77 gene families called the Barley Gene Family Database (BGFD: http://barleygfdb.com). BGFD is a free, user-friendly, and web-accessible platform that provides data on barley family genes. BGFD provides intuitive visual displays to facilitate studies of the physicochemical properties, gene structure, phylogenetic relationships, and motif organization of genes. Massive multi-omics datasets have been acquired and processed to generate an atlas of expression pattern profiles and genetic variation in BGFD. The platform offers several practical toolkits to conduct searches, browse, and employ BLAST functions, and the data are downloadable.ConclusionsBGFD will aid research on the domestication and adaptive evolution of barley; it will also facilitate the screening of candidate genes and exploration of important agronomic traits in barley.

Mechanism of Early Flowering in a Landrace Naked Barley eam8.l Mutant

The EARLY MATURITY 8 (EAM8) gene of barley is homologous to the EARLY FLOWERING 3 (ELF3) gene in Arabidopsis, as loss-of-function mutations in this circadian clock gene promote rapid flowering. A previous study demonstrated that the early flowering phenotype of a hulless barley, Lalu, was due to allele eam8.l carrying an alternative splicing mutation in intron 3 that led to intron retention. In the present study, we verified that eam8.l encoded a truncated protein. Although EAM8 was expressed at a higher level in Lalu than in other barley lines with a longer growth period, it did not negatively regulate flowering time. This result further proved that the eam8.l protein was nonfunctional in regulating flowering in barley. The early flowering phenotype of Lalu plants was strongly dependent on the biosynthesis of gibberellin (GA). The eam8.l mutation stopped the suppression of GA biosynthesis, and Lalu accumulated excessive GA, especially in leaves. This was achieved through the upregulated expression of genes in the GA pathway, including GA20ox2, LFY1, SOC1, PAP2, and FPF3. The mutation of the EAM8 gene also abolished the inhibition of FLOWERING LOCUS T-like (FT1) gene expression at night. During the night, expression levels of the FT1 gene were higher than those during the day in Lalu. However, the GA-dependent pathway and FT1 gene mechanism are two independent pathways that promote flowering in Lalu. Alleles of EAM8, therefore, demonstrated an important breeding value in barley, which is probably effective in many other day-length-sensitive crop plants as well; thus, they could be used to tune adaptation in different geographic regions and climatic conditions, a critical issue in times of global warming.

Unraveling the genetics of polyamine metabolism in barley for senescence-related crop improvement

We explored the polyamine (PA) metabolic pathway genes in barley (Hv) to understand plant development and stress adaptation in Gramineae crops with emphasis on leaf senescence. Bioinformatics and functional genomics tools were utilized for genome-wide identification, comprehensive gene features, evolution, development and stress effects on the expression of the polyamine metabolic pathway gene families (PMGs). Three S-adenosylmethionine decarboxylases (HvSAMDCs), two ornithine decarboxylases (HvODCs), one arginine decarboxylase (HvADC), one spermidine synthase (HvSPDS), two spermine synthases (HvSPMSs), five copper amine oxidases (HvCuAOs) and seven polyamine oxidases (HvPAOs) members of PMGs were identified and characterized in barley. All the HvPMG genes were found to be distributed on all chromosomes of barley. The phylogenetic and comparative assessment revealed that PA metabolic pathway is highly conserved in plants and the prediction of nine H. vulgare miRNAs (hvu-miR) target sites, 18 protein-protein interactions and 961 putative CREs in the promoter region were discerned. Gene expression of HvSAMDC3, HvCuAO7, HvPAO4 and HvSPMS1 was apparent at every developmental stage. SPDS/SPMS gene family was found to be the most responsive to induced leaf senescence. This study provides a reference for the functional investigation of the molecular mechanism(s) that regulate polyamine metabolism in plants as a tool for future breeding decision management systems.

Immunological clustering of the spring barley gene pool in the conditions of the Ryazan region

The article presents the results of field studies of the collection gene pool of spring barley in the conditions of the Ryazan branch of the Federal State Budgetary Scientific Institution "Federal Scientific Agroengineering Center VIM" in 2017-2021 against the natural background of the development of fungal diseases. The aim of the research was to carry out immunological clustering of the collection gene pool of spring barley in the conditions of the Ryazan region and to identify the most promising forms for inclusion in crosses as parental forms. It was revealed that the vast majority of the studied varieties belonged to the group of highly resistant varieties. It was found that more than half of the varieties (57.8%) of the studied collection possessed complex resistance to a group of pathogens (reticulated (Perenophora teres Drechs), dark brown mottling (Bipolaris sorokiniana Shoem), powdery mildew (Erisiphe gramminis D.C.f.sp. hordei Marchal), dusty smut (Usnilago nuda Jen.)). spring barley. The following varieties showed high complex stability: Nur, Reliable, Moskovsky 3, Moskovsky 2, Dvina, Kalita, Hopper, Clear, Griv, Miar, Risk, Choice (Russia); Timerkhan (Tatarstan); Divosny, Gonor, Yakub, Batka, Fest, Khago (Belarus); Hetman, Kharkiv 102, Vinnytsia 17 (Ukraine); Ilek-1, Ilek-34 (Kazakhstan); Delphin (France); Linga, Irbe (Latvia); Izotta, Graice (Germany); Prosa, Pejas (Czech Republic); Collie (UK); B-934 (Canada). The greatest approximate productivity over the years of research has been revealed in the following varieties: Notable (Russia), Gonar (Belarus), Vivaldi (Austria), Eufel, Pioneer (France), Stratus (Poland), which have an advantage over the Yaromir standard by 0.3 – 0.7 t/ha. Reliable variety (Russia) had the highest resistance to lodging out of the entire studied gene pool of spring barley – 8.6 points. The use of a comprehensive ranking assessment revealed the priority of varieties of the Belarusian selection Divosny, Gonar and Czech varieties Pegas, Prosa, which occupy leading positions on the rating scale in terms of resistance to lodging, disease damage and productivity.

Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation

Key messageStructural variants (SV) of 23 barley inbreds, detected by the best combination of SV callers based on short-read sequencing, were associated with genome-wide and gene-specific gene expression and, thus, were evaluated to predict agronomic traits.In human genetics, several studies have shown that phenotypic variation is more likely to be caused by structural variants (SV) than by single nucleotide variants. However, accurate while cost-efficient discovery of SV in complex genomes remains challenging. The objectives of our study were to (i) facilitate SV discovery studies by benchmarking SV callers and their combinations with respect to their sensitivity and precision to detect SV in the barley genome, (ii) characterize the occurrence and distribution of SV clusters in the genomes of 23 barley inbreds that are the parents of a unique resource for mapping quantitative traits, the double round robin population, (iii) quantify the association of SV clusters with transcript abundance, and (iv) evaluate the use of SV clusters for the prediction of phenotypic traits. In our computer simulations based on a sequencing coverage of 25x, a sensitivity > 70% and precision > 95% was observed for all combinations of SV types and SV length categories if the best combination of SV callers was used. We observed a significant (P < 0.05) association of gene-associated SV clusters with global gene-specific gene expression. Furthermore, about 9% of all SV clusters that were within 5 kb of a gene were significantly (P < 0.05) associated with the gene expression of the corresponding gene. The prediction ability of SV clusters was higher compared to that of single-nucleotide polymorphisms from an array across the seven studied phenotypic traits. These findings suggest the usefulness of exploiting SV information when fine mapping and cloning the causal genes underlying quantitative traits as well as the high potential of using SV clusters for the prediction of phenotypes in diverse germplasm sets.

FIND-IT: Accelerated trait development for a green evolution.

Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low–mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.

The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication.

SUMMARYThe distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene‐rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco‐geographical ranges. We defined and compared variant data across the pericentromeric and non‐pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single‐nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome‐wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two‐row and six‐row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non‐synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be ‘highly deleterious’. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.

Genomewide identification and analysis of the OSCA gene family in barley (Hordeum vulgare L.)

The hyperosmolality-gated calcium-permeable channels (OSCA) are considered to be osmotic sensors that play an important role in the early stages of hyperosmotic stress response. We analysed the physicochemical properties, chromosome distribution, phylogeny, gene structure and expression pattern of the OSCA gene family in barley, and investigated the expression of HvOSCA genes in barley under drought stress by quantitative real-time polymerase chain reaction (qRT-PCR). Finally, 14 members of the OSCA gene family were identified from barley, all containing the RSN1_7TM domain and often accompanied by the RSN1_TM and PHM7_cyt domains. According to the phylogenetic relationship, they were divided into four subgroups, and each with similar gene structures. Two types of duplicate events in the HvOSCA genes family evolved under the effect of purification selection. By analysing the cis-acting elements in the HvOSCA promoter, it was speculated that the barley OSCA gene family is involved in the regulation of multiple signalling pathways. The expression of HvOSCA genes in barley tissues and their relative expression under drought stress revealed that the gene family plays a role in plant organ differentiation, growth and development and coping with abiotic stress. These results provide new valuable information for the functional analysis of HvOSCA genes and the genetic improvement of barley, and provide an important reference for follow-up research.

Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism

Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 (EGT1) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery's known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.

Exogenous expression of barley HvWRKY6 in wheat improves broad-spectrum resistance to leaf rust, Fusarium crown rot, and sharp eyespot

Systemic acquired resistance (SAR) is a broad-spectrum plant defense phenomena controlled by the salicylic acid receptor NPR1. Key regulators of the SAR signaling pathway showed great potentials to improve crop resistance to various diseases. In our previous investigation, a barley transcription factor gene HvWRKY6 was identified as downstream of NPR1 during SAR. However, the broad-spectrum resistance features and molecular mechanisms of HvWRKY6 remain to be explored. In this study, a transgenic wheat line exogenously expressing HvWRKY6 showed improved resistance to leaf rust, Fusarium crown rot (FCR), and sharp eyespot. The model pathogen Pseudomonas syringae pv. tomato DC3000 was employed to induce the SAR response in wheat plants' leaf region adjacent to the infiltration area. Transcriptome sequencing revealed activation of broad-spectrum defense responses by expressing HvWRKY6 in a pathogen-independent manner. Based on the differentially expressed genes in plant hormone signal transduction, we speculated that the enhanced resistance in HvWRKY6-OE wheat transgenic line was associated with activation of the salicylic acid pathway and suppression of the abscisic acid and jasmonic acid pathways. These findings suggest that the transgenic line HvWRKY6-OE might be applied for the genetic improvement of wheat to several fungal diseases; the underlying resistance mechanism was clarified.

Genomic and Pathogenic Diversity of Barley Yellow Mosaic Virus and Barley Mild Mosaic Virus Isolates in Fields of China and Their Compatibility with Resistance Genes of Cultivated Barley.

Plant viruses transmitted by the soilborne plasmodiophorid Polymyxa graminis constantly threaten global production of cereal crops. Although the yellow mosaic virus disease of barley has been known to be present for a long time in China, the understanding of the diversity of the viral pathogens and their interactions with host resistance remains limited. In this study, we conducted a nationwide survey of P. graminis and the barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) it transmits, followed by genomic and pathogenic diversity analyses of both viruses. BaYMV and BaMMV were found exclusively in the region downstream of the Yangtze River, despite the national distribution of its transmission vector P. graminis. Analysis of the genomic variations of BaYMV and BaMMV revealed an elevated rate of nonsynonymous substitutions in the viral genome-linked protein (VPg), in which most substitutions were located in its interaction surface with the host eukaryotic translation initiation factor 4E (eIF4E). VPg sequence diversity was associated with the divergence in virus pathogenicity that was identified through multiple field trials. The majority of the resistance genes, including the widely applied rym4 and rym5 (alleles of eIF4E), as well as the combination of rym1/11 and rym5, are not sufficient to protect cultivated barley against viruses in China. Collectively, these results provide insights into virulence specificity and interaction mode with host resistance in cultivated barley, which has significant implications in breeding for the broad-spectrum resistance barley varieties.

Characterization of Siccibacter sp. Strain C2 a Novel Rhizobacterium that Enhances Tolerance of Barley to Salt Stress.

Plant growth promoting rhizobacteria (PGPR) arouse an increasing interest as an eco-friendly solution for improving crop tolerance to environmental stresses. In this study, we report the characterization of a novel halotolerant PGPR strain (named C2) identified in a screen of rhizospheric bacterial isolates from southeast of Tunisia. Phylogenetic analysis showed that strain C2 is most likely affiliated to the genus Siccibacter with Siccibacter turicensis as the closest species (98.19%). This strain was able to perform phosphate solubilization and production of indole acetic acid (IAA), siderophores, hydrogen cyanide (HCN), as well as different hydrolytic enzymes (proteases, amylases, cellulases, and lipases). The potential of strain C2 in enhancing salt stress tolerance of Hordeum vulgare was also investigated. Our greenhouse inoculation assays showed that strain C2 promotes barley growth in the presence of 400mM NaCl by increasing biomass, root length, and chlorophyll contents. It has a positive effect on the photosynthetic efficiency, concomitantly with lower intercellular CO2 contents, compared to non-inoculated plants. Moreover, barley inoculation with strain C2 under salt stress, resulted in higher accumulation of proline and soluble sugars and alleviate the oxidative stress by decreasing hydrogen peroxide and malondialdehyde contents. Remarkably, this positive effect corroborates with a significant activation in the expression of a subset of barley stress responsive genes, including HVA1, HvDREB1, HvWRKY38 and HvP5CS. In summary, Siccibacter sp. strain C2 is able to enhance barley salt stress tolerance and should be leveraged in developing sustainable practices for cereal crop production.