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Background: Ca 2+ and H 2 O 2 are second messengers that regulate a wide range of cellular events in response to different environmental and developmental cues. In plants, stress-induced H 2 O 2 has been shown to initiate characteristic Ca 2+ signatures; however, a clear picture of the molecular connection between H 2 O 2 -induced Ca 2+ signals and H 2 O 2 -induced cellular responses is missing, particularly in cereal crops such as barley. Here, we employed RNA-seq analyses to identify transcriptome changes in roots and leaves of barley after H 2 O 2 treatment under conditions that inhibited the formation of cytosolic Ca 2+ transients. To that end, plasma membrane Ca 2+ channels were blocked by LaCl 3 application prior to stimulation of barley tissues with H 2 O 2 ., Results: We examined the expression patterns of 4246 genes that had previously been shown to be differentially expressed upon H 2 O 2 application. Here, we further compared their expression between H 2 O 2 and LaCl 3  + H 2 O 2 treatment. Genes showing expression patterns different to the previous study were considered to be Ca 2+ -dependent H 2 O 2 -responsive genes. These genes, numbering 331 in leaves and 1320 in roots, could be classified in five and four clusters, respectively. Expression patterns of several genes from each cluster were confirmed by RT-qPCR. We furthermore performed a network analysis to identify potential regulatory paths from known Ca 2+ -related genes to the newly identified Ca 2+ -dependent H 2 O 2 responsive genes, using the recently described Stress Knowledge Map. This analysis indicated several transcription factors as key points of the responses mediated by the cross-talk between H 2 O 2 and Ca 2+ ., Conclusion: Our study indicates that about 70% of the H 2 O 2 -responsive genes in barley roots require a transient increase in cytosolic Ca 2+ concentrations for alteration in their transcript abundance, whereas in leaves, the Ca 2+ dependency was much lower at about 33%. Targeted gene analysis and pathway modeling identified not only known components of the Ca 2+ signaling cascade in plants but also genes that are not yet connected to stimuli-associated signaling. Potential key transcription factors identified in this study can be further analyzed in barley and other crops to ultimately disentangle the underlying mechanisms of H 2 O 2 -associated signal transduction mechanisms. This could aid breeding for improved stress resistance to optimize performance and productivity under increasing climate challenges., Competing Interests: Declarations. Ethical approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Legumes are well-known for symbiotic nitrogen fixation, whereas associative nitrogen fixation for nonlegume plants needs more attention. Most associative nitrogen-fixing bacteria are applied in their original plant species and need further study for broad adaptation. Additionally, if isolated nitrogen-fixing bacteria could function under fertilizer conditions, it is often ignored. Here, among 21 nitrogen-fixing bacteria isolated from barrenness-tolerance Jerusalem artichoke (JA), Stenotrophomonas sp. SI-NJAU-1 excelled in nitrogen fixation and boosted the growth of JA, wheat, barley, and rice. Additionally, SI-NJAU-1 was proven to decrease the application of compound fertilizers by 30%. To further promote plant growth, Gln K and gln B of SI-NJAU-1, which are crucial for bacterial ammonium assimilation, were mutated. Deletion of gln K but not gln B in SI-NJAU-1 reduced the activity of glutamine synthetase (GS) and the unadenylylated GS and the content of glutamine, which led to ammonium secretion outside and significantly increased the biomass of barley. This work expands the scope of associative nitrogen-fixing endophytes, affirming their potential for plant growth promotion.

Curated resources at centralized repositories provide high-value service to users by enhancing data veracity. Curation, however, comes with a cost, as it requires dedicated time and effort from personnel with deep domain knowledge. In this paper, we investigate the performance of a large language model (LLM), specifically generative pre-trained transformer (GPT)-3.5 and GPT-4, in extracting and presenting data against a human curator. In order to accomplish this task, we used a small set of journal articles on wheat and barley genetics, focusing on traits, such as salinity tolerance and disease resistance, which are becoming more important. The 36 papers were then curated by a professional curator for the GrainGenes database (https://wheat.pw.usda.gov). In parallel, we developed a GPT-based retrieval-augmented generation question-answering system and compared how GPT performed in answering questions about traits and quantitative trait loci (QTLs). Our findings show that on average GPT-4 correctly categorized manuscripts 97% of the time, correctly extracted 80% of traits, and 61% of marker-trait associations. Furthermore, we assessed the ability of a GPT-based DataFrame agent to filter and summarize curated wheat genetics data, showing the potential of human and computational curators working side-by-side. In one case study, our findings show that GPT-4 was able to retrieve up to 91% of disease related, human-curated QTLs across the whole genome, and up to 96% across a specific genomic region through prompt engineering. Also, we observed that across most tasks, GPT-4 consistently outperformed GPT-3.5 while generating less hallucinations, suggesting that improvements in LLM models will make generative artificial intelligence a much more accurate companion for curators in extracting information from scientific literature. Despite their limitations, LLMs demonstrated a potential to extract and present information to curators and users of biological databases, as long as users are aware of potential inaccuracies and the possibility of incomplete information extraction., (Published by Oxford University Press 2025. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Background: The two-component system (TCS) serves as a common intracellular signal transduction pathway implicated in various processes of plant development and response to abiotic stress. With regard to the important cereal crop barley, only partial information about the occurrence of TCS signaling elements in the genome and putative functions is available., Results: In this study, we identified a total of 67 non-redundant TCS genes from all subgroups of the phosphorelay in the latest barley reference genome. Functional annotation and phylogenetic characterization was combined with a comprehensive gene expression analysis of the signaling components. Expression profiles hint at potential functions in vegetative and reproductive organs and tissue types as well as diverse stress responses. Apparently, a distinct subset of TCS genes revealed a stringent grain-specificity not being expressed elsewhere in the plant. By using laser capture microdissection (LCM)-based transcript analysis of barley grain tissues, we refined expression profiles of selected TCS genes and attributed them to individual cell types within the grain. Distinct TCS elements are exclusively expressed in the different maternal and filial cell types, particularly in the endosperm transfer cell (ETC) region. These genes are deemed to be selected in the domestication process of modern cultivars. Moreover, barley plants transformed with a synthetic sensor (TCSn::GFP) showed a high and specific activity in the ETC region of grains monitoring transcriptional output of the signaling system., Conclusions: The results provide comprehensive insights into the TCS gene family in the temperate cereal crop barley and indicate implications in various agronomic traits. The dataset is valuable for future research in different aspects of plant development and will be indispensable not only for barley, but also for other crops of the Poaceae., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Background: Over the years, nanoparticles have emerged as a promising approach for improving crop growth, yield, and overall agricultural sustainability. However, there has been growing concern about the potential adverse effects of nanoparticles in the agricultural sector and the environment. The present study aimed to investigate the detrimental effects of high (1000 mg L -1 ) concentrations of copper oxide nanoparticles (CuO NPs) on barley seedlings. The equivalent concentrations of CuO bulk and the ionic form of copper were also used in the experiments for comparative analysis. CuO NPs were characterized by Field Emission-Scanning Electron Microscopy, Dynamic Light Scattering, Zeta Potential analysis, and X-ray Diffraction prior to the application. Barley seedlings were subjected to the foliar application of CuO NP, CuO bulk, ionic Cu, and control group. The presence of CuO NPs in barley leaves was confirmed 72 hours after treatment by energy-dispersive X-ray analysis., Results: The results showed a CuO NPs treatment led to an impairment of nutrient balance in barley leaves. An increase in hydrogen peroxide content followed by the higher specific activity of catalase and ascorbate peroxidase was also observed in response to CuO NPs, CuO bulk, and Cu 2+ ions. The profile of phytohormones including auxins (IAA and IBA), Gibberellins (GA 1 , GA 4 , and GA 9 ), abscisic acid (ABA), ethylene (ET), and jasmonic acid (JA) significantly affected by CuO NPs, CuO bulk, and Cu 2+ ions. The transcripts of the PR1 gene involved in systemic acquired resistance (SAR) and LOX-1 and PAL involved in induced systemic resistance (ISR) were significantly upregulated in response to CuO NPs treatment., Conclusion: Our findings suggest that the systemic resistances in barley seedlings were induced by higher accumulation of ABA, ET, and JA under CuO NPs treatment. The activation of systemic resistances indicated the involvement of both SAR and SAR pathways in the response to CuO NPs in barley., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Maximizing microbial functions for improving crop performance requires better understanding of the important drivers of plant-associated microbiomes. However, it remains unclear the forces that shapes microbial structure and assembly, and how plant seed-microbiome interactions impact grain quality. In this work, we characterized the seed endophytic microbial communities of malting barley from different geographical locations and investigated associations between microbial (bacterial and fungal) species diversity and malt quality traits. Host genotype, location, and interactions (genotype x location) significantly impacted the seed endophytic microbial communities. Taxonomic composition analysis identified the most abundant genera for bacterial and fungal communities to be Bacillus (belonging to phylum Firmicutes) and Blumeria (belonging to phylum Ascomycota), respectively. We observed that a greater proportion of bacterial amplicon sequence variants (bacterial ASVs) were shared across genotypes and across locations while the greater proportion of the fungal ASVs were unique to each genotype and location. Association analysis showed a significant negative correlation between bacterial alpha diversity indices (Faith PD and Shannon indices) and malt quality traits for barley protein (BP), free amino nitrogen (FAN), diastatic power (DP) and alpha amylase (AA), while fungal alpha diversity (Shannon and Simpson) showed significant negative relationship with β-D-glucan content. In addition, some bacterial and fungal genera were significantly associated with malt extract (ME) -a key trait for maltsters and brewers. We conclude that barley genotype, location, and their interactions shape the seed endophytic microbiome and is key to microbiome manipulation and management during barley production and/or malting., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Base editors are precise editing tools that employ deaminases to modify target DNA bases. The DYW-family of cytosine deaminases is structurally and phylogenetically distinct and might be harnessed for genome editing tools. We report a novel CRISPR/Cas9-cytosine base editor using SsdA, a DYW-like deaminase and bacterial toxin. A G103S mutation in SsdA enhances C-to-T editing efficiency while reducing its toxicity. Truncations result in an extraordinarily small enzyme. The SsdA-base editor efficiently converts C-to-T in rice and barley protoplasts and induces mutations in rice plants and mammalian cells. The engineered SsdA is a highly efficient genome editing tool., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

The advanced molecular tools provide critical inputs in uncovering the regulatory mechanisms underlying plants' adaptation to abiotic stress. Presented holistic studies were done on the barley crown tissue being essential for plant performance under various environmental stimuli. To investigate the effect of brassinosteroids (BRs), the known players in stress management, on molecular response of this tissue to drought, the genotypes with different BRs signal transduction efficiency were employed. Large-scale transcriptomic and proteomic profiling confirmed the specific re-modeling of behavior of the BRs-insensitive barley uzu1.a mutant under drought. On the other hand, a set of genes expressed independently of the genotype was identified, including dehydrin encoding genes. This study also uncovered the candidate genes to be linkers of phytohormones crosstalk. Importantly, we detected the converging upregulation of several proteins and encoding genes under drought, including late embryogenesis abundant proteins and chaperones; they represent a promising target for cereals' improvement. Moreover, the greatest variation between genotypes in accumulation of BRs in the crown tissue exposed to drought was observed for castasterone. Presented multi-omics, high-throughput results enhanced the understanding of molecular response to drought in crown tissue. The new insight was provided into the relationships between gene expression, protein and phytohormone content in barley plants of different BRs signaling., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Kuczyńska et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Barley (Hordeum vulgare ssp. vulgare) is one of the oldest founder crops in human civilization and has been widely dispersed across the globe to support human society as a livestock feed and a raw material for the brewing industries. Since the early half of the 20th century, it has been used for innovative research on cytogenetics, biochemistry, and genetics, facilitated by its mode of reproduction through self-pollination and its true diploid status, which have contributed to the accumulation of numerous germplasm and mutant resources. In the era of molecular genomics and biology, a multitude of barley genes and their related regulatory mechanisms have been identified and functionally validated, providing a paradigm for equivalent studies in other Triticeae crops. This review highlights important advances on barley research over the past decade, focusing mainly on genomics and genomics-assisted germplasm exploration, genetic dissection of developmental and adaptation-related traits, and the complex dynamics of yield and quality formation. In the coming decade, the prospect of integrating these innovations in barley research and breeding shows great promise. Barley is proposed as a reference Triticeae crop for the discovery and functional validation of new genes and the dissection of their molecular mechanisms. The application of precise genome editing as well as genomic prediction and selection, further enhanced by artificial intelligence-based tools and applications, is expected to promote barley improvement to efficiently meet the evolving global demands for this important crop., (Copyright © 2024 The Author. Published by Elsevier Inc. All rights reserved.)

We applied a systems biology approach to gain a deep insight into the regulatory mechanisms of barley (Hordeum vulgare ) under drought and waterlogging stress conditions. To identify informative models related to stress conditions, we constructed meta-analysis and two distinct weighted gene co-expression networks. We then performed module trait association analyses. Additionally, we conducted functional enrichment analysis of significant modules to shed light on the biological performance of underlying genes in the two contrasting stresses. In the next step, we inferred the gene regulatory networks between top hub genes of significant modules, kinases, and transcription factors (TFs) using a machine learning algorithm. Our results showed that at power=10, the scale-free topology fitting index (R2) was higher than 0.8 and the connectivity mean became stable. We identified 31 co-expressed gene modules in barley, with 13 and 14 modules demonstrating significant associations with drought and waterlogging stress, respectively. Functional enrichment analysis indicated that these stress-responsive modules are involved in critical processes, including ADP-rybosylation factors (ARF) protein signal transduction, ethylene-induced autophagy, and phosphoric ester hydrolase activity. Specific TFs and kinases, such as C2C2-GATA, HB-BELL, and MADS-MIKC, were identified as key regulators under these stress conditions. Furthermore, certain TFs and kinases established unique connections with hub genes in response to waterlogging and drought conditions. These findings enhance our understanding of the molecular networks that modulate barley's response to drought and waterlogging stresses, offering insights into the regulatory mechanisms essential for stress adaptation.

A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry., Competing Interests: Competing interests: K.B.B., C.D., G.B.F., M.E.J., Q.L., M.T.S.N., P.R.P., M.W.R., B.S., N.W.T. and C.V. are employees of the Carlsberg Research Laboratory. The other authors declare no competing interests., (© 2025. The Author(s).)

Partial root-zone drying irrigation (PRD) has been widely employed to regulate crop root development and responses to environmental fluctuations. However, its role in reprogramming rhizospheric microorganisms and inducing plant stress tolerance remains largely unexplored. This study aimed to investigate the effects of PRD on the response of barley (Hordeum vulgare) plants to low temperatures under various irrigation regimes. Under low temperature, barley plants subjected to PRD exhibited a significantly enhanced net photosynthetic rate, stomatal conductance, and maximum quantum efficiency of photosystem II compared to fully irrigated plants. Additionally, these plants showed a reduction in relative conductance. These results suggest that PRD could be a viable strategy for enhancing crop stress tolerance through irrigation management. Metabolomic analysis revealed that PRD influenced the accumulation of glutathione and 9-octadecenamide in roots under low temperature, which was corroborated by transcriptome profiling data. Furthermore, the study highlighted the close association between this regulatory process and rhizosphere core microorganisms, such as Sphingobium and Mortierella, enriched in barley roots under PRD. This study revealed the mechanism underlying plant stress tolerance induction by PRD and the roles of rhizosphere microorganisms in this process. Also, the current study suggests that PRD is a promising strategy for enhancing crop stress tolerance through effective irrigation management., (© 2025 Society for Experimental Biology and John Wiley & Sons Ltd.)

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests., (© 2024. The Author(s).)

Leaf stripe disease, caused by Pyrenophora graminea , is a seed-borne fungal disease that significantly impacts hulless barley ( Hordeum vulgare var. nudum ) production on the Qinghai-Tibet Plateau. This study aimed to identify genetic factors conferring resistance to the leaf stripe by analyzing an F 3 population derived from a cross between the resistant landrace Teliteqingke and the susceptible landrace Dulihuang. Genetic analysis revealed that resistance in Teliteqingke was governed by two dominant genes. Using bulked segregant analysis combined with an SNP array (BSA-SNP) and RNA-seq, we identified two candidate regions on chromosomes 3H and 7H. Further analysis focused on chromosome 3H, which revealed a candidate genomic region containing seven potential disease-resistance genes. Among these, RT-qPCR experiments demonstrated significant expression induction of HORVU.MOREX.r3.3HG0232110.1 (encoding a RING/U-box superfamily protein) and HORVU.MOREX.r3.3HG0232410.1 (encoding a bZIP transcription factor) showed significant expression induction following inoculation with P. graminea . These genes are strong candidates for the resistance mechanism against leaf stripes in Teliteqingke. These results provide a foundation for functional validation of these genes and offer valuable insights for breeding disease-resistant hulless barley.

Keymessage: In this first QTL mapping study of embryo size in barley, novel and stable QTL were identified and candidate genes underlying a significant locus independent of kernel size were identified based on orthologous analysis and comparison of the whole-genome assemblies for both parental genotypes of the mapping population. Embryo, also known as germ, in cereal grains plays a crucial role in plant development. The embryo accounts for only a small portion of grain weight but it is rich in nutrients. Larger embryo translates to a more nutritious grain and larger store of energy reserves, which can benefit seed germination and seedling establishment. However, reports on quantitative trait loci (QTL) affecting embryo size in barley is rare. To understand the genetic basis of embryo size in barley, a population consisting of 201 F9 recombination inbred lines (RILs) was assessed in four environments. Three regions affecting various characteristics of embryo size including embryo length (EL), embryo width (EW) and embryo area (EA) were consistently identified. They located on chromosomes 2H, 4H and 7H, respectively. Among them, the QTL on 7H was not significantly affected by kernel size. Phenotypic variances explained by this QTL for EL, EW and EA were 11.8%, 9.3% and 12.7%, respectively. Taken advantage of the available genomic assemblies of the two parental genotypes, candidate genes for this locus on 7H were identified. In addition, significant correlations between embryo size and early vigour and kernel traits were detected. To our knowledge, the present study is for the first time reporting QTL conferring embryo size by directly measuring the characteristics as quantitative trait in barley, which would broaden our understanding of the genetic basis of barley embryo size and offer valuable targets for future breeding programmes., Competing Interests: Declarations. Conflict of interest: The authors declare that there are no conflicts of interest., (© 2025. Crown.)

Awns in barley have different shapes including awnless, straight, hooded, crooked, and leafy awns. The hooded awns are characterized by an appendage of the lemma, which forms a trigonal or cap-shaped structure, and even blossoms and yields fruits on barley awn. In the lemma primordia of wild-type (straight awn), cells divide and elongate to form the straight awn. However, in the lemma primordia of KNOX3 mutant (hooded awn), cells divide at various orientations without elongating, and they form hooded awns. This phenomenon is due to the upregulation of KNOX3 expression via insertion of a tandem direct duplication of 305 bp in the intron IV. Here, we summarize the development of barley hooded awn research in the following two aspects: on the one hand, the morphology, development of hooded awns, and the expression regulation of the KNOX3 gene. The latter includes ectopic expression of the KNOX3 gene, gene interactions among awn-related genes, the regulatory relationship between class I KNOX genes and hormones, as well as the influence of abiotic stresses. On the other hand, the potential performance of hooded awns in barley for yield breeding is discussed. Hooded awns have potential application value in forage, which could compensate for the disadvantage of the long straight awn in the barley straw used for feed in modern cultivars. In addition, the hooded awn produces ectopic meristems to develop complete florets, which is an interesting question and helps to understand the development, adaptation, and evolution of plant floral organs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Studying genetic variability through the phenotypic performance of genotypes is crucial in the breeding program. Therefore, evaluating both yield performance and stability across diverse environments is essential in yield trials to identify high-yield potential and stable cultivars. In this study, we employed 12 univariate and 10 multivariate stability models to analyze how genotype (G), environment (E), and their interaction (G × E) affect the yield performance of 32 barley genotypes across 10 environments. The environmental main effect explained 81.3% of the total variation, compared to 18.6% for genotypes and G × E interaction effects. Using the GGE biplot 'which-won-where' polygon, we categorized environments into five groups and genotypes into six groups, identifying eight genotypes with mean grain yield (GY) superior to the overall mean (4.43 tons ha - 1 ). Spearman's correlation analysis indicated significant positive correlations (P < 0.01) between GY and various stability parameters such as linear regression coefficients (b i ), Perkins and Jinks's stability parameters (B i ), environmental variance (S xi 2 ) and Tai's environmental effects (α i ), among others, as univariate stability measures. Additionally, nonparametric measures such as Nassar and Huhn's (S I 6 and S I 3 ) and Thennarasu's (NP I (3) and NP I (4) ), TOP-rank stability and the yield stability index (YSI), showed significant correlations with GY. Both univariate and multivariate stability models highlighted genotypes G32, G1, and G27 as the most stable, exhibiting minimal yield variation across environments. Furthermore, G15, followed by G13, G7, and G9, demonstrated high stability based on multivariate measures. Accordingly, it might be safe to utilize the stability parameters of different groups concerning static and dynamic concepts of stability to avoid the possibility of estimating the same concept of stability. This study emphasizes the importance of utilizing a combination of univariate and multivariate stability models to assess genotype stability comprehensively and select "ideal genotypes" that offer both high yield potential and stability., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Barley leaf stripe, a disease mainly caused by Pyrenophora graminea (P. graminea) infection, severely affects barley yield and quality and is one of the most widespread diseases in barley production. However, little is known about the underlying molecular mechanisms of leaf stripe resistance. In this study, the transcript expression profiles of normal and infected leaves of resistant Tibetan hulless barley (Hordeum vulgare L. var. nudum Hook. f.) variety Kunlun 14 and susceptible variety Z1141 were analyzed by RNA sequencing (RNA-seq). The results showed a total of 7,669 and 5,943 differentially expressed genes (DEGs) were found in resistant and susceptible Kunlun 14 and Z1141, respectively, with 8,916 DEGs found between Kunlun 14 and Z1141. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the 8,916 DEGs identified many significantly enriched categories and pathways, of which a plant-pathogen interaction pathway, containing a total of 102 genes (100 known genes and two novel genes), was found, that was very important for the study of the leaf stripe resistance mechanism. Using RNA-seq, small RNA sequencing (miRNA-seq) combined with degradome sequencing (degradome-seq), four pairs associated with leaf-stripe miRNAs and target genes were obtained, namely Hvu-miR168-5p and Argonaute1 (HvAGO1), Hvu-novel-52 and growth-regulating factor 6 (HvGRF6), Hvu-miR6195 and chemocyanin-like protein (CLP), and Hvu-miR159b and gibberellin-dependent MYB (GAMYB). Transformation of the important target gene HvAGO1 into Arabidopsis verified that HvAGO1 could against Botrytis cinerea. Then RNA-seq and miRNA-seq of Arabidopsis transformed with overexpressed of HvAGO1 were performed. Based on the above research results, we constructed a Protein-Protein Interaction (PPI) network of barley leaf stripe resistance. This study lays the foundation for the study of the barley leaf stripe resistance mechanism and provides new targets for the genetic improvement of disease-resistant barley varieties., Competing Interests: Declarations. Institutional review board statement: Not applicable. Informed consent: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Salinization poses a significant challenge in agriculture. Identifying salt-tolerant plant germplasm resources and understanding their mechanisms of salt tolerance are crucial for breeding new salt-tolerant plant varieties. However, one of the primary obstacles to achieving this goal in crops is the physiological complexity of the salt-tolerance trait. In a previous study, we developed a salt-tolerant barley doubled haploid (DH) line, designated as DH20, through mutagenesis combined with microspore culture, establishing it as an idea model for elucidating the mechanisms of salt tolerance. In this study, ion homeostasis, key osmotic agents, antioxidant enzyme activities and gene expression were compared between Hua30 (the original material used as a control) and DH20. The results indicated that under salt treatment, DH20 exhibited significantly higher shoot fresh and dry weight, relative plant height, shoot K + /Na + ratio, improved stomatal guard cell function, and better retention of chloroplast ultrastructure compared to Hua30. Notably, the K + efflux in DH20 was significantly lower while the Na + and H + efflux was significantly higher than those in Hua30 under salt stress in mesophyll cells. Furthermore, the activities of ascorbate peroxidase, superoxide dismutase, and peroxidase, along with the levels of proline, betaine, malondialdehyde, and soluble protein, were correlated with ion efflux and played a vital role in the response of DH20 to salt stress. Compared to Hua30, the relative expression levels of the HvSOS1, HvSOS2, HvSOS3, HvHKT1;3, HvNHX1, HvNHX2, and HvNHX3 genes, which showed a strong correlation with Na + , K + , and H + efflux, exhibited significant differences at 24 h under salt stress in DH20. These findings suggest that ion homeostasis, key osmolytes, antioxidant enzyme activities, and associated gene expression are coordinated in the salt tolerance of DH20, with K + retention and Na + and H + efflux serving as important mechanisms for coping with salt stress. These findings present new opportunities for enhancing salinity tolerance, not only in barley but in other cereals as well, including wheat and rice, by integrating this trait with other traditional mechanisms. Furthermore, MIFE measurements of NaCl-induced ion fluxes from leaf mesophyll provide plant breeders with an efficient method to screen germplasm for salinity stress tolerance in barley and potentially other crops. Clinical trial number: Not applicable., Competing Interests: Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161-176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns. We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Key Message: Enhancing salt tolerance genetically through defining the genetic and physiological mechanisms intergenerational and transgenerational stress memory that contributes to sustainable agriculture by reducing the reliance on external inputs such as irrigation and improving the adaptability of barley to changing climate conditions. Salinity stress poses a substantial challenge to barley production worldwide, adversely affecting crop yield, quality, and agricultural sustainability. To address this, the present study utilized a genome-wide association san (GWAS) to identify genetic associations underlying intergenerational and transgenerational stress memory in response to salinity in a diverse panel of 138 barley accessions. We compared seeds from a second-generation group without salinity exposure (C1C2) to seeds from groups that experienced single-generation salt stress two generations ago (S1C2; transgenerational memory) or one generation ago (C1S2; intergenerational memory), as well as seeds from a group exposed to salinity across both generations (S1S2; combined memory effects). Our results revealed that historical salt stress, irrespective of the number of prior generations affected, induced significant changes in traits such as spike length, spikelets per spike, grains per spike, grain weight, thousand-kernel weight, and markedly increment in antioxidant components levels of enzymatic and non-enzymatic antioxidants. These findings indicate that prior exposure to salinity leaves lasting physiological and biochemical effects that enhance the plant's ability to respond to subsequent stress. Notably, the GWAS analysis identified highly significant genetic associations and candidate genes such as HORVU.MOREX.r3.4HG0383450 linked to most of these traits under salinity exposure histories. In conclusion, intergenerational and transgenerational stress memory plays a pivotal role in enhancing barley's salt tolerance, offering valuable insights for breeding programs aimed at developing resilient barley cultivars., Competing Interests: Declarations. Conflict of interest: The authors have no competing interests. Ethical Approval: The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors. Data Availability Statement: All data supporting the findings of this study are available within the paper and its supplementary materials published online., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: Genetic variation for malting quality as well as metabolomic and near-infrared features was identified. However, metabolomic and near-infrared features as additional omics-information did not improve accuracy of predicted breeding values. Significant attention has recently been given to the potential benefits of metabolomics and near-infrared spectroscopy technologies for enhancing genetic evaluation in breeding programs. In this article, we used a commercial barley breeding population phenotyped for grain yield, grain protein content, and five malting quality traits: extract yield, wort viscosity, wort color, filtering speed, and β-glucan, and aimed to: (i) investigate genetic variation and heritability of metabolomic intensities and near-infrared wavelengths originating from leaf tissue and malted grain, respectively; (ii) investigate variance components and heritabilities for genomic models including metabolomics (GOBLUP-MI) or near-infrared wavelengths (GOBLUP-NIR); and (iii) evaluate the developed models for prediction of breeding values for traits of interest. In total, 639 barley lines were genotyped using an iSelect9K-Illumina barley chip and recorded with 30,468 metabolomic intensities and 141 near-infrared wavelengths. First, we found that a significant proportion of metabolomic intensities and near-infrared wavelengths had medium to high additive genetic variances and heritabilities. Second, we observed that both GOBLUP-MI and GOBLUP-NIR, increased the proportion of estimated genetic variance for grain yield, protein, malt extract, and β-glucan compared to a genomic model (GBLUP). Finally, we assessed these models to predict accurate breeding values in fivefold and leave-one-breeding-cycle-out cross-validations, and we generally observed a similar accuracy between GBLUP and GOBLUP-MI, and a worse accuracy for GOBLUP-NIR. Despite this trend, GOBLUP-MI and GOBLUP-NIR enhanced predictive ability compared to GBLUP by 4.6 and 2.4% for grain protein in leave-one-breeding-cycle-out and grain yield in fivefold cross-validations, respectively, but differences were not significant (P-value > 0.01)., Competing Interests: Declarations. Conflict of interest: On behalf of all authors, the corresponding authors states that there is no conflict of interest. Consent for publication: Not applicable. Ethics approval: Not applicable. Consent to participate: Not applicable., (© 2025. The Author(s).)

Background: Genebanks around the globe serve as valuable repositories of genetic diversity, offering not only access to a broad spectrum of plant material but also critical resources for enhancing crop resilience, advancing scientific research, and supporting global food security. To this end, traditional genebanks are evolving into biodigital resource centers where the integration of phenotypic and genotypic data for accessions can drive more informed decision-making, optimize resource allocation, and unlock new opportunities for plant breeding and research. However, the curation and availability of interoperable phenotypic and genotypic data for genebank accessions is still in its infancy and represents an obstacle to rapid scientific discoveries in this field. Therefore, effectively promoting FAIR (i.e., findable, accessible, interoperable, and reusable) access to these data is vital for maximizing the potential of genebanks and driving progress in agricultural innovation., Findings: Here we provide whole genome sequencing data of 812 barley (Hordeum vulgare L.) plant genetic resources and 298 European elite materials released between 1949 and 2021, as well as the phenotypic data for 4 disease resistance traits and 3 agronomic traits. The robustness of the investigated traits and the interoperability of genomic and phenotypic data were assessed in the current publication, aiming to make this panel publicly available as a resource for future genetic research in barley., Conclusions: The data showed broad phenotypic variability and high association mapping potential, offering a key resource for identifying genebank donors with untapped genes to advance barley breeding while safeguarding genetic diversity., (© The Author(s) 2025. Published by Oxford University Press GigaScience.)

In this study, the drought-responsive gene HvFBX158 from barley was transferred to Arabidopsis thaliana , and overexpression lines were obtained. The phenotypic characteristics of the transgenic plants, along with physiological indicators and transcription level changes of stress-related genes, were determined under drought treatment. Under drought stress, transgenic plants overexpressing HvFBX158 exhibited enhanced drought tolerance and longer root lengths compared to wild-type plants. Additionally, malondialdehyde and hydrogen peroxide contents were significantly lower in transgenic lines, while superoxide dismutase activity was elevated. Quantitative RT-PCR showed that the expression levels of drought and stress response genes, including AtP5CS, AtDREB2A, AtGSH1, AtHSP17.8 , and AtSOD , were significantly upregulated. Transcriptome analysis further confirmed that HvFBX158 regulated multiple stress tolerance pathways. In summary, the overexpression of the HvFBX158 gene enhanced drought tolerance in Arabidopsis thaliana by regulating multiple stress response pathways. This study provides a practical basis for improving drought-resistant barley varieties and lays a foundation for subsequent research on F-box family genes for stress resistance in barley.

Barley leaf stripe is an important disease caused by Pyenophora graminea that affects barley yields in the world. Ascorbic acid (AsA) interacts with key elements of a complex network orchestrating plant defense mechanisms, thereby influencing the outcome of plant-pathogen interaction. Myo-inositol oxygenase (MIOX) is a pivotal enzyme involved in plants development and environmental stimuli. However, MIOX has described functions in plants but has not been characterized in fungi. In this study, we characterized the Pgmiox gene in P. graminea pathogenesis through annotated on the metabolic pathway of ascorbic acid aldehyde. Our analysis suggested that the Pgmiox protein had a typical conserved MIOX domain. Multiple alignment analysis indicated that the P. graminea MIOX orthologue clustered with MIOX proteins of Pyrenophora species. RNA interference successfully reduced transcript abundance of Pgmiox in six transformant lines compared to wild type, and the transformants were further less virulent on the host plant barley. Transformants of Pgmiox had significant reductions in vegetative growth and pathogenicity, which had increased resistance to tebuconazole and carbendazim. In addition, Pgmiox is associated with ionic, drought, osmotic, oxidative, and heavy metal stress tolerance in P. graminea. In conclusion, our findings reveal that Pgmiox may be widely utilized by fungi to enhance pathogenesis and holds significant potential for the development of durable P. graminea resistance through genetic modifications., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Mixed-linkage (1,3; 1,4)-β-D-glucan (MLG) impacts the food and industrial end-uses of barley, but the molecular mechanism of variations in MLG content remains unclear. MLG content usually increases in Waxy-mutated barley. This study applied transcriptomic, proteomic, and metabolomic analyses to Waxy-mutated recombinant inbred lines with higher MLG content and wild-type lines with lower MLG content, and identified candidate genes and pathways regulating MLG content through combining preliminary gene function analysis. MLG biosynthesis differed significantly during late grain development in the Waxy-mutated and wild-type barley lines. The MLG increase was closely associated with strongly active sugar and starch metabolism and stress-responsive plant hormones, particularly abscisic acid (ABA) signaling process. Stress-responsive transcript factors ILR3, BTF3, RGGA, and PR13 protein bind to CslF6, which is critical for barley MLG biosynthesis, and the stress-responsive gene ASR1 also had a positive effect on MLG increase. Waxy mutation enhances barley stress responses by activating ABA- or other stress-responsive plant hormones signaling processes, which facilitates MLG biosynthesis. This study provides a new approach for elucidating the variations in MLG content of barley grains., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Drought is an important abiotic factor constricting crop production globally. Although the roles of JAZ proteins in regulating jasmonic acid signalling and plant responses to environmental stress are well documented, their specific functions and underlying mechanisms remain little known. In this study, JAZ proteins in barley were thoroughly analyzed, revealing a total of 11 members classified into three phylogenetic subgroups. HvJAZ2, based on its distinct expression patterns, is considered a key candidate gene for regulating drought tolerance in barley. Using the HvJAZ2 knockout mutants, we revealed that the gene negatively regulates drought tolerance by inhibiting barley root growth. Notably, the jaz2 mutants upregulated the expression of root development genes, including SHR1, PLT1, PLT2 and PLT6. plt2 and plt1/plt2 mutants exhibited suppressed root development and reduced drought tolerance. Analysis of interactions between HvJAZ2 and other proteins showed that HvJAZ2 does not directly interact with HvPLT1/2/6, but interacts with some other proteins. BIFC and LCA assays further confirmed the nuclear interaction between HvJAZ2 and HvMYC2. Y1H and Dual-Luciferase experiments demonstrated that HvMYC2 can bind to and activate the HvPLT2 promoter. In summary, HvJAZ2 negatively regulates root development and drought tolerance in barley by suppressing HvPLT2 expression through interacting with HvMYC2., (© 2024 John Wiley & Sons Ltd.)

The effectiveness of fungicides to control foliar fungal crop diseases is being diminished by the increasing spread of resistance to fungicides. One approach that may help to maintain efficacy is remediation of resistant populations by sensitive ones. However, the success of such approaches can be compromised by re-incursion of resistance through aerial spore dispersal, although knowledge of localized gene flow is lacking. Here, we report on a replicated mark-release-recapture field experiment with several treatments set up to study spore-dispersal-mediated gene flow of a mutated allele that confers demethylase inhibitor resistance in Pyrenophora teres f. teres ( Ptt ). Artificial inoculation of the host, barley ( Hordeum vulgare ), was successful across the 12-ha trial, where the introduced sensitive and resistant populations were, respectively, 6- and 13-fold the DNA concentration of the native Ptt population. Subsequent disease pressure remained low, which hampered spread of the epidemic to such an extent that gene flow was not detected at, or beyond, 2.5 m from source points. In the absence of gene flow, plots were assessed for treatment effects; fungicide applied to populations that contained 14.3% of allele mutation increased in frequency to 24.5%, whereas sensitive populations had no change in structure. Untreated controls of the native Ptt population remained genetically stable, yet untreated controls that were inoculated with sensitive Ptt had half the resistance frequency of the native population structure. The trial demonstrates the potential for management to remediate fungicide-resistant pathogen populations, where localized gene flow is minimal, to safeguard chemical crop protection into the future., Competing Interests: The author(s) declare no conflict of interest.

Genome-wide association study (GWAS) is a powerful tool for identifying marker-trait associations that can accelerate breeding progress. Yet, its power is typically constrained in newly established breeding programs where large phenotypic and genotypic datasets have not yet accumulated. Expanding the dataset by inclusion of data from well-established breeding programs with many years of phenotyping and genotyping can potentially address this problem. In this study we performed single- and multi-population GWAS on heading date and lodging in four barley breeding populations with varying combinations of row-type and growth habit. Focusing on a recently established 6-rowed winter (6RW) barley population, single-population GWAS hardly resulted in any significant associations. Nevertheless, the combination of the 6RW target population with other populations in multi-population GWAS detected four and five robust candidate quantitative trait loci for heading date and lodging, respectively. Of these, three remained undetected when analysing the combined populations individually. Further, multi-population GWAS detected markers capturing a larger proportion of genetic variance in 6RW. For multi-population GWAS, we compared the findings of a univariate model (MP1) with a multivariate model (MP2). While both models surpassed single-population GWAS in power, MP2 offered a significant advantage by having more realistic assumptions while pointing towards robust marker-trait associations across populations. Additionally, comparisons of GWAS findings for MP2 and single-population GWAS allowed identification of population-specific loci. In conclusion, our study presents a promising approach to kick-start genomics-based breeding in newly established breeding populations., Competing Interests: Competing interests: Nordic Seed A/S own and market the studied barley breeding programs. Ethics approval: All data presented in this manuscript required no ethical approval., (© 2024. The Author(s).)

One of the main signal transduction pathways that modulate plant growth and stress responses, including drought, is the action of phytohormones. Recent advances in omics approaches have facilitated the exploration of plant genomes. However, the molecular mechanisms underlying the response in the crown of barley, which plays an essential role in plant performance under stress conditions and regeneration after stress treatment, remain largely unclear. The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. Moreover, we assumed that due to the strong connection between strigolactones and branching the hvdwarf14.d mutant, with dysfunctional receptor of strigolactones, manifests the most abundant alternations in crowns and phenotype under drought. Finally, we expected to identify components underlying the core response to drought which are independent of the genetic background. Large-scale analyses were conducted using gibberellins-biosynthesis, brassinosteroids-signaling, and strigolactones-signaling mutants, as well as reference genotypes. Detailed phenotypic evaluation was also conducted. The obtained results clearly demonstrated that hormonal disorders caused by mutations in the HvGA20ox2 , HvBRI1 , and HvD14 genes affected the multifaceted reaction of crowns to drought, although the expression of these genes was not induced by stress. The study further detected not only genes and proteins that were involved in the drought response and reacted specifically in mutants compared to the reaction of reference genotypes and vice versa , but also the candidates that may underlie the genotype-universal stress response. Furthermore, candidate genes involved in phytohormonal interactions during the drought response were identified. We also found that the interplay between hormones, especially gibberellins and auxins, as well as strigolactones and cytokinins may be associated with the regulation of branching in crowns exposed to drought. Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.

The barley stripe mosaic virus (BSMV) uses its genomic RNA components (alpha, beta, and gamma) as an efficient method for studying gene functions. It is a newly developed method that utilizes gene transcript suppression to determine the role of plant genes. BSMV derived from virus induced gene silencing (VIGS) is capable of infecting various key farming crops like barley, wheat, rice, corn, and oats. Nevertheless, the growing acceptance and enhancement of BSMV-VIGS will benefit all kinds of plants. Abiotic stresses such as drought and salt are highly affecting plant growth, development, and production. BSMV-induced temporal gene knockdown is performed during particular stressful situations to determine their specific function. The quick physiological and biochemical changes aid in confirming the role of the target genes. VIGS has a significant role to improve crop genetics and breeding, despite having certain restrictions. Thus, exploring the possible solution and addressing these difficulties will enhance the technology in the continuous advancement of plant manufacturing. BSMV-mediated VIGS has become popular in functional genomics; gene function can be determined without permanent transformation. In general, BSMV-mediated VIGS will be very helpful in the ongoing effort to develop resilient crops., Competing Interests: Declarations. Ethical statements: Not applicable. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Plants are increasingly exposed to stress-induced factors, including heavy metals. Zinc, although it is a microelement, at high concentrations can be phytotoxic to plants by limiting their growth and development. The presented research confirmed the inhibition effect of Zn on morphological and physiological parameters in barley plants. However, the effect was Zn dose dependent (50 µM, 100 µM, and 200 µM), as well as part of the plants (above ground or roots). To mitigate the negative effects of Zn, plants were sprayed with 0.1% silicon. Silicon was proven to have a positive effect on mitigating the inhibitory effects of Zn-induced stress. In most cases, an increase in both morphological (length, elongation, fresh and dry weights, and weather content) and physiological (relative chlorophyll content and fluorescence) parameters was observed. This occurrence was dependent on the Zn dose. Epigenetic analyses confirmed differences in the DNA methylation level, both between plants subjected to stress at different strengths (50 µM, 100 µM, and 200 µM Zn) and between plants sprayed with Si or not. The differences indicate that silicon affects the epigenome of barley plants, thereby modifying the response of plants to stress factors. This modification may be the basis for plants to acquire resistance as "epigenetic memory".

Phased, small interfering RNAs (PhasiRNAs) play a crucial role in supporting male fertility in grasses. Earlier work in maize (Zea mays) and rice (Oryza sativa)-and subsequently many other plant species-identified premeiotic 21-nucleotide (nt) and meiotic 24-nt phasiRNAs. More recently, a group of premeiotic 24-nt phasiRNAs was discovered in the anthers of 2 Pooideae species, barley (Hordeum vulgare) and bread wheat (Triticum aestivum). Whether premeiotic 24-nt phasiRNAs and other classes of reproductive phasiRNAs are conserved across Pooideae species remains unclear. We conducted comparative RNA profiling of 3 anther stages in 6 Pooideae species and 1 Bambusoideae species. We observed complex temporal accumulation patterns of 21-nt and 24-nt phasiRNAs in Pooideae and Bambusoideae grasses. In Bambusoideae, 21-nt phasiRNAs accumulated during meiosis, whereas 24-nt phasiRNAs were present in both premeiotic and postmeiotic stages. We identified premeiotic 24-nt phasiRNAs in all 7 species examined. These phasiRNAs exhibit distinct biogenesis mechanisms and potential Argonaute effectors compared to meiotic 24-nt phasiRNAs. We show that specific Argonaute genes coexpressed with stage-specific phasiRNAs are conserved across Bambusoideae and Pooideae species. Our degradome analysis identified a set of conserved miRNA target genes across species, while 21-nt phasiRNA targets were species-specific. Cleavage of few targets was observed for 24-nt phasiRNAs. In summary, this study demonstrates that premeiotic 24-nt phasiRNAs are present across Bambusoideae and Pooideae families, and the temporal accumulation of other classes of 21-nt and 24-nt phasiRNA differs between bamboo and Pooideae species. Furthermore, targets of the 3 classes of phasiRNAs may be rapidly evolving or undetectable., Competing Interests: Conflict of interest statement. The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Alopecurus aequalis is a winter annual or short-lived perennial bunchgrass which has in recent years emerged as the dominant agricultural weed of barley and wheat in certain regions of China and Japan, causing significant yield losses. Its robust tillering capacity and high fecundity, combined with the development of both target and non-target-site resistance to herbicides means it is a formidable challenge to food security. Here we report on a chromosome-scale assembly of A. aequalis with a genome size of 2.83 Gb. The genome contained 33,758 high-confidence protein-coding genes with functional annotation. Comparative genomics revealed that the genome structure of A. aequalis is more similar to Hordeum vulgare rather than the more closely related Alopecurus myosuroides., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Chitosan (CS), derived from the partial deacetylation and hydrolysis of chitin, varies in the degree of deacetylation, molecular weight, and origin, influencing its biological effects, including antifungal properties. In plants, CS triggers immune responses and stimulates biomass growth. Previously, we found that the antifungal activity of CS was strongly dependent on its physicochemical properties. This study revealed that the chitosan batch CS&#95;10 with the strongest antifungal activity also effectively activated plant immune responses and promoted biomass growth. Barley treated with CS&#95;10 exhibited systemic acquired resistance (SAR), characterized by micronecrotic reactions upon Puccinia hordei ( Ph ) inoculation and reduced symptoms following Fusarium graminearum ( Fg ) infection, representing biotrophic and necrotrophic pathogens, respectively. CS&#95;10 treatment (concentration 200 ppm) also enhanced plant biomass growth (by 11% to 15%) and promoted the accumulation of salicylic acid (SA), a hormone that regulates both plant immune responses and growth. Low levels of exogenous SA applied to plants mirrored the stimulation observed with CS&#95;10 treatment, suggesting SA as a key regulator of CS&#95;10-induced responses. Transcriptomic analysis identified SA-regulated genes as drivers of enhanced immunity and biomass stimulation. Thus, CS&#95;10 not only fortifies plant defenses against pathogens like Ph and Fg but also boosts growth through SA-dependent pathways.

In barley having adherent hulls, an irreversible connection between the pericarp with both palea and lemma is formed during grain maturation. A mutation in the NUDUM 1 ( NUD1 ) gene prevents this connection and leads to the formation of barley with non-adherent hulls. A genetic model of two isogenic lines was used to elucidate the genetic mechanisms of hull adhesion: a doubled haploid line having adherent hulls and its derivative with non-adherent hulls obtained by targeted mutagenesis of the NUD1 gene. Comparative transcriptomics analysis of the grain coats was performed at two stages of development: the milk stage, when the hulls can still be easily detached from the pericarp, and the dough stage when the hull adhesion process occurs. It was shown that the main differences in the transcriptomes lie in the genes related to DNA replication and chromatin assembly, cell wall organization, and cuticle formation. Meanwhile, genes involved in lipid biosynthesis mostly show minor differences in expression between stages and genotypes and represent a limited set of active genes. Among the 3-ketoacyl-CoA synthase (KCS) genes active during grain development, candidates for key enzymes responsible for very long-chain fatty acid elongation were identified.

Cadmium (Cd) is a toxic heavy metal that poses risks to crop production and food safety worldwide. This study evaluated whether manganese (Mn) addition could mitigate Cd toxicity and reduce Cd accumulation in barley seedlings. Hydroponically grown seedlings of Cd-tolerant (WSBZ) and Cd-sensitive (Dong17) barley cultivars were treated with 0.1 μM and 1 μM Cd as well as 0.2 mM Mn alone and in a combination with 0.1 or 1.0 μM Cd for 21 days. Cd exposure caused the dramatic alteration of growth and physiological parameters by disrupting chloroplast, and increased Cd accumulation in both genotypes. However, Mn addition markedly alleviated the negative impacts of all examined parameters caused by Cd stress. Cd addition enhanced expression of anti-oxidative enzyme related genes, including HvSOD, HvCAT, HvAPX, HvPOD in the two barley genotypes exposed to Cd stress. The expression analysis showed nearly all HvNRAMPs genes are dramatically up regulated by both Mn and Cd, with WSBZ having higher expression than Dong 17. Notably, HvNRAMP1 showed the highest expression due to Mn addition, highlighting its crucial role in Mn uptake and transportation in barley. Moreover, Cd stress and Mn addition increased and suppressed the expression of HvYSL5, HvHMA2 and HvHMA3, respectively. Conversely, the expression of HvYSL2, HvIRT1 and HvMTP8 was upregulated by both Mn and Cd treatments, with a further increase observed in the combined Cd and Mn treatments. It may be concluded that sufficient Mn supply is quite important for reducing Cd uptake and accumulation in plants., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Conflicts of Interest The authors have no conflict of interest to declare., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited., Methods: This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments., Results: A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis -acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix-loop-helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and provides a reference for the molecular mechanism of Qingke gene evolution., Competing Interests: The authors declare that they have no competing interest., (© 2024 Li et al.)

Nitrogen (N) is a critical element for plant growth and development. Hence, improving nitrogen use efficiency (NUE) is vital for reducing costs and the environmental impact of agricultural practices. Understanding the genetic control of N metabolism is crucial to improve NUE, especially in agronomically important plants, such as barley (Hordeum vulgare). Using bioinformatics and functional genomics tools, we identified and characterized sixteen barley nitrogen metabolism-related gene families (HvNMGs) on a genome-wide scale, analysing gene features and evolution. These genes, located on six of seven barley chromosomes, are highly conserved in plants (including barley, rice, and Arabidopsis), as shown by phylogenetic analysis. We further explored the evolutionary relationships of NMGs through a genome-to-genome synteny analysis, which indicated higher conservation of NMGs between barley and other monocots, suggesting that these orthologous pairs predate species divergence. Protein-protein interaction analyses revealed that all of the HvNMGs show interactions, mainly with each other. The H. vulgare miRNAs target sites (hvu-miR) prediction identified six hvu-miR in 4 HvNMGs (HvGABA-T2, HvALDH10-1, HvALDH10-2 and HvARGAH), indicating their potential involvement in stress responses. The expression patterns analysis of publicly available RNA-seq data revealed that HvNMGs are expressed in all developmental stages of barley, and they respond to different stress conditions, indicating their essential role in plant growth, development and stress response. The organ-specific expression analysis, conducted using qPCR, of HvNMGs revealed higher expression of HvNiR and HvNRs in the leaf and significantly higher expression of HvARGAH and HvALDH10 in the spike than in other tissues, showing that some of the genes may be particularly important in some tissues than others. This data provides a foundation for understanding HvNMG function and could be used to improve barley yield by enhancing NUE - an important goal for both crop productivity and environmental sustainability., Competing Interests: Declaration of competing interest None Declared., (Copyright © 2024. Published by Elsevier Ltd.)

Barley (Hordeum vulgare L.) is widely cultivated across diverse soil types, including acidic soils where aluminum (Al) toxicity is the major limiting factor. The relative Al sensitivity of barley highlights the need for a deeper understanding of early molecular responses in root tip (the primary target of Al toxicity) to develop Al-tolerant cultivars. Integrative N 6 -methyladenosine (m6A) modification, transcriptomic, and metabolomic analyses revealed that elevated auxin and jasmonic acid (JA) levels modulated Al-induced root growth inhibition by repressing genes involved in cell elongation and proliferation. Additionally, these pathways promoted pectin demethylation via up-regulation of genes encoding pectin methylesterases (PMEs). The up-regulation of citrate efflux transporter genes including Al-activated citrate transporter 1 (HvAACT1), and ATP-binding cassette (ABC) transporters like HvABCB25, facilitated Al exclusion and vacuolar sequestration. Enhanced activity within the phenylpropanoid pathway supported antioxidant defenses and internal chelation through the production of specific flavonoids and altered cell wall composition via lignin unit modulation. Notably, several Al-responsive genes, including HvABCB25 and transcription factors (TFs), exhibited m6A modification changes, with two microtubule associated protein 65 (MAP65) members displaying opposing regulatory patterns at both transcriptional and m6A levels, underscoring the crucial role of m6A modification in gene expression regulation. This comprehensive study provides valuable insights into the epitranscriptomic regulation of gene expression and metabolite accumulation in barley root tip under Al stress., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Foliar fungal diseases are a major limitation in organic naked barley (Hordeum vulgare L.) production. The lack of conventional fungicides in organic systems increases reliance on genetic resistance. We evaluated the severity of barley stripe rust (Puccinia striiformis f. sp. hordei Westend), leaf rust (Puccina hordei sp. hordei), spot blotch (Cochliobolus sativus, anamorph Bipolaris sorokiniana (S. Ito & Kurib.) Drechsler ex Dastur), and scald (Rhynchosporium commune Zaffarano, McDonald and Linde sp. nov) on a naked barley diversity panel of 350 genotypes grown in 13 environments to identify quantitative trait loci associated with disease resistance. Genome-wide association analyses across and within environments found 10 marker trait associations for barley stripe rust, four marker trait associations for leaf rust, one marker trait association for scald, and five marker trait associations for spot blotch. Structure analysis identified six Ward groups based on genotypic diversity. Resistance to susceptible allele ratios were high for stripe rust and spot blotch, moderate for leaf rust, and low for scald. Combined phenotypic analysis values for each disease overlayed by a principal component analysis found distinct resistance and susceptibility patterns for barley stripe rust and scald. Most significant marker trait associations were previously identified in the literature, providing confirmation and potential new sources of disease resistance for genetic improvement of naked barley germplasm., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Heveins are one of the most important groups of plant antimicrobial peptides. So far, various roles in plant growth and development and in response to biotic and abiotic stresses have reported for heveins. The present study aimed to identify and characterize the hevein genes in two-row and six-row cultivars of barley. In total, thirteen hevein genes were identified in the genome of two-row and six-row cultivars of barley. The identified heveins were identical in two-row and six-row cultivars of barley and showed a high similarity with heveins from other plant species. The hevein coding sequences produced open reading frames (ORFs) ranged from 342 to 1002 bp. Most of the identified hevein genes were intronless, and the others had only one intron. The hevein ORFs produced proteins ranged from 113 to 333 amino acids. Search for conserved functional domains showed CBD and LYZ domains in barley heveins. All barley heveins comprised extracellular signal peptides ranged from 19 to 35 amino acids. The phylogenetic analysis divided barley heveins into two groups. The promoter analysis showed regulatory elements with different frequencies between two-row and six-row cultivars. These cis-acting elements included elements related to growth and development, hormone response, and environmental stresses. The expression analysis showed high expression level of heveins in root and reproductive organs of both two-row and six-row cultivars. The expression analysis also showed that barley heveins is induced by both biotic and abiotic stresses. The results of antimicrobial activity prediction showed the highest antimicrobial activity in CBD domain of barley heveins. The findings of the current study can improve our knowledge about the role of hevein genes in plant and can be used for future studies., Competing Interests: Declarations. Competing Interests: The authors have declared that no competing interests exist. Ethical Approval: Not applicable. Consent to Participate: No human subjects or other vulnerable groups have been used for the study. Consent for Publication: Not applicable., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Drought is one of the most devastating abiotic stresses worldwide, which severely limits crop yield. Tibetan wild barley is a treasure trove of useful genes for crop improvement including drought tolerance. Here, we detected large-scale changes of gene expression in response to drought stress with a substantial difference among contrasting Tibetan barley genotypes XZ5 (drought-tolerant), XZ54 (drought-sensitive) and cv. Tadmor (drought-tolerant). Drought stress led to upregulations of 142 genes involved in transcription, metabolism, protein synthesis, stress defense, transport and signal transduction in XZ5, but those genes were down-regulated or unchanged in XZ54 and Tadmor. We identified and functionally characterized a novel multiple organellar RNA editing factors 8 (HvMORF8), which was up-regulated by drought stress in XZ5, but unchanged in XZ54 and Tadmor under drought stress. Phylogenetic analysis showed that orthologues of HvMORF8 can be traced back to the closest gymnosperm species such as Cycas micholitzii, implicating a potential evolutionary origin for MORF8 from a common ancestor in early seed plants. Virus-induced HvMORF8 silencing in XZ5 led to hypersensitivity to drought stress, demonstrating it is a positive regulator of drought tolerance in barley. RNA sequencing of BSMV:HvMORF8 and control plants reveals that silencing of HvMORF8 suppresses genes involved in osmolytes transport, cell wall modification and antioxidants, resulting in water metabolism disorder and overaccumulation of reactive oxygen species (ROS) under drought stress. Therefore, we propose HvMORF8-mediated regulatory drought tolerance mechanisms at transcriptomic level in XZ5, providing new insight into the genetic basis of plastid RNA editing function of HvMORF8 for barley drought tolerance., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Barley (Hordeum vulgare) is a climate-resilient crop widely cultivated in both highly productive and suboptimal agricultural systems, and its ability to adapt to multiple biotic and abiotic stresses has contributed significantly to food security. Greenbug is a destructive insect pest for global barley production, and new greenbug resistance genes are needed to overcome the challenges posed by diverse greenbug biotypes in fields. CI 2458 is a Chinese landrace exhibiting a unique resistance profile to a set of 14 greenbug biotypes, which suggests the presence of a new greenbug resistance gene in CI 2458. A recombinant inbred line population from the cross Weskan × CI 2458 was developed, evaluated for responses to greenbug biotype F, and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing. Linkage analysis revealed a single gene, designated Rsg4, conditioning greenbug resistance in CI 2458. Rsg4 was delimited to a 1.14 Mb interval between SNP markers S3H&#95;666512114 and S3H&#95;667651446 in the terminal region of chromosome arm 3HL, with genetic distances of 1.2 cM proximal to S3H&#95;667651446 and 1.1 cM distal to S3H&#95;666512114. Allelism tests confirmed that Rsg4 is a new greenbug resistance gene independent of Rsg1 and Rsg3, which reside in the same chromosome arm. Rsg4 differs from Rsg1 alleles and Rsg3 in its resistance to greenbug biotype TX1, one of the most widely virulent biotypes. The introgression of Rsg4 into locally adapted barley cultivars is of agronomic importance, and kompetitive allele-specific polymerase chain reaction (KASP) markers flanking Rsg4, KASP-Rsg336-1 and KASP-Rsg336-2, enable rapid pyramiding of Rsg4 with other resistance genes to develop durable greenbug-resistant cultivars., (Published 2024. This article is a U.S. Government work and is in the public domain in the USA. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Pangenomes are collections of annotated genome sequences of multiple individuals of a species 1 . The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants 2 . Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems., Competing Interests: Competing interests: K.B., C.D., M.E.J., S.M.K., Q.L., E.M., P.R.P., B.S., H.C.T., M.T.S.N., C.V. and M.W.R. are current or previous Carlsberg A/S employees. P.A.P. and D.V. are SECOBRA Recherches employees. The other authors declare no competing interests., (© 2024. The Author(s).)

In vitro plant embryogenesis and microcallus formation are systems which are required for plant regeneration, a process during which cell reprogramming and proliferation are critical. These systems offer many advantages in breeding programmes, such as doubled-haploid production, clonal propagation of selected genotypes, and recovery of successfully gene-edited or transformed plants. However, the low proportion of reprogrammed cells in many plant species makes these processes highly inefficient. Here we report a new strategy to improve in vitro plant cell reprogramming using small molecule inhibitors of mammalian leucine rich repeat kinase 2 (LRRK2), which are used in pharmaceutical applications for cell reprogramming, but never used in plants before. LRRK2 inhibitors increased in vitro embryo production in three different systems and species, microspore embryogenesis of oilseed rape and barley, and somatic embryogenesis in cork oak. These inhibitors also promoted plant cell reprogramming and proliferation in Arabidopsis protoplast cultures. The benzothiazole derivative JZ1.24, a representative compound of the tested molecules, modified the expression of the brassinosteroid (BR)-related genes BIN2, CPD, and BAS1, correlating with an activation of BR signaling. Additionally, the LRRK2 inhibitor JZ1.24 induced the expression of the embryogenesis marker gene SERK1-like. The results suggest that the use of small molecules from the pharmaceutical field could be extended to promote in vitro reprogramming of plant cells towards embryogenesis or microcallus formation in a wider range of plant species and in vitro systems. This technological innovation would help to develop new strategies to improve the efficiency of in vitro plant regeneration, a major bottleneck in plant breeding., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier GmbH.. All rights reserved.)

As a result of extensive selection, two polyploid grass weeds, Hordeum glaucum (northern barley grass; 2n = 4x = 28) and Bromus diandrus (ripgut brome; 2n = 8x = 56), have evolved resistance to glyphosate, in Australia. Previous research suggested amplification of 5-enolpyruvylshikimate-3-Phosphate synthase (EPSPS) gene confers resistance in these two weed species. The objective of this research was to investigate the genomic organization of the EPSPS gene in these two species through molecular cytogenetic analyses of fluorescence in situ hybridization (FISH) to understand possible mechanism of amplification of this gene. EPSPS copy number of H. glaucum and B. diandrus plants was estimated via quantitative polymerase chain reaction. The susceptible plants of both species had one copy of EPSPS, whereas the resistant plants of H. glaucum and B. diandrus had 14-17 and 16-32 copies, respectively. FISH analysis of glyphosate-susceptible (Hg-RWS) H. glaucum, revealed four faint signals of the EPSPS gene in two pairs of homologous chromosomes, at the telomeric region. The glyphosate-resistant H. glaucum (Hg-YP1) also showed amplification of EPSPS gene at telomeric regions in two pairs of homologous chromosomes, but the signals were brighter and appeared as cluster of EPSPS genes. Similarly, the glyphosate-susceptible B. diandrus (Bd-S) plants showed faint signals of EPSPS gene on two homologous chromosomes, at the telomeric position. However, samples of two glyphosate-resistant, B. diandrus, Bd-SA988 and Bd-Vic showed much brighter hybridization signals of EPSPS gene, located at the telomere on two homologous chromosomes, suggesting an increase in EPSPS gene copies at this position. Overall, unequal crossover during meiosis may have triggered the initial EPSPS gene duplication sparking the evolution of glyphosate resistance., (© 2024 Society for Experimental Biology and John Wiley & Sons Ltd.)

Introduction: Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known., Objectives: This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits., Methods: Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes., Results: There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA 4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed., Conclusion: Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

In root research, hydroponic plant cultivation is commonly used and soil experiments are rare. We investigated the response of 12-day-old barley roots, cultivated in soil-filled rhizotrons, to different soil water potentials (SWP) comparing a modern cultivar (cv. Scarlett) with a wild accession ICB181243 from Pakistan. Water potentials were quantified in soils with different relative water contents. Root anatomy was studied using histochemistry and microscopy. Suberin and lignin amounts were quantified by analytical chemistry. Transcriptomic changes were observed by RNA-sequencing. Compared with control with decreasing SWP, total root length decreased, the onset of endodermal suberization occurred much closer towards the root tips, amounts of suberin and lignin increased, and corresponding biosynthesis genes were upregulated in response to decreasing SWP. We conclude that decreasing water potentials enhanced root suberization and lignification, like osmotic stress experiments in hydroponic cultivation. However, in soil endodermal cell suberization was initiated very close towards the root tip, and root length as well as suberin amounts were about twofold higher compared with hydroponic cultivation., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Winter barley (Hordeum vulgare) production areas in the middle and lower reaches of the Yangtze River are severely threatened by barley yellow mosaic disease, which is caused by Barley yellow mosaic virus and Barley mild mosaic virus. Improving barley disease resistance in breeding programs requires knowledge of genetic loci in germplasm resources. In this study, bulked segregant analysis (BSA) identified a novel major quantitative trait loci (QTL) QRym.ZN1-7H for barley yellow mosaic disease resistance in an F 2 population derived from the cross between "Nongke 1-6" (H. vulgare) and "Zaoshu 3" (H. vulgare). This QTL, originating from bulbous barley (Hordeum bulbosum), demonstrated stability and was further validated in another F 2 population derived from the cross between "Nongke 2-6" (H. vulgare) and "Supi 1" (H. vulgare). QRym.ZN1-7H accounted for 10.61%-19.34% of the phenotypic variance. The QTL was further fine mapped to the 14- to 39-Mb interval on barley chromosome 7H. Transcriptome analysis identified 53 and 35 differentially expressed genes in roots and leaves (at QRym.ZN1-7H locus), respectively, with nine genes differentially expressing in both tissues. HORVU.MOREX.r3.7HG0650990, a member of the disease resistance protein family (NBS-LRR class), is the most likely candidate gene for QRym.ZN1-7H. Enrichment analysis indicated that QRym.ZN1-7H may be involved in signal transduction in plant innate immune response. This study laid a foundation for barley disease resistance breeding., (© 2025 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)