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At least 19 recordsLinked to original sources
PubMed2025

A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum.

Wild plants can contribute valuable genes to their domesticated relatives1. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley's closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes2. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.

Hordeum↗
PubMedDate not supplied

Collection of Hordeum spontaneum C. Koch emend. Bacht. from Southwest Asia studied in the neighborhood of Moscow.

Wild barley Hordeum spontaneum C. emend. is of interest from several aspects (Bakhteev, 1974). It is not only a very near relative of cultivated barley H. sativum Jessen, but also a potentially very promising donor for use in hybridization. With these facts in mind and, in particular, recalling N. I. Vavilov's remarks [on the occasion of publication of R. E. Regel's article "on the origin of cultivated barleys" (1917)], appropriate investigations were started. In the present case 77 specimens of H. spontaneum, collected by S. Sakamoto (Japan) in the countries of South West Asia, were studied with reference to several morphological and biological features including winter hardiness.

Adaptation, Physiological↗
PubMed2026

Cloning, Transformation, and Reporter Gene Analysis of the SalT Promoter in Barley (Hordeum vulgare).

Constitutive gene expression can lead to pleiotropic effects. Therefore, spatial or temporal restriction of expression via specific promoters provides a more targeted approach. This study aimed to clone the SalT promoter and analyze its activity in transgenic barley using GFP and GUS reporter genes. The T-DNA constructs carrying the SalT promoter were introduced into barley cv. Golden Promise, and transgenic plants were confirmed through PCR, hygromycin selection, and Southern hybridization. Both constructs, SalT-GFP and SalT-GUS, were transformed in barley cv. Golden Promise. Here, we characterized the expression pattern of the SalT promoter in barley and utilized it to drive the expression of reporter genes GFP and GUS. The SalT promoter was isolated from rice genomic DNA, cloned into the pNos-AB-M vector, and confirmed through PCR and restriction analysis. Subsequently, GFP and GUS genes were cloned under the SalT promoter in the same vector. The constructs were then subcloned into the p6U vector for plant expression. Agrobacterium-mediated genetic transformation of barley cultivar "Golden Promise" was conducted, resulting in successful integration of the transgenes. Callus induction, regeneration, and root formation efficiency were assessed, demonstrating the potential of the SalT promoter to drive gene expression during various stages of plant development. Molecular analyses, including PCR and Southern hybridization, confirmed the presence and integration of transgenes in the barley genome. Furthermore, GFP fluorescence and GUS staining analyses revealed strong expression of the respective genes under control of the SalT promoter in different plant tissues. This study provides insights into the application of the SalT promoter for genetic manipulation and functional characterization in barley, offering opportunities for crop improvement and biotechnological applications.

Hordeum↗
PubMed1978

Analysis of plant genomes. III. Denaturation and reassociation properties of cryptic satellite DNAs in barley (Hordeum vulgare) and wheat (Triticum aestivum).

A cryptic satellite fraction was isolated from barley and wheat by preparatory ultracentrifugation of total DNA in Ag+-Cs2SO4 density gradients and was characterized by studying its denaturation-reassociation properties. Wheat satellite DNA underwent thermal denaturation as a single component with a Tm of 81 degrees C while barley satellite DNA consisted of one major (Tm = 82.5 degrees C) and one minor (Tm = 91 degrees C) component. When the barley and wheat satellites were reassociated and then melted, the Tm values were found to be 6--7 degrees C lower than those of the corresponding native DNA preparations. Examination of the C0t curves of these two satellite DNAs revealed the presence of a major, fast reassociating and a minor, slow reassociating fraction. The fast reassociating DNA fraction of barley was found to have a complexity of 9.7 . 10(5) daltons while that of wheat satellite was 5.8 . 10(5) daltons. Since these satellites reassociated with about 4--5% base mismatching, as judged by their deltsTm (6--7 degrees C), they each appear to consist of rather similar base sequences.

Centrifugation, Density Gradient↗
PubMed1978

The plastid membranes of barley (Hordeum vulgare). Light-induced appearance of mRNA coding for the apoprotein of the light-harvesting chlorophyll a/b protein.

Illumination of dark-grown barley plants induces a massive insertion of the light-harvesting chlorophyll a/b protein into the developing thylakoid membrane. In addition to the onset of chlorophyll synthesis, light induces specifically the appearance of a prominent mRNA species which codes for a polypeptide of Mr 29500. This component was identified as a precursor of the apoprotein of the light-harvesting chlorophyll a/b protein. The precursor has an Mr larger than the authentic protein by approximately 4000. Studies of the chlorophyll-b-less mutant chlorina f2 of barley offer the first clue to the mechanism which controls the light-dependent mRNA formation. The induction of the mRNA coding for the aproprotein of the light-harvesting chlorophyll a/b protein does not seem to be linked directly to the assembly process of the light-harvesting structure and does not require chlorophyll b. It is proposed that light exerts its influence on the mRNA formation by a reaction which is different from the phototransformation of protochlorophyll(ide) to chlorophyll(ide).

Cell Membrane↗
PubMed1978

A modified Giemsa C-banding technique for Hordeum species.

A Giemsa C-banding technique with a hot 1 N HCl hydrolysis step has been developed for barley chromosomes. This step makes it easy to obtain well separated C-banded chromosomes. To compare this technique with other C-banding techniques, chromosomes of H. vulgare cv. York were stained by both this technique and a modification of the technique of Kimber et al. (1976). With respect to centromeric and intercalary bands, both techniques produce a similar banding pattern, but telomeric bands observed by the modified technique of Kimber et al. (1976) were not detected by our procedure. This indicates that telomeric heterochromatin may be different chemically and/or structurally from the centromeric and intercalary heterochromatin and its appearance dependent upon the C-banding technique. The procedure described provides a relatively rapid technique for C-banding of barley chromosomes.

Azure Stains↗
PubMed1978

[High-yield isolation of chloroplast DNA from Hordeum vulcare barley protoplasts].

A fraction of intact chloroplasts free of other cell components in isolated from barley leaf chloroplasts. Instead of mechanical desintegration of plant tissue, the method described includes the cellulysine treatment, thus increasing the yeild of chloroplast DNA. The mean content of DNA per barley chloroplast is found to be 1.10(-4) g. Base composition of barley chloroplast DNA is 39.8 mol.% of G+C. The treatment of chloroplast DNA with restriction endonuclease EcoRI results in the appearance of 17-19 bands under agarose gel electrophoresis.

Cellulose↗
PubMedDate not supplied

[Phytochrome system and synthesis of lipoquinones in the plastids of etiolated hordeum seedlings].

Short pulses of red light induce in etiolated barley seedlings an enhanced synthesis of plastidic benzoquinones and vitamin K1, which can be reverted by subsequent irradiation with short pulses of far-red. As compared to the dark there is more formation of plastoquinone-9 than alpha-tocopherol. The enhanced formation of vitamin K1 is coupled with a concomitant decrease in the level of the second naphthoquinone vitamin "K". The data show that active phytochrome Pfr, also in its ground state, induces the light triggered lipoquinone synthesis which is connected to thylakoid formation. The red light induction of enhanced plastoquinone-9 synthesis cannot be fully reverted by subsequent far-red and seems to be a very fast phytochrome response.

Chlorophyll↗
PubMedDate not supplied

[The influence of phytochrome on the formation of individual carotenoids in etiolated hordeum seedlings].

Short time red pulses, given 6 times for 5 min within 36 h, induce in etiolated barley seedlings an enhanced synthesis of the main chloroplast carotenoids beta-carotene, violaxanthine, lutein and neoxanthine. The level of antheraxanthine and zeaxanthine decreases by red light treatment. These red light effects are reverted by subsequent short time far-red pulses. The results show that the white light induced change in the accumulation rate of individual carotenoids is initiated and regulated by active phytochrome Pfr. In the case of neoxanthin and zeaxanthin the red light effects cannot be fully reverted by far-red; this points to a very fast phytochrome reaction.

Carotenoids↗
PubMed2025

On the origin of the late-flowering ppd-H1 allele in barley.

To breed for climate resilient crops, an understanding of the genetic and environmental factors influencing adaptation is critical. Barley provides a model species to study adaptation to climate change. Here we present a detailed analysis of genetic variation at a major photoperiod response locus and relate this to the domestication history and dispersal of barley. The PPD-H1 locus (a PSEUDO-RESPONSE REGULATOR 7) promotes flowering under long-day conditions, and a natural mutation at this locus resulted in a recessive, late-flowering ppd-H1 allele. This mutation proved beneficial in high-latitude environments such as Northern Europe, where it allows extended vegetative growth during long spring days. We infer the origin of the mutated late-flowering ppd-H1 allele by re-sequencing a large geo-referenced collection of 942 Hordeum spontaneum, 5 Hordeum agriocrithon and 1110 domesticated (Hordeum vulgare) barleys. We demonstrate that the late-flowering phenotype originated from Desert-type wild barley in the Southern Levant and present evidence suggesting a post-domestication origin of the mutated ppd-H1 allele.

Hordeum↗
PubMed2026

Genomic and evolutionary analysis reveals dynamic variations of MKK3 gene, a key regulator for seed dormancy in barley.

Barley (Hordeum vulgare L.) is an important crop in the world, and its seed dormancy is primarily controlled by a mitogen-activated protein kinase kinase 3 (MKK3) gene. Although kinase activity of MKK3 and its roles in barley post-domestication have been widely studied, the pre-domestication evolution of MKK3 and the spread of nondormant alleles among global barley varieties remain largely unexplored. In this study, we analyzed MKK3 sequences in barley and its wild progenitor (Hordeum spontaneum K. Koch) and identified two polymorphic miniature inverted-repeat transposable elements (MITEs). Comparative analyses indicated that the insertions/excision of the MITEs predated the current estimates of barley domestication. Examination of the barley pangenomes coupled with droplet digital polymerase chain reaction revealed extensive copy number variation of MKK3 and suggested that transposons likely contributed to tandem amplification of the MKK3 gene on chromosome 5H. Additionally, approximately 1-Kb MKK3 sequences were found on chromosomes 1H and 6H. Further analysis indicated that these short MKK3 sequences were captured by a CACTA transposon that also contained fragments from four other expressed genes. The acquisition of MKK3 was estimated to be between 1.9 and 2.5 million years ago. Together, these findings illuminate the dynamic pre-domestication evolution of the MKK3 gene and identify three divergent MKK3 haplotype groups including a unique lineage predominant in Ethiopian germplasm. This study highlights the contribution of transposons to structural diversification and evolutionary differentiation of the MKK3 locus and provides helpful information for understanding the complex history of MKK3 gene in barley and also for improving preharvest sprouting tolerant varieties under distinct natural conditions.

Hordeum↗
PubMed2026

Finlay-Wilkinson random regression for yield and yield stability prediction in cereals.

Year-to-year climate variability poses a challenge for agriculture by increasing crop yield variability; therefore, there is a need to identify genotypes that can withstand these fluctuations. With the right selection criteria, genotypes with yield stability across variable environmental conditions can be selected. Methods such as Finlay-Wilkinson random regression (FWRR) may allow us to use sparse datasets-common in plant breeding pipelines-and incorporate genomic data to leverage phenotypic information from related genotypes to predict yield stability. Our objective was to examine how the number of environments and the variance among those environments affect stability predictions. We also integrate FWRR as a genomic prediction tool for characterizing yield stability, comparing it to the traditional genomic prediction models as a reference. We used three datasets: one highly unbalanced dataset for oats (Avena sativa L.) and two completely balanced datasets with different numbers of environments for barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.). We fit standard Finlay-Wilkinson (FW) and FWRR models to estimate grain yield and stability under various scenarios. We found that the estimated stability values obtained were similar using balanced datasets for FW or FWRR. FWRR also achieved moderate predictive ability for stability using unbalanced datasets under 10-fold cross-validation (CV1) with new genotypes. In terms of environmental representation, selecting the right set of environments for inclusion in the model was more important than adding more environments. Our results suggest the possibility of using FWRR to select stable genotypes earlier in line development, as well as to design resource-efficient stability-testing schemes.

Hordeum↗
PubMed2026

Discovering common and population-specific QTLs for leaf rust resistance in different Barley populations.

Multi-population GWAS lead to identification of common and population-specific QTLs for leaf rust resistance in barley. Genome-wide association studies (GWAS) are a powerful tool for detecting genetic markers associated with traits of interest. However, these studies are typically restricted to a single population, and transferability of identified marker effects across populations is challenged by population differences in linkage, allele frequencies, epistatic effects, and environmental context. When comparing GWAS results between populations, a lack of overlapping signals is often interpreted as a lack of common quantitative trait loci (QTLs), although such discrepancies may result from differences in statistical power to detect signals. In barley (Hordeum vulgare L.), where genetic leaf rust resistance is rapidly overcome by evolving pathogens, identification of cross-population robust and potentially transferable resistance loci is a key task. Here, we present a mixed model approach for multi-population GWAS that estimates correlated marker effects in multiple populations and use this to test for significant effects across and within populations. Applying this model to four barley breeding populations revealed both common and population-specific QTL effects for leaf rust resistance, including loci colocalizing with known Rph genes and novel regions with plausible candidate genes. Multi-population GWAS increased power, revealing signals not detected by GWAS within populations. We categorized the reported QTLs into three groups based on marker-associated allele effects: (1) consistent effect direction across populations, (2) differing effect direction across populations, and (3) present in a single population. The study highlights the transferability and limitations of leaf rust resistance QTLs across different barley populations and provides a general statistical framework to support robust marker-assisted selection across populations.

Quantitative Trait Loci↗
PubMed1976

Multi-temperature effects on Hill reaction activity of barley chloroplasts.

1. The relationship between temperature and Hill reaction activity has been investigated in chloroplasts isolated from barley (Hordeum vulgare L. cv. Abyssinian). 2. An Arrhenius plot of the photoreduction of 2,6-dichlorophenolindophenol (DCIP) showed no change in slope over the temperature range 2--38degreesC. The apparent Arrhenius activation energy (Ea) for the reaction was 48.1 kJ/mol. 3. In the presence of an uncoupler of photophosphorylation, methylamine, the Ea for DCIP photoreduction went through a series of changes as the temperature was increased. Changes were found at 9, 20, 29 and 36degreesC. The Ea was highest below 9degreesC at 63.7 kJ/mol. Between 9 and 20degreesC the Ea decreased to 40.4 kJ/mol and again to 20.2 kJ/mol between 20 and 29degreesC. Between 29 and 36degreesC there was no further increase in activity with increasing temperature. The temperature-induced changes at 9, 20 and 29degreesC were reversible. At temperatures above 36degreesC (2 min) a thermal and largely irreversible inactivation of the Hill reaction occurred. 4. Temperature-induced changes in Ea were also found when ferricyanide was substituted for DCIP or gramicidin D for methylamine. The addition of an uncoupler of photophosphorylation was not required to demonstrate temperature-induced changes in DCIP photoreduction following the exposure of the chloroplasts to a low concentration of cations. 5. The photoreduction of the lipophilic acceptor, oxidized 2, 3, 5, 6-tetramethyl-p-phenylenediamine, also showed changes in Ea in the absence of an uncoupler. 6. The temperature-induced changes in Hill activity at 9 and 29degreesC coincided with temperature-induced changes in the fluidity of chloroplast thylakoid membranes as detected by measurements of electron spin resonance spectra. It is suggested that the temperature-induced changes in the properties and activity of chloroplast membranes are part of a control mechanism for regulation of chloroplast development and photosynthesis by temperature.

2,6-Dichloroindophenol↗
PubMed2026

Decoding the molecular basis of blue grain color codominance in Qingke: Integrative analysis of RNA-seq, DNA methylation, and miRNA-seq.

The grains on single spike of the F1 generation from the cross between blue- and white-grained Qingke (Hordeum vulgare L. var. nudum Hook. f.) are randomly distributed in blue and white colors. This study integrated data from RNA-seq, DNA methylation, and miRNA-seq to analyze this trait. The results showed that the HvF3'5'H gene is likely central to the development of this codominant phenotype. Through cross-validation of three omics approaches, it was found that the HvMYB gene targeted by miR858-z, as well as the WRKY24 and At3g44326 genes targeted by novel-m0152-5p, novel-m0153-5p, and novel-m0154-5p, are correlated with DNA methylation. qRT-PCR analysis confirmed that the four aforementioned genes exhibited variety-specific and developmental stage-specific expression patterns. This study dissects the regulatory network underlying the codominant blue and white grain color divergence on a single Qingke spike from a multi-omics perspective.

DNA Methylation↗
PubMed1977

Subcellular distribution of calcium within root meristem cells.

The barley root (Hordeum vulgare) of 3-day old seedlings were treated with potassium oxalate to study the distribution of calcium among plant cell organelles. The best results were obtained by previously treating the root with 10(-3) M CaCl2 followed by an incubation for 20 min with potassium oxalate. The unstained sections for electronmicroscopy showed the deposits of calcium oxalate as a granular or a dark layer on the mitochondria, endoplasmic reticulum and the nucleare envelope. Within all the cells, dark bodies, like vacuoles, were noticed.

Calcium↗