Cultivated Barley Research Articles

The potential of wild barley (Hordeum vulgare subsp. spontaneum C. Koch.) to improve early shoot and root traits of cultivated barley

The potential of wild barley (Hordeum vulgare subsp. spontaneum C. Koch.) to improve early shoot and root traits of cultivated barley

Halotolerant phosphate solubilizing bacteria isolated from arid area in Tunisia improve P status and photosynthetic activity of cultivated barley under P shortage

Forty-seven (47) bacterial strains were isolated from soil of Gabes (an arid region in southern Tunisia) and were screened for their ability to produce Indole-3-Acetic Acid (IAA) and to solubilize phosphate (P). The characterization and molecular identification of the most successful P-solubilizing bacteria (PSB) were then carried out. When grown on suitable artificial media, the most salt-tolerant strains also showed the highest P solubilization capacity (up to 126.8 μg ml−1 of released phosphorus after 7 day incubation) and the strongest ability to produce IAA (up to 101.86 μg ml−1 after 3 day incubation). Overall, bacterial isolates displayed a different tolerance to varying pH, temperatures, and salinity. The molecular identification revealed that 11 strains belonged to three genera: Bacillus, Pseudomonas and Mesorhizobium. Inoculation of barley with P-solubilizing bacteria under tricalcium phosphate-induced P shortage significantly improved plant growth (biomass, shoot height, and root length) together with increasing total chlorophyll contents and photosynthetic activity. This was concomitant with (i) higher P uptake and translocation and (ii) increased phosphorus absorption and utilization efficiencies (PAE and PUE), which is indicative of a better plant P nutrition under P scarcity. Taken together, we provide strong arguments showing that bacteria native to extreme environments display PSB potential making them promising candidates to mitigate low Pi availability for crop plants.

Design of potential Ilp markers for Hordeum vulgare and H. marinum Atg2, Atg7, Atg8 genes

Aim. Design of potential intron length polymorphism markers for ATG2, ATG7, ATG8 genes. Methods. Use of classical bioinformatics methods to search for loci encoding ATG2, ATG7, ATG8 in the Hordeum marinum genome based on homology with cultivated barley genes; analysis of exon-intron structure of genes, design of ILP markers. Results. The sequences of ATG2, ATG7, ATG8 genes in H. marinum were determined. Analyzed differences in the exon-intron structure of the ATG2, ATG7, ATG8 loci in cultivated (H. vulgare) and salt-resistant wild barley (H. marinum). 25 potential ILP markers were designed for introns that showed significant interspecies length polymorphism: 13 for ATG2, 6 for ATG7, 3 for ATG8A, 2 for ATG8B and 1 for ATG8D. Conclusions. Based on gene structure comparative analysis of the autophagosome formation proteins ATG2, ATG7, ATG8 of cultivated H. vulgare and salt-tolerasnt H. marinum, a number of introns are recommended for further use as a potential source of ILP markers for the study of interspecies genetic differentiation of cereals.

LncRNA cis- and trans-regulation provides new insight into drought stress responses in wild barley.

Drought is one of the most common abiotic stresses that affect barley productivity. Long noncoding RNA (lncRNA) has been reported to be widely involved in abiotic stress, however, its function in the drought stress response in wild barley remains unclear. In this study, RNA sequencing was performed to identify differentially expressed lncRNAs (DElncRNA) among two wild barley and two cultivated barley genotypes. Then, the cis-regulatory networks were according to the chromosome position and the expression level correction. The GO annotation indicates that these cis-target genes are mainly involved in "ion transport transporter activity" and "metal ion transport transporter activity". Through weighted gene co-expression network analysis (WGCNA), 10 drought-related modules were identified to contract trans-regulatory networks. The KEGG annotation demonstrated that these trans-target genes were enriched for photosynthetic physiology, brassinosteroid biosynthesis, and flavonoid metabolism. In addition, we constructed the lncRNA-mediated ceRNA regulatory network by predicting the microRNA response elements (MREs). Furthermore, the expressions of lncRNAs were verified by RT-qPCR. Functional verification of a candidate lncRNA, MSTRG.32128, demonstrated its positive role in drought response and root growth and development regulation. Hormone content analysis provided insights into the regulatory mechanisms of MSTRG.32128 in root development, revealing its involvement in auxin and ethylene signal transduction pathways. These findings advance our understanding of lncRNA-mediated regulatory mechanisms in barley under drought stress. Our results will provide new insights into the functions of lncRNAs in barley responding to drought stress.

Differential reduction in cadmium accumulation in barley under cadmium-salt co-exposure involves specific HMA genes and antioxidative responses

Salinity and heavy metal accumulation adversely affect agricultural productivity and environmental sustainability. Little information exists about the combinatory effect of various stresses on plants, but it is assumed that stress interaction may trigger a specific response. Here, we assessed the combinatory effect of salinity and cadmium on various physiological and molecular traits in two cultivated barley genotypes with contrasting salinity tolerance; Rihane (RH, salt tolerant) and Lemsi (LM, salt sensitive). Studied genotypes were hydroponically exposed to CdCl2 (30 µM), NaCl (300 mM) or the combined Cd-NaCl stresses for 15 days. Salinity and to a lesser degree Cd-NaCl stress significantly reduced growth, leaf water content, chlorophyll pigments, and K uptake, and increased Na and Cl contents for both genotypes, with LM being more affected than RH. Cd content in roots was higher than in shoots for both genotypes either under Cd alone or when combined with NaCl. Interestingly, NaCl addition reduced Cd accumulation in both roots and shoots of the two barley genotypes, suggesting that the interaction of NaCl and Cd on their uptake and accumulation is antagonistic. The tolerant genotype (RH) accumulated lower Cd levels in shoots and roots than the salt-sensitive one (LM). Cd-NaCl stress significantly lowered H2O2 and MDA contents relative to NaCl treatment alone. The activity of several antioxidant enzymes was essentially higher in RH than in LM, under the different stresses. These responses were in concomitant with an enhanced expression of specific Heavy Metal ATPases (HvHMA) genes, mainly in RH, which can partially, explain the reduced Cd accumulation in this genotype. Overall, these findings suggest the possibility of cultivating salt-tolerant barley genotypes in saline soils slightly contaminated with Cd, whereas barley sensitive genotypes could be assessed for phytoremediation purposes.

Possibilities of using the tetraploid interspecific hybrid <i>Hordeum bulbosum</i> L. × <i>Hordeum vulgare</i> L. in obtaining new recombinant barley lines

Background. Hordeum bulbosum L. is the only wild species of the genus Hordeum, the gene pool of which is successfully used in introgressive hybridization to increase the genetic diversity of H. vulgare L. When creating introgression forms based on hybrids of H. vulgare with H. bulbosum, it is necessary to take into consideration the ploidy of the parent species, and their genetic features that determine the intensity of the process of H. bulbosum chromosomes elimination in embryogenesis. The purpose of our investigation was to study the features associated with the elimination of bulbous barley chromosomes in embryos obtained in various combinations of crosses involving the tetraploid hybrid H. bulbosum with H. vulgare for its effective use in obtaining introgression lines of H. vulgare. Material and methods. The analysis was performed on 9-15 days old embryos obtained in crosses of the tetraploid hybrid F2 (H. bulbosum A17 (4x) × H. vulgare ‘Borwina’ (4x)) (HbHbHvHv) with ‘Igri’ (2x) and ‘Borwina’ (2x) barley varieties, with H. bulbosum A17 (4x), as well as during its self-pollination. The chromosomal composition of embryos of different ages was analyzed on squashed embryo slides using genomic in situ hybridization (GISH). Results. Among the 11-15 days old embryos obtained from self-pollination of the hybrid, approximately half of the studied ones were mixoploids, while in other embryos the majority of cells contained only the genomic material of H. vulgare. The elimination process was very intensive in crosses of the hybrid with the barley varieties ‘Igri’ (2x) and ‘Borwina’ (2x), and by day 10-11 after pollination cells containing only the genomic material of H. vulgare predominated in all embryos, regardless of the direction of crossing and the variety used. Hybrid embryos with a stable chromosomal composition resulted from a cross of a tetraploid hybrid with H. bulbosum A17 (4x). Embryos with recombinant H. vulgare chromosomes carrying alien genetic material of bulbous barley were identified in all types of crosses. Conclusion. The most efficient way for the mass production of introgression lines of cultivated barley varieties based on the partially fertile hybrid F2 (H. bulbosum A17 (4x) × H. vulgare ‘Borwina’ (4x)), is the crossing with varieties of H. vulgare (2x). The progeny from such crosses will contain only cultivated barley plants, among which it is possible to identify forms with the introgression of H. bulbosum and use already the first generation from their self-pollination for selecting H. vulgare lines carrying the genetic material of bulbous barley in both homologs.

A GDSL-motif Esterase/Lipase Affects Wax and Cutin Deposition and Controls Hull-Caryopsis Attachment in Barley.

The cuticle covering aerial organs of land plants is well known to protect against desiccation. Cuticles also play diverse and specialized functions, including organ separation, depending on plant and tissue. Barley shows a distinctive cuticular wax bloom enriched in β-diketones on leaf sheaths, stem nodes and internodes and inflorescences. Barley also develops a sticky surface on the outer pericarp layer of its grain fruit leading to strongly adhered hulls, 'covered grain', important for embryo protection and seed dispersal. While the transcription factor-encoding gene HvNUDUM (HvNUD) appears essential for adherent hulls, little is understood about how the pericarp cuticle changes during adhesion or whether changes in pericarp cuticles contribute to another phenotype where hulls partially shed, called 'skinning'. To that end, we screened barley lines for hull adhesion defects, focussing on the Eceriferum (= waxless, cer) mutants. Here, we show that the cer-xd allele causes defective wax blooms and compromised hull adhesion, and results from a mutation removing the last 10 amino acids of the GDS(L) [Gly, Asp, Ser, (Leu)]-motif esterase/lipase HvGDSL1. We used severe and moderate HvGDSL1 alleles to show that complete HvGDSL1 function is essential for leaf blade cuticular integrity, wax bloom deposition over inflorescences and leaf sheaths and pericarp cuticular ridge formation. Expression data suggest that HvGDSL1 may regulate hull adhesion independently of HvNUD. We found high conservation of HvGDSL1 among barley germplasm, so variation in HvGDSL1 unlikely leads to grain skinning in cultivated barley. Taken together, we reveal a single locus which controls adaptive cuticular properties across different organs in barley.

The transcriptome landscape of developing barley seeds.

Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.

The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome.

Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical-chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops.

The Difference in Shoot Metabolite Profiles of a Wild and a Cultivated Barley Genotype in Response to Four Nitrogen Forms

Plants can utilize different N forms, including organic and inorganic N resources, and show great differences in the utilization efficiency of each N form among species and genotypes within a species. Previously, we found that the Tibetan wild barley genotype (XZ16) was better in the utilization of organic nitrogen in comparison with the cultivated barley genotype (Hua30). In this study, the metabolite profiles of the two barley genotypes were comprehensively compared in their response to four N forms, including nitrate (NO3−), ammonium (NH4+), urea, and glycine. The macro and micro nutrient concentrations in shoots were mostly found to be higher in the nitrate and urea treatments than in ammonium and glycine in both the genotypes. XZ16 had higher concentrations of nutrient ions in the glycine treatment, but Hua30 accumulated more nutrients in the ammonium treatment. Among a total of 163 differentially regulated metabolites, the highest up-regulation and highest down-regulation values were found in XZ16 in the glycine and urea treatments, respectively. Some important metabolites, such as proline, glutamine, serine, asparagine, L-homoserine, aspartic acid, putrescine, ornithine, and 4-aminobutyrate, were up-regulated in the glycine treatment in both the genotypes with a higher fold change in XZ16 than that in Hua30. Similarly, fructose-6-PO4, aconitic acid, and isocitrate were only up-regulated in XZ16 in the glycine treatment. Here, we concluded that the genotype XZ16 exhibited a better response to the glycine treatment, while Hua30 showed a better response to the NH4+ treatment, which is attributed to the better utilization of glycine-N and NH4+-N, respectively.

Evaluation of a plant salinity-stress B2-protein gene in wild barley (Hordeum spontaneum) and cultivated barley (Hordeum vulgare L.)

Dehydration-inducing conditions are major factors affecting plants geographic distribution worldwide. Salinity is a major factor affecting crop productivity and survival. Advances in molecular studies enabled scientists to explore salinity and genetic factors that control and contribute to salinity tolerance in plants. We previously identified clones from barley substractive library “from plants growing under high salinity regime” that was similar to previously identified B2-protein gene. In the current study, the relative expression of the B2-protein gene is assessed in wild barley (Hordeum spontaneum) and cultivated barley (Hordeum vulgare L) varieties. Our results indicated that the relative expression of the B2 gene displayed 8.00, 10.34, 12.12 and 11.37 folds at 100 mM NaCl and 4.28, 3.62, 2.70 and 1.58 folds at 200 mM NaCl compared to the non-salt stressed control in wild barley, Giza 129, Giza 132 and Giza 123, respectively. The full-length sequence of the B2 gene (1449 bp) was successfully assembled “accession number MT249004” from wild barley. Comparison studies of the wild barley B2 sequence to its published homologue in cultivated barley indicated the presence of an extra 23 bp long sequence, but its deduced amino acids sequence is five a.a. residues shorter (354 vs. 359 a.a.) with 96.1 % identity. Computational analysis at the protein level indicated the presence of differences in the physicochemical properties between the two proteins. Also, the subcellular localization prediction of the protein revealed the detection of the former protein in the nucleus and the later in the chloroplast. However, the protein modelling and structure prediction do not reveal differences since around 60 % of the protein is disordered. On the other hand, B2-protein interaction predicted networks composed of proteins directly or indirectly associated with the stress responses. In conclusion, the B2- protein gene is a promising candidate for dehydration stress tolerance.

Dehydrin genes allelic variations in some genotypes of local wild and cultivated barley (Hordeum L.) in Syria

Dehydrin genes allelic variations in some genotypes of local wild and cultivated barley (Hordeum L.) in Syria

Genomic resources for a historical collection of cultivated two-row European spring barley genotypes

Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.

Integrated transcriptome and metabolome analysis reveals the divergent evolution of low-P tolerance in cultivated and Tibetan wild barley

Most arable lands in the world are quite low in available phosphorus (P), becoming an important factor restricting crop yield. However, the genotypic difference of low-P tolerance in barley is rarely understood at molecular level. In this study, low-P responses of three barley genotypes were explored by physiological, transcriptomic and metabolomic analysis. The results showed that low-P-tolerant genotypes Zaoaibai (cultivar) and X130 (Tibetan wild accession) showed less growth inhibition compared to low-P-sensitive Salooni2 under low-P stress. Omics analysis showed that many genes involved in Pi acquisition and transport were more upregulated in Zaoaibai, which had relatively higher concentrations of shoot P and glucose-6-phosphate, indicating that enhancement of P acquisition, P translocation and P availability contributed to low-P tolerance in Zaoaibai. On the other hand, the genes and metabolites involved in biosynthesis of Pi-free lipids were highly expressed and more abundant in X130, suggesting that remodeling of membrane lipids by replacing phospholipids with Pi-free lipids is an important strategy for X130 in its adaptation to low-P stress. The divergent evolution of low-P tolerance in Zaoaibai and X130 could be driven by diverse ecological factors in Eastern China (low soil P) and Tibet Plateau (high soil P and low temperature), respectively.

Study of wild barley species in Southern Dagestan conditions

Wild-growing barley is widely distributed in Dagestan from the coastal lowland to the subalpine zone and is a good fodder and soil-strengthening plant. The study of wild-growing species of barley in the aspect: distribution, systematic diversity, significance are devoted to the works of prominent scientists (Vavilov, Grossheim, Lvov, Kobylyansky, Omarov, Zhukovsky, Tsvelev), which, in the context of the distribution and use of species of the genus Barley in Dagestan, are summarized by Omarov D.S. [6] Wild species are of interest as carriers of valuable breeding traits and can be included in breeding and genetic programs for the possible introgression of valuable genes into the cultivated barley genotype in order to create new promising varieties with a high adaptive potential. At the Dagestan Experimental Station of VIR in 2020-2022 a field study of 114 samples of wild-growing barley species from the VIR collection was carried out to identify the breeding value of these "wild" forms of plants. The sample included representatives of five species: H.spontaneum, H.bulbosum, H.murinum, H.hrasdanicum, and H.glaucum of different ecological and geographical origin. The samples were evaluated for resistance to barley fungal diseases widespread in the region (powdery mildew, dwarf and yellow rust). Interspecific and intraspecific differentiation in terms of resistance to these biotic factors is shown. Resistant forms recommended as sources and susceptible forms as testers are noted.

Phenotypic characterization and seed viability test in ex-situ conserved Ethiopian cultivated barley (Hordeum vulgare L.) landraces

BackgroundNowadays, most of the Ethiopian barley landraces had been lost from farmer’s field and exclusively found ex-situ conserved at the Ethiopian Biodiversity Institute (EBI). Those ex-situ conserved are generally believed to be representative of the original population and possess high genetic diversity and important unique genes that are useful for tackling the various biotic and abiotic stresses in the face of the current climate change. Thus, this research was aimed at testing the performance of 150 ex-situ conserved landraces that had been collected from Arsi and Bale highlands, Southeastern Ethiopia. The landraces were tested at multiple test locations over two years (2021 and 2022).ResultsAll the tested landraces showed a good germination rate regardless of their long storage duration. In addition, performance of all the qualitative traits revealed a varying frequency for each character state. For example, most of the accessions (51.3%) had six kernel row numbers (KRN). All the remaining accessions had two rows (28.7%) and irregular KRN with variable lateral florets (20%). Likewise, some of the quantitative traits considered showed a significant variation among the landraces. However, there observed a significant variation for all the interaction effects in some of the traits considered signifying the importance of considering environment effects while targeting genetic selection and improvement of ex-situ conserved germplasms. The phenotypic coefficients of variation (PCV) were considerably high to medium in most of the traits considered including seed yield per hectare (SYPH) but with no associated higher genotypic coefficients of variation (GCV). Moreover, all the traits showed a far greater phenotypic coefficient of variation (PCV) to that of genotypic coefficients of variation (GCV) once again suggesting the pronounced effect of environmental factors to the variation. This was far supported by the significantly higher absolute magnitudes in phenotypic correlation compared to their corresponding genotypic correlation in most of the traits. Low estimates of heritability and genetic advance observed in all the traits considered except seed yield per hectare indicate importance of the trait for selection in Ethiopian barley improvement programs. Clustering patterns of the accessions, in narrow sense, revealed the existence of low divergence among the samples.ConclusionEthiopian barley landraces are promising candidates for further yield improvement and conservation. However, further regular testing and screening should be conducted for the ex-situ conserved landraces because of the current erratic climate change. In addition, more robust molecular marker systems could be used to clearly reveal the extents of genetic diversity and to facilitate the breeding and conservation of Ethiopian barley landraces.

Identification of transcriptionally active transposons in Barley

BackgroundThe genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants.ResultsWe analyzed the barley full-length cDNA (FLcDNA) sequences and detected 71 unique FLcDNAs exhibiting significant sequence similarity to the extant transposase proteins. These FLcDNAs were then used to search against the genome of a malting barley cultivar ‘Morex’, seven new intact transposons were identified. Sequence alignments indicated that six intact transposons contained the entire FLcDNAs whereas another one served as 3’ untranslated region (3’ UTR) of a barley gene. Our reverse transcription-PCR (RT-PCR) experiment further confirmed the expression of these six transposons and revealed their differential expression. We conducted genome-wide transposon comparisons and detected polymorphisms of three transposon families between the genomes of ‘Morex’ and other three genotypes including the wild barley (Hordeum spontaneum, B1K-04-12) and two cultivated barley varieties, ‘Golden Promise’ and ‘Lasa Goumang’. Lastly, we screened the transcripts of all annotated barley genes and found that some transposons may serve as the coding regions (CDSs) or UTRs of barley genes.ConclusionWe identified six newly expressed transposons in the barley genome and revealed the recent mobility of three transposon families. Our efforts provide a valuable resource for understanding the effects of transposons on barley genome evolution and for developing novel molecular tools for barley genetic improvement and other research.

QTL mapping of nitrogen use efficiency traits at the seedling and maturity stages under different nitrogen conditions in barley (Hordeum vulgare L.)

AbstractNitrogen (N) is an essential element for plant growth and development. The identification and utilization of N use efficiency (NUE) loci are essential for breeding high NUE cultivars. In this study, 15 NUE traits were measured in a recombinant inbred line population containing 121 lines derived from the cross between a cultivated barley (Baudin) and a wild barley (CN4027). The hydroponic culture was conducted with normal N and low N treatments in one‐time frame, and field trials were conducted with N sufficiency and N deficiency treatments in two growing seasons. Twenty‐two quantitative trait loci (QTLs) and four clusters were detected. Of them, the five stable QTLs Qgna.sau‐3H for grain N concentration, Qtna.sau‐3H for total N accumulation per plant, Qnhi.sau‐3H for N harvest index, Qnutegy.sau‐3H for N utilization efficiency for grain yield and Qanutedm.sau‐3H.1 for N utilization efficiency for aboveground dry matter were co‐located on chromosome 3H flanked by the markers bpb6282426 and bpb4786261. These two novel QTL clusters simultaneously controlled NUE traits at the seedling and maturity stages. Some genes related to NUE traits in intervals of the major QTLs were predicted. The significant relationships between NUE traits and agronomic and physiological traits were detected and discussed. In conclusion, this study uncovers the most promising genomic regions for the marker‐assisted selection of NUE traits to improve NUE in barley.

Chromosome Rearrangement in Elymus dahuricus Revealed by ND-FISH and Oligo-FISH Painting.

As a perennial herb in Triticeae, Elymus dahuricus is widely distributed in Qinghai-Tibetan Plateau and Central Asia. It has been used as high-quality fodders for improving degraded grassland. The genomic constitution of E. dahuricus (2n = 6x = 42) has been revealed as StStHHYY by cytological approaches. However, the universal karyotyping nomenclature system of E. dahuricus is not fully established by traditional fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). In this study, the non-denaturing fluorescent in situ hybridization (ND-FISH) using 14 tandem-repeat oligos could effectively distinguish the entire E. dahuricus chromosomes pairs, while Oligo-FISH painting by bulked oligo pools based on wheat-barley collinear regions combined with GISH analysis, is able to precisely determine the linkage group and sub-genomes of the individual E. dahuricus chromosomes. We subsequently established the 42-chromosome karyotype of E. dahuricus with distinctive chromosomal FISH signals, and characterized a new type of intergenomic rearrangement between 2H and 5Y. Furthermore, the comparative chromosomal localization of the centromeric tandem repeats and immunostaining by anti-CENH3 between cultivated barley (Hordeum vulgare L.) and E. dahuricus suggests that centromere-associated sequences in H subgenomes were continuously changing during the process of polyploidization. The precise karyotyping system based on ND-FISH and Oligo-FISH painting methods will be efficient for describing chromosomal rearrangements and evolutionary networks for polyploid Elymus and their related species.

Organ-enriched gene expression during floral morphogenesis in wild barley.

Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.