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A physical, genetic and functional sequence assembly of the barley genome (2012)

K. F. Mayer ; R. Waugh ; J. W. Brown ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 491(7426): 711-6. doi: 10.1038/nature11543.

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Publication Date: 2012-10-19

Description: Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉International Barley Genome Sequencing Consortium -- Mayer, Klaus F X -- Waugh, Robbie -- Brown, John W S -- Schulman, Alan -- Langridge, Peter -- Platzer, Matthias -- Fincher, Geoffrey B -- Muehlbauer, Gary J -- Sato, Kazuhiro -- Close, Timothy J -- Wise, Roger P -- Stein, Nils -- BB/100663X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2012 Nov 29;491(7426):711-6. doi: 10.1038/nature11543. Epub 2012 Oct 17.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23075845" target="_blank"〉PubMed〈/a〉

Keywords: Alternative Splicing/genetics ; Codon, Nonsense/genetics ; Crops, Agricultural/genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics ; Hordeum/classification/*genetics ; Molecular Sequence Annotation ; Physical Chromosome Mapping ; Polymorphism, Single Nucleotide/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; *Sequence Analysis, DNA ; Transcriptome/genetics

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Stored xylem sap from wheat and barley in drying soil contains a transpiration inhibitor with a large molecular size (1993)

MUNNS, R. ; PASSIOURA, J. B. ; MILBORROW, B. V. ; [et al.]

Oxford, UK : Blackwell Publishing Ltd

Plant, cell & environment 16 (1993), S. 0

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ISSN: 1365-3040

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Xylem sap was collected from wheat and barley growing in a drying soil, and the effect of the sap on transpiration was detected by a bioassay with detached wheat leaves. The inhibitory activity of fresh sap was small, and could be largely accounted for by the abscisic acid content (about 2×10-5mol m-3). When fresh sap was stored at -20°C for several days, the activity increased. Maximum activity developed after a week. This increase in activity was due to a compound that increased in size with storage at -20°C. When fresh sap was fractionated with filters of different molecular size exclusion characteristics, and the separated fractions stored at -20°C for a week, activity developed only in the fraction containing compounds smaller than 0·3 kDa. However, when sap already stored at -20°C was fractionated, activity was only in fractions containing compounds larger than 0·3 kDa. The increase in activity and in size did not occur with storage in liquid nitrogen (-196°C) or at -80°C. These results suggest that storage at -20°C causes the aggregation or polymerization of a small compound with low activity to form a large compound with high activity. This change is not catalysed by an enzyme because it can occur in a fraction from which molecules larger than 0·3 kDa are removed. It is probably promoted by high solute concentrations when ice crystals form. Sap collected from plants in soils of high water potential had little or no activity after storage at -20°C.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1365-3040.1993.tb00509.x

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A newly identified barley gene, Dhn12, encoding a YSK2 DHN, is located on chromosome 6H and has embryo-specific expression (2000)

Choi, D. -W. ; Close, T. J.

Springer

Theoretical and applied genetics 100 (2000), S. 1274-1278

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ISSN: 1432-2242

Keywords: Key words Bacterial artificial chromosome (BAC) library ; Dehydrin ; DHN ; Embryo-specific expression ; Hordeum vulgare

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Dehydrins are water-soluble lipid-associating proteins that accumulate during low-temperature or water-deficit conditions, and are thought to play a role in freezing- and drought-tolerance in plants. Dhn genes exist as multi-gene families in plants. Previously, we screened lambda genomic libraries of two barley cultivars in an effort to isolate all of the barley Dhn genes. We identified 11 unique Dhn genes and estimated a total of 13 Dhn genes in the barley genome. To extend the collection, we used an alternative source of clones, a 1.5×Morex barley BAC library. In this library, we found nine Dhn genes that we described previously and one new Dhn gene, Dhn12. The Dhn12 gene encodes an acidic YSK2 dehydrin. The Dhn12 gene is located on chromosome 6H, and shows a different expression pattern from all other Dhn genes identified previously. RT-PCR results show that Dhn12 expression is embryo-specific. Dhn12 is not expressed in seedling shoots under any of the conditions tested, including non-stressed as well as dehydrated, or cold-, ABA- or NaCl-treated seedlings.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220051434

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Map locations of barley Dhn genes determined by gene-specific PCR (2000)

Choi, D.-W. ; Koag, M. C. ; Close, T. J.

Springer

Theoretical and applied genetics 101 (2000), S. 350-354

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ISSN: 1432-2242

Keywords: Key words Dehydrin ; Dhn ; Hordeum vulgare ; PCR-based mapping

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract We previously identified 11 unique barley Dhn genes and found, using wheat-barley addition lines, that these genes are dispersed on four chromosomes 3H, 4H, 5H, 6H. In the present work, more precise positions of barley Dhn genes were determined using gene-specific PCR and 100 doubled haploid lines developed from a cross of Dicktoo and Morex barley. Dhn10 is located on 3H between saflp106 and ABG4. Dhn6 is at the previously determined position on 4H between SOLPRO and BCD265a. Dhn1 and Dhn2 are at the previously determined position on 5H between mR and saflp172. The Dhn locus previously called Dhn4a on barley 5H or Dhn2.2 on T. monococcum 5A is in fact Dhn9 and maps to a revised position between BCD265b and saflp218. Dhn3, Dhn4, Dhn7 and Dhn5 each map to the same position on chromosome 6H, suggesting that the previously reported separation of Dhn3, Dhn4 and Dhn5 may reflect limitations in the accuracy of Southern blot data. In addition to clarifying the map positions of these important stress-related genes, these results illustrate the advantage of gene-specific probes for the mapping of individual genes in a multi-gene family.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220051490

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Genetic studies of Triticeae dehydrins: assignment of seed proteins and a regulatory factor to map positions (1998)

Werner-Fraczek, J. E. ; Close, T. J.

Springer

Theoretical and applied genetics 97 (1998), S. 220-226

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ISSN: 1432-2242

Keywords: Key words Dehydrin genes ; Wheat ; Barley ; Triticeae ; Regulatory factor

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract A collection of 200 wheat (Triticum aestivum L. cv ‘Chinese Spring’) cytogenetic stocks (nullisomic, tetrasomic, nulli-tetrasomic, ditelosomic and deletion lines, addition and substitution stocks from intra- and inter-specific crosses) was utilized to determine the proteins encoded by some of the wheat and barley dehydrin genes, using a western blot procedure. Proteins extracted from seeds were reacted with antibodies that recognize dehydrins in a wide range of plants, including wheat and barley. Proteins encoded by dehydrin loci in chromosome arms 4DS, 5BL and 6AL of ‘Chinese Spring’ wheat were assigned by this method. There was also evidence of a regulatory factor on 5B in the vicinity of the dhn genes, and on 5H in wheat-barley addition lines, that is required for a normal level of expression of seed dehydrins in hexaploid wheat. Further understanding of this putative regulatory factor would be helpful for the interpretation of linkage studies that may relate dehydrin gene expression to phenotypes such as dehydration, salinity or low-temperature tolerance.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220050888

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The barley (Hordeum vulgare L.) dehydrin multigene family: sequences, allele types, chromosome assignments, and expression characteristics of 11 Dhn genes of cv Dicktoo (1999)

Choi, D.-W. ; Zhu, B. ; Close, T. J.

Springer

Theoretical and applied genetics 98 (1999), S. 1234-1247

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ISSN: 1432-2242

Keywords: Key words Dehydrin ; Multigene family ; LEA ; COR ; RAB ; Barley ; Triticeae

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Dehydrins (LEA D11 proteins) have been identified in both higher and lower plants, and are associated with tolerance to, or response to the onset of, low temperature or dehydration. Several studies have suggested that specific alleles of Dhn genes may contribute to a number of phenotypic traits, including the emergence of seedlings in cool or saline soils and the frost tolerance of more-mature plants. However, an incomplete collection of the Dhn multigene family in any system and nucleic acid cross-hybridization between Dhn gene-family members have limited the precision of these studies. We attempted to overcome these impediments by determining the nucleotide sequences of the entire Dhn multigene family in barley and by developing gene-specific probes. We identified 11 unique Dicktoo Dhn genes. Seven appear to be alleles of Dhn genes identified previously in other barley cultivars. Another, Dhn9, appears to be orthologous to a Triticum durum Dhn gene. A statistical analysis of the total collection of genomic clones brings the estimated size of the barley Dhn gene family to 13. Allelic differences in the protein-coding regions appear to result principally from duplications of entire Φ-segments or single amino-acid substitutions, suggesting that polypeptide structural constraints have been a strong force in the evolution of Dhn alleles. Chromosome mapping by PCR with wheat-barley addition lines established the presence of Dhn genes in four barley chromosomes (3H, 4H, 5H, 6H). RT-PCR demonstrated that the Dhn genes are differentially regulated under dehydration, low temperature and ABA treatment, consistent with putative regulatory elements located upstream of the respective Dhn coding regions. This whole-genome, gene-specific study unifies what previously seemed to be disparate-mapping, expression, and genetic-variation data for Dhn genes in the Triticeae and other plant systems.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220051189

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Nuclear and cytoplasmic localization of maize embryo and aleurone dehydrin (1994)

Asghar, Rehana ; Fenton, R. D. ; DeMason, Darleen A. ; [et al.]

Springer

Protoplasma 177 (1994), S. 87-94

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ISSN: 1615-6102

Keywords: Aleurone ; Cytoplasm ; Dehydrins ; Embryo ; Nucleus ; Scutellum

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Summary The subcellular location of dehydrins was determined by immunomicroscopy in maize kernels imbibed in the presence of ABA. Antibodies were specific to the consensus sequence that exists near the carboxy terminus of virtually all dehydrins. Aleurone, scutellar epithelium, scutellar provascular strands, and the outermost embryonic leaves contained the highest concentration of dehydrins. In these tissues, and in scutellar parenchyma cells and inner embryonic leaves, dehydrins were present in the cytoplasm and associated with nuclei. In shoot and root apex cells, dehydrins appeared to be present principally in the cytoplasm. This localization pattern of dehydrins, together with the known amino acid sequences and phosphorylation patterns, leads to analogies with other proteins that are present in both the nucleus and cytoplasm of eukaryotic cells.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF01378983

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Expression of the barley dehydrin multigene family and the development of freezing tolerance (2000)

Zhu, B. ; Choi, D.-W. ; Fenton, R. ; [et al.]

Springer

Molecular genetics and genomics 264 (2000), S. 145-153

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ISSN: 1617-4623

Keywords: Dehydrin LEA D11 Multigene family Barley Freezing tolerance

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract. Dehydrins (DHNs; LEA D11) are one of the typical families of plant proteins that accumulate in response to dehydration, low temperature, osmotic stress or treatment with abscisic acid (ABA), or during seed maturation. We previously found that three genes encoding low-molecular-weight DHNs (Dhn1, Dhn2 and Dhn9) map within a 15-cM region of barley chromosome 5H that overlaps a QTL for winterhardiness, while other Dhn genes encoding low- and high-molecular-weight DHNs are located on chromosomes 3H, 4H and 6H. Here we examine the expression of specific Dhn genes under conditions associated with expression of the winterhardiness phenotype. Plants grown at 4°C or in the field in Riverside, California developed similar, modest levels of freezing tolerance, coinciding with little low-MW Dhn gene activity. Dicktoo (the more tolerant cultivar) and Morex (the less tolerant) grown in Saskatoon, Canada had higher levels of expression of genes for low-MW DHNs than did the same cultivars in Riverside, with expression being higher in Dicktoo than Morex. Dehydration or freeze-thaw also evoked expression of genes for low MW DHNs, suggesting that the dehydration component of freeze-thaw in the field induces expression of genes encoding low-MW DHNs. These observations are consistent with the hypothesis that the major chilling-induced DHNs help to prime plant cells for acclimation to more intense cold, which then involves adaptation to dehydration during freeze-thaw cycling. A role for chromosome 5H-encoded DHNs in acclimation to more intense cold seems possible, even though it is not the basis of the major heritable variation in winterhardiness within the Dicktoo × Morex population.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s004380000299

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