Barley Sequencing


Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley P E, Muehlbauer G J, Scholz U, Korol A, Mayer K F X, Waugh R, Langridge P, Graner A, Stein N. A sequence-ready physical map of barley anchored genetically by two million SNPs. Plant Physiol. 164 (2014) 412-423.
Braumann I, Stein N, Hansson M. Reduced chlorophyll biosynthesis in heterozygous barley magnesium chelatase mutants. Plant Physiol. Biochem. 78 (2014) 10-14.
Lüpken T, Stein N, Perovic D, Habekuss A, Serfling A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Ariyadasa R, Martis M M, Mayer K F X, Niks R E, Collins N C, Friedt W, Ordon F. High resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV. Mol. Breed. 33 (2014) 477-488.
Mascher M, Jost M, Kuon J-E, Himmelbach A, Assfalg A, Beier S, Scholz U, Graner A, Stein N. Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol. 15 (2014) R78.
Mascher M, Stein N. Genetic anchoring of whole-genome shotgun assemblies. Front. Genet. 5 (2014) 208.
Mazaheri M, Kianian P M A, Mergoum M, Valentini G L, Seetan R, Pirseyedi S M, Kumar A, Gu Y Q, Stein N, Kubaláková M, Doležel J, Denton A M, Kianian S F. Transposable element junctions in marker development and genomic characterization of barley. Plant Genome (2014)
Middleton C P, Senerchia N, Stein N, Akhunov E D, Keller B, Wicker T, Kilian B. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One 9 (2014) e85761.
Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E, Pecchioni N, Francia E. The barley Frost resistance-H2 locus. Funct. Integr. Genomics (2014) Epub ahead of print:.
Poursarebani N, Ma L, Schmutzer T, Houben A, Stein N. FISH mapping for physical map improvement in the large genome of barley - a case study on chromosome 2H. Cytogenet. Genome Res. (2014) accepted.
Stein N, Steuernagel B. Advances in sequencing the barley genome. In: Tuberosa R, Graner A, Frison E (Eds.): Genomics of Plant Genetic Resources. Vol. 1: Managing, sequencing and mining genetic resources. Springer Science+Business Media Dordrecht. (2014) 391-403.
Wendler N, Mascher M, Nöh C, Himmelbach A, Scholz U, Ruge-Wehling B, Stein N. Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant Biotechnol. J. (2014) in press.
Schmutzer T, Ma L, Poursarebani N, Bull F, Stein N, Houben A, Scholz U. Kmasker - a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet. Genome Res. 142 (2014) 66-78.
Yang P, Habekuss A, Ordon F, Stein N. Analysis of bymovirus resistance genes on proximal barley chromosome 4HL provides the basis for precision breeding for BaMMV/BaYMV resistance. Theor. Appl. Genet. (2014) Epub ahead of print:.
Yang P, Lüpken T, Habekuss A, Hensel G, Steuernagel B, Kilian B, Ariyadasa R, Himmelbach A, Kumlehn J, Scholz U, Ordon F, Stein N. PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc. Natl. Acad. Sci. U.S.A. 111 (2014) 2104-2109.

Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G. Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. Theor. Appl. Genet. 126 (2013) 1575-1586.
Koppolu R, Anwar N, Sakuma S, Tagiri A, Lundqvist U, Pourkheirandish M, Rutten T, Seiler C, Himmelbach A, Ariyadasa R, Youssef H M, Stein N, Sreenivasulu N, Komatsuda T, Schnurbusch T. Six-rowed spike4 (Vrs4) controls spikelet determinacy and row-type in barley. Proc. Natl. Acad. Sci. U. S. A. 110 (2013) 13198-13203.
Lüpken T, Stein N, Perovic D, Habekuss A, Kramer I, Hähnel U, Steuernagel B, Scholz U, Zhou R, Ariyadasa R, Taudien S, Platzer M, Martis M, Mayer K, Friedt W, Ordon F. Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.). Theor. Appl. Genet. 126 (2013) 1201-1212.
Mascher M, Muehlbauer G J, Rokhsar D S, Chapman J, Schmutz J, Barry K, Munoz-Amatriain M, Close T J, Wise R P, Schulman A H, Himmelbach A, Mayer K F X, Scholz U, Poland J A, Stein N, Waugh R. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76 (2013) 718-727.
Mascher M, Richmond T A, Gerhardt D J, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov E D, Hedley P E, Gonzales A M, Morrell P L, Kilian B, Blattner F R, Scholz U, Mayer K F, Flavell A J, Muehlbauer G J, Waugh R, Jeddeloh J A, Stein N. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 76 (2013) 494-505.
Mascher M, Wu S, Amand P S, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 8 (2013) e76925.
Matthies I E, Weise S, Förster J, Korzun V, Stein N, Röder M S. Nitrogen-metabolism related genes in barley - haplotype diversity, linkage mapping and associations with malting and kernel quality parameters. BMC Genet. 14 (2013) e77.
Muñoz-Amatriaín M, Eichten S R, Wicker T, Richmond T A, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer K F X, Taudien S, Platzer M, Jeddeloh J A, Springer N M, Muehlbauer G J, Stein N. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 14 (2013) R58.
Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis M M, Graner A, Schweizer P, Scholz U, Mayer K F X, Stein N. Conserved synteny-based anchoring of the barley genome physical map. Funct. Integr. Genomics 13 (2013) 339-350.
Sakuma S, Pourkheirandish M, Hensel G, Kumlehn J, Stein N, Tagiri A, Yamaji N, Ma J F, Sassa H, Koba T, Komatsuda T. Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley. New Phytol. 197 (2013) 939-948.
Yang P, Perovic D, Habekuss A, Zhou R, Graner A, Ordon F, Stein N. Gene-based high-density mapping of the gene rym7 conferring resistance to Barley mild mosaic virus (BaMMV). Mol. Breed. 32 (2013) 27-37.

Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat. Genet. 44 (2012) 1388-1392.
Houston K, Druka A, Bonar N, Macaulay M, Lundquist J, Franckowiak J, Morgante M, Stein N, Waugh R. Analysis of the barley bract suppression gene Trd1. Theor. Appl. Genet. 125 (2012) 33-45.
Huynh B L, Mather D E, Schreiber A W, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis J C R, Edwards J, Shirley N, Langridge P, Fleury D. Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. Plant Mol. Biol. 80 (2012) 299-314.
Kohl S, Hollmann J, Blattner F R, Radchuk V, Andersch F, Steuernagel B, Schmutzer T, Scholz U, Krupinska K, Weber H, Weschke W. A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq. BMC Plant Biol. 12 (2012) 154.
Mayer K F X, Waugh R, Langridge P, Close T J, Wise R P, Graner A, Matsumoto T, Sato K, Schulman A, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Madishetty K, Svensson J T, Bhat P, Moscou M, Resnik J, Muehlbauer G J, Hedley P, Liu H, Morris J, Frenkel Z, Korol A, Bergès H, Taudien S, Felder M, Groth M, Platzer M, Himmelbach A, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Morgante M, Nussbaumer T, Gundlach H, Martis M, Poland J, Pfeifer M, Moisy C, Tanskanen J, Zuccolo A, Spannagl M, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Tanaka T, Wannamaker S, Schmutzer T, Brown J W S, Fincher G B, Stein N. A physical, genetic and functional sequence assembly of the barley genome. Nature 491 (2012) 711-716.
Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N. High resolution mapping of Dense spike-ar ( to the genetic centromere of barley chromosome 7H. Theor. Appl. Genet. 124 (2012) 373-384.
Zakhrabekova S, Gough S P, Braumann I, Müller A H, Lundqvist J, Ahmann K, Dockter C, Matyszczak I, Kurowska M, Druka A, Waugh R, Graner A, Stein N, Steuernagel B, Lundqvist U, Hansson M. Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 4326-4331.

Comadran J, Ramsay L, Mackenzie K, Hayes P, Close T J, Muehlbauer G, Stein N, Waugh R. Patterns of polymorphism and linkage disequilibrium in cultivated barley. Theor. Appl. Genet. 122 (2011) 523-531.
Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R. Genetic dissection of barley morphology and development. Plant Physiol. 155 (2011) 617-627.
Mayer K F X, Martis M, Hedley P E, Šimková H, Liu H, Morris J A, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23 (2011) 1249-1263.
Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, Dejong P, Wu C C, Graner A, Langridge P, Stein N. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics 12 (2011) 247.
Sharma S, Sharma S, Kopisch-Obuch F J, Keil T, Laubach E, Stein N, Graner A, Jung C. QTL analysis of root-lesion nematode resistance in barley: 1. Pratylenchus neglectus. Theor. Appl. Genet. 122 (2011) 1321-1330.
Wicker T, Mayer K F X, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23 (2011) 1706-1718.

Cockram J, White J, Zuluaga D L, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey M J, Werner P, Harrap D, Tapsell C, Liu H, Hedley P E, Stein N, Schulte D, Steuernagel B, Marshall D F, Thomas W T, Ramsay L, Mackay I, Balding D J, Consortium T A, Waugh R, O'Sullivan D M. Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc. Natl. Acad. Sci. U. S. A. 107 (2010) 21611-21616.
Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Guzy-Wrobelska J, Ramsay L, Druka I, Grant I, Macaulay M, Vendramin V, Shahinnia F, Radovic S, Houston K, Harrap D, Cardle L, Marshall D, Morgante M, Stein N, Waugh R. Exploiting induced variation to dissect quantitative traits in barley. Biochem. Soc. Trans. 38 (2010) 683-688.
Nair S K, Wang N, Turuspekov Y, Pourkheirandish M, Sinsuwongwat S, Chen G X, Sameri M, Tagiri A, Honda I, Watanabe Y, Kanamori H, Wicker T, Stein N, Nagamura Y, Matsumoto T, Komatsuda T. Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proc. Natl. Acad. Sci. U.S.A. 107 (2010) 490-495.
Vu G T, Wicker T, Buchmann J P, Chandler P M, Matsumoto T, Graner A, Stein N. Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley. Funct. Integr. Genomics 10 (2010) 509-521.

To initiate a cross database search for genomic data, please enter a keyword query into the text box. Some query examples:

search for a trait: barley low nitrogen
search for salt-stressed barley gene OXO2: OXO2_HORVU

Please note! By default, faceted search is reducing search results to those, which has direct genome annotations. If you like to see more, please enable indirect links or all hits in the filter panel.