Barley Sequencing

Publications

2014
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. dx.doi.org/10.1104/pp.113.228213
Braumann I, Stein N, Hansson M. Reduced chlorophyll biosynthesis in heterozygous barley magnesium chelatase mutants. Plant Physiol. Biochem. 78 (2014) 10-14. dx.doi.org/10.1016/j.plaphy.2014.02.004
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. dx.doi.org/10.1007/s11032-013-9966-1
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. dx.doi.org/10.1186/gb-2014-15-6-r78
Mascher M, Stein N. Genetic anchoring of whole-genome shotgun assemblies. Front. Genet. 5 (2014) 208. dx.doi.org/10.3389/fgene.2014.00208
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) dx.doi.org/10.3835/plantgenome2013.10.0036
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. dx.doi.org/10.1371/journal.pone.0085761
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:. dx.doi.org/10.1007/s10142-014-0360-9
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. dx.doi.org/10.1159/000356460
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:. dx.doi.org/10.1007/s00122-014-2324-9
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. dx.doi.org/10.1073/pnas.1320362111

2013
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. dx.doi.org/10.1007/s00122-013-2075-z
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. dx.doi.org/10.1073/pnas.1221950110
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. dx.doi.org/10.1007/s00122-013-2047-3
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. dx.doi.org/10.1111/tpj.12319
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. dx.doi.org/10.1111/tpj.12294
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. dx.doi.org/10.1371/journal.pone.0076925
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. dx.doi.org/10.1186/1471-2156-14-77
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. dx.doi.org/10.1186/gb-2013-14-6-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. dx.doi.org/10.1007/s10142-013-0327-2
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. dx.doi.org/10.1111/nph.12068
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. dx.doi.org/10.1007/s11032-013-9842-z

2012
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. dx.doi.org/10.1038/ng.2447
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. dx.doi.org/10.1007/s00122-012-1814-x
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. dx.doi.org/10.1007/s11103-012-9949-3
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. dx.doi.org/10.1186/1471-2229-12-154
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. dx.doi.org/10.1038/nature11543
Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N. High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theor. Appl. Genet. 124 (2012) 373-384. dx.doi.org/10.1007/s00122-011-1712-7
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. dx.doi.org/10.1073/pnas.1113009109

2011
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. dx.doi.org/10.1007/s00122-010-1466-7
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. dx.doi.org/10.1104/pp.110.166249
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. dx.doi.org/10.1105/tpc.110.082537
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. dx.doi.org/10.1186/1471-2164-12-247
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. dx.doi.org/10.1007/s00122-011-1533-8
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. dx.doi.org/10.1105/tpc.111.086629

2010
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. dx.doi.org/10.1073/pnas.1010179107
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. dx.doi.org/10.1042/BST0380683
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. dx.doi.org/10.1073/pnas.0909097107
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. dx.doi.org/10.1007/s10142-010-0173-4

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