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Title:   Author  item
                                            MAYER, KLAUS - German Research Center For Environmental Healthitem
                                            WAUGH, ROBBIE - The James Hutton Instituteitem
                                            LANGRIDGE, PETER - University Of Adelaideitem
                                            CLOSE, TIMOTHY - University Of Californiaitem
                                            Wise, Rogeritem
                                            GRANER, ANDREAS - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            MATSUMOTO, TAKASHI - National Institute Of Agrobiological Sciences (NIAS)item
                                            SATO, KAZUHIRO - Okayama Universityitem
                                            SCHULMAN, ALAN - University Of Helsinkiitem
                                            MUEHLBAUEER, GARY - University Of Minnesotaitem
                                            STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            ARIYADASA, RUVINI - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            SCHULTE, DANIELA - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            POURSAREBANI, NASER - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            ZHOU, RUONAN - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            STEUERNAGEL, BURKHARD - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            MASCHER, MARTIN - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            SCHOLZ, UWE - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            SHI, BUJUN - Adelaide Universityitem
                                            MADISHETTY, KAVITHA - University Of Californiaitem
                                            SVENSSON, JAN - University Of Californiaitem
                                            BHAT, PRASANNA - University Of Californiaitem
                                            MOSCOU, MATTHEW - University Of Californiaitem
                                            RESNIK, JOSH - University Of Californiaitem
                                            HEDLEY, PETE - The James Hutton Instituteitem
                                            LIU, HUI - The James Hutton Instituteitem
                                            MORRIS, JENNY - The James Hutton Instituteitem
                                            FRENKEL, ZEEV - University Of Haifaitem
                                            KOROL, AVRAHAM - University Of Haifaitem
                                            BERGES, HELENE - Institut National De La Recherche Agronomique (INRA)item
                                            TAUDIEN, STEFAN - Leibniz Instituteitem
                                            FELDER, MARIUS - Leibniz Instituteitem
                                            GROTH, MARCO - Leibniz Instituteitem
                                            PLATZER, MATTHIAS - Leibniz Instituteitem
                                            HIMMELBACH, AXEL - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            LONARDI, STEFANO - University Of Californiaitem
                                            DUMA, DENISA - University Of Californiaitem
                                            ALPERT, MATTHEW - University Of Californiaitem
                                            CORDERO, FRANCESA - University Of Torinoitem
                                            BECCUTI, MARCO - University Of Torinoitem
                                            CIARDO, GIANFRANCO - University Of Californiaitem
                                            MA, YAQIN - University Of Californiaitem
                                            WANAMAKER, STEVE - University Of Californiaitem
                                            CATTONARO, FEDERICA - University Of Udineitem
                                            VENDRAMIN, VERA - University Of Udineitem
                                            SCALABRIN, SIMONE - University Of Udineitem
                                            RADOVIC, SLOBODANKA - University Of Udineitem
                                            WING, ROD - University Of Arizonaitem
                                            MORGANTE, MICHELE - University Of Udineitem
                                            NUSSBAUMER, THOMAS - German Research Center For Environmental Healthitem
                                            GUNDLACH, HEIDRUN - German Research Center For Environmental Healthitem
                                            MARTIS, MIHAELA - German Research Center For Environmental Healthitem
                                            Poland, Jesseitem
                                            SPANNAGL, MANUEL - German Research Center For Environmental Healthitem
                                            PFEIFER, MATTHIAS - German Research Center For Environmental Healthitem
                                            MOISY, CEDRIC - University Of Helsinkiitem
                                            TANSKANEN, JAAKO - University Of Helsinkiitem
                                            ZUCCOLO, ANDREA - University Of Udineitem
                                            RUSSELL, JOANNE - The James Hutton Instituteitem
                                            DRUKA, ARNIS - The James Hutton Instituteitem
                                            MARSHALL, DAVID - The James Hutton Instituteitem
                                            BAYER, MICHA - The James Hutton Instituteitem
                                            SAMPATH, DHARANYA - The Genome Analysis Centreitem
                                            FEBRER, MELANIE - The Genome Analysis Centreitem
                                            CACCAMO, MARIO - The Genome Analysis Centreitem
                                            TANAKA, TSUYOSHI - National Institute Of Agrobiological Sciences (NIAS)item
                                            PLATZER, MATTHIAS - Leibniz Instituteitem
                                            FINCHER, GEOFFREY - University Of Adelaideitem
                                            SCHMUTZER, THOMAS - Leibniz Institute Of Plant Genetics And Crop Plant Research
  Submitted to: Nature
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 8/30/2012
                                    Publication  Date: 11/29/2012
                                    Citation: Mayer, K., Waugh, R., Langridge, P., Close, T.J., Wise, R.P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbaueer, G.J., Stein, N., 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., Hedley, P., Liu, H., Morris, J., Frenkel, Z., Korol, A., Berges, 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.A., Spannagl, M., Pfeifer, M., Moisy, C., Tanskanen, J., Zuccolo, A., Russell, J., Druka, A., Marshall, D., Bayer, M., Sampath, D., Febrer, M., Caccamo, M., Tanaka, T., Platzer, M., Fincher, G., Schmutzer, T. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-716.Interpretive Summary: Barley is among the world’s earliest domesticated crop species and represents the fourth most abundant cereal in both area and harvest.  Approximately three-quarters of global production is used for animal feed, 20% is malted for use in alcoholic and non-alcoholic beverages, and 5% as an ingredient in a range of different food products.  Consumption of barley grain or grain products provides human health benefits due to its high dietary fiber content and has led to its renaissance as a true ‘functional food'.  More importantly, due to the barley plant being widely adapted and generally more stress-tolerant than its close relative wheat, it remains the major food source for many people in poor countries, and an ideal crop in harsh and marginal environments.  As a diploid inbreeding temperate crop, barley has traditionally been considered a model for plant genetic research. 

Crop improvement strategies, even in the commercial sector remain largely traditional, with the vision of true genome assisted breeding currently unfulfilled.  A challenge to the scientific community is therefore to provide a full genome sequence, or an appropriate enabling surrogate, that will facilitate advances in both fundamental and breeding research.  

In response to this challenge, we present a novel paradigm for delivering barley genome resources as a model for the Triticeae, the tribe that includes bread and durum wheat, and rye.    

We introduce the concept of a barley genome, an integrated, multi-layered informational resource that provides access to the majority of all barley genes in a highly structured physical and genetic framework.  In association with comparative sequence and transcriptome data, the barley genome provides a new molecular and cellular insight into the biology of the species, providing a platform to advance gene discovery and genomics assisted crop improvement in this staple crop.

Impact:  Genome based tools and informational resources will promote new approaches to broaden the germplasm base, facilitate new breeding strategies and accelerate rates of genetic gain.  This resource provides new knowledge of broad significance to plant scientists and breeders, enabling growers to produce nourishing, disease resistant, and higher yielding crops.
                                Technical Abstract: Barley (Hordeum vulgare L.) is amongst the oldest of our domesticated crop plants and remains one of the world’s most important crop species.  It has a diploid genome of 5.1 gigabases, almost twice the size of those of human and maize.  To meet global demand for food, fuel and fibre, it is commonly agreed that reference genome sequences of our crop plants are urgently required in order to enable genome assisted crop improvement.  Here we present the genome of the barley cultivar (cv.) Morex.  Despite comprising >84% repetitive sequence, we are able to provide 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 with a cumulative length of 4.98 Gbp, 4.56 Gbp assigned to individual chromosome arms and more than 3.9 Gbp anchored to a high-resolution genetic map.  Projecting a deep whole genome shotgun (WGS) assembly, cDNAs and RNA-seq data onto this framework provides support for 79,379 transcript clusters, with 75,258 anchored to the WGS.  A ‘high confidence’ (HC) set of 26,159 genes has homology support from other plant genomes.  These HC genes exhibit dynamic patterns of gene expression with extensive developmental and tissue specific post-transcriptional regulation.  Alternative splicing and premature stop codons (PTCs) are abundant and appear strongly correlated with spatial and temporal regulation.  Non-coding transcripts and novel transcribed regions (nTARs) are similarly abundant and more than 2000 appear evolutionarily conserved.  Combined evidence therefore indicates that post-transcriptional processing in barley forms an important regulatory layer.  WGS survey sequences from diverse barley cultivars and a wild accession reveal a landscape of extensive single nucleotide variation (SNV) and evidence for islands of reduced diversity likely a product of recent breeding history.  The barley gene-ome represents a new paradigm for genome assisted research in a very large crop genome.


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