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Title: A physical, genetic and functional sequence assembly of the barley genome

Author
item MAYER, KLAUS - German Research Center For Environmental Health
item WAUGH, ROBBIE - The James Hutton Institute
item LANGRIDGE, PETER - University Of Adelaide
item CLOSE, TIMOTHY - University Of California
item Wise, Roger
item GRANER, ANDREAS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item MATSUMOTO, TAKASHI - National Institute Of Agrobiological Sciences (NIAS)
item SATO, KAZUHIRO - Okayama University
item SCHULMAN, ALAN - University Of Helsinki
item MUEHLBAUEER, GARY - University Of Minnesota
item STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item ARIYADASA, RUVINI - Leibniz Institute Of Plant Genetics And Crop Plant Research
item SCHULTE, DANIELA - Leibniz Institute Of Plant Genetics And Crop Plant Research
item POURSAREBANI, NASER - Leibniz Institute Of Plant Genetics And Crop Plant Research
item ZHOU, RUONAN - Leibniz Institute Of Plant Genetics And Crop Plant Research
item STEUERNAGEL, BURKHARD - Leibniz Institute Of Plant Genetics And Crop Plant Research
item MASCHER, MARTIN - Leibniz Institute Of Plant Genetics And Crop Plant Research
item SCHOLZ, UWE - Leibniz Institute Of Plant Genetics And Crop Plant Research
item SHI, BUJUN - Adelaide University
item MADISHETTY, KAVITHA - University Of California
item SVENSSON, JAN - University Of California
item BHAT, PRASANNA - University Of California
item MOSCOU, MATTHEW - University Of California
item RESNIK, JOSH - University Of California
item HEDLEY, PETE - The James Hutton Institute
item LIU, HUI - The James Hutton Institute
item MORRIS, JENNY - The James Hutton Institute
item FRENKEL, ZEEV - University Of Haifa
item KOROL, AVRAHAM - University Of Haifa
item BERGES, HELENE - Institut National De La Recherche Agronomique (INRA)
item TAUDIEN, STEFAN - Leibniz Institute
item FELDER, MARIUS - Leibniz Institute
item GROTH, MARCO - Leibniz Institute
item PLATZER, MATTHIAS - Leibniz Institute
item HIMMELBACH, AXEL - Leibniz Institute Of Plant Genetics And Crop Plant Research
item LONARDI, STEFANO - University Of California
item DUMA, DENISA - University Of California
item ALPERT, MATTHEW - University Of California
item CORDERO, FRANCESA - University Of Torino
item BECCUTI, MARCO - University Of Torino
item CIARDO, GIANFRANCO - University Of California
item MA, YAQIN - University Of California
item WANAMAKER, STEVE - University Of California
item CATTONARO, FEDERICA - University Of Udine
item VENDRAMIN, VERA - University Of Udine
item SCALABRIN, SIMONE - University Of Udine
item RADOVIC, SLOBODANKA - University Of Udine
item WING, ROD - University Of Arizona
item MORGANTE, MICHELE - University Of Udine
item NUSSBAUMER, THOMAS - German Research Center For Environmental Health
item GUNDLACH, HEIDRUN - German Research Center For Environmental Health
item MARTIS, MIHAELA - German Research Center For Environmental Health
item Poland, Jesse
item SPANNAGL, MANUEL - German Research Center For Environmental Health
item PFEIFER, MATTHIAS - German Research Center For Environmental Health
item MOISY, CEDRIC - University Of Helsinki
item TANSKANEN, JAAKO - University Of Helsinki
item ZUCCOLO, ANDREA - University Of Udine
item RUSSELL, JOANNE - The James Hutton Institute
item DRUKA, ARNIS - The James Hutton Institute
item MARSHALL, DAVID - The James Hutton Institute
item BAYER, MICHA - The James Hutton Institute
item SAMPATH, DHARANYA - The Genome Analysis Centre
item FEBRER, MELANIE - The Genome Analysis Centre
item CACCAMO, MARIO - The Genome Analysis Centre
item TANAKA, TSUYOSHI - National Institute Of Agrobiological Sciences (NIAS)
item PLATZER, MATTHIAS - Leibniz Institute
item FINCHER, GEOFFREY - University Of Adelaide
item 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.