Location: Corn Insects and Crop Genetics ResearchTitle: A physical, genetic and functional sequence assembly of the barley genome Author
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.