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Title: Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

item MUNOZ-AMATRIAIN, MARIA - University Of California
item LONARDI, STEFANO - University Of California
item LUO, MINGCHENG - University Of California
item MADISHETTY, KAVITHA - University Of California
item SVENSSON, JAN - University Of California
item MOSCOU, MATTHEW - University Of California
item WANAMAKER, STEVE - University Of California
item JIANG, TAO - University Of California
item KLEINHOFS, ANDRIS - Washington State University
item MUEHLBAUER, GARY - University Of Minnesota
item Wise, Roger
item STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item MA, YAQIN - University Of California
item RODRIGUEZ, EDMUNDO - University Of California
item KUDRNA, DAVE - University Of Arizona
item BARTOS, JAN - Institute Of Experimental Botany
item BHAT, PRASANNA - University Of California
item Chao, Shiaoman
item CONDAMINE, PASCAL - University Of California
item HEINEN, SHANE - University Of Minnesota
item RESNIK, JOSH - University Of California
item WING, ROD - University Of Arizona
item WITT, HEATHER - University Of California
item ALPERT, MATTHEW - University Of California
item BECCUTI, MARCO - University Of California
item BOZDAG, SERDAR - University Of California
item CORDERO, FRANCESCA - University Of California
item MIREBRAHIM, HAMID - University Of California
item OUNIT, RACHID - University Of California
item WU, YONGHUI - University Of California
item YOU, FRANK - US Department Of Agriculture (USDA)
item ZHENG, JIE - University Of California
item DOLEZEL, JAROSLAV - Institute Of Experimental Botany
item GRIMWOOD, JANE - Department Of Energy Joint Genome
item SCHMUTZ, JEREMY - Department Of Energy Joint Genome
item DUMA, DENISA - University Of California
item ALTSCHMIED, LOTHAR - Leibniz Institute Of Plant Genetics And Crop Plant Research
item BLAKE, TOM - Montana State University
item Bregitzer, Paul
item COOPER, LOL - Oregon State University
item DILBIRLIGI, MUHARREM - Washington State University
item FALK, ANDERS - Swedish University Of Agricultural Sciences
item FEIZ, LEILA - Montana State University
item GRANER, ANDREAS - Leibniz Institute Of Plant Genetics And Crop Plant Research
item GUSTAFSON, PERRY - Retired ARS Employee
item HAYES, PATRICK - Oregon State University
item LEMAUX, PEGGY - University Of California
item MAMMADOV, JAFAR - Virginia Tech
item CLOSE, TIMOTHY - University Of California

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/24/2015
Publication Date: 10/1/2015
Citation: Munoz-Amatriain, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J., Moscou, M., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G., Wise, R.P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bartos, J., Bhat, P., Chao, S., Condamine, P., Heinen, S., Resnik, J., Wing, R., Witt, H., Alpert, M., Beccuti, M., Bozdag, S., Cordero, F., Mirebrahim, H., Ounit, R., Wu, Y., You, F., Zheng, J., Dolezel, J., Grimwood, J., Schmutz, J., Duma, D., Altschmied, L., Blake, T., Bregitzer, P.P., Cooper, L., Dilbirligi, M., Falk, A., Feiz, L., Graner, A., Gustafson, P., Hayes, P., Lemaux, P., Mammadov, J., Close, T. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal. 84(1):216-227. doi: 10.1111/tpj.12959.

Interpretive Summary: Barley is among the world’s earliest domesticated crop species and represents the fourth most abundant cereal produced in both area and harvest. 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'. Moreover, the barley plant is widely adapted and generally more stress-tolerant than its close relative wheat, thus 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. However, the barley genome is large and highly repetitive which hinders the development of a complete nucleotide sequence. To gain access to the gene-rich portion of the barley genome as resource for breeding for important traits in for example, malting quality, disease resistance and drought stress, we identified and sequenced the barley gene-space containing 17,386 genes. We demonstrate the utility of this sequence resource by identifying candidate genes for malting quality improvement. These sequences and their annotations can be accessed and exported via an online interface ( or through a new version of the Windows software HarvEST:Barley (download from This resource provides a platform to advance gene discovery and genomics-assisted crop improvement in this staple crop. 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.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.