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 Corn Insects and Crop Genetics Research: Ames, IA
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Title:   Author  item
                                            MUNOZ-AMATRIAIN, MARIA - University Of Californiaitem
                                            LONARDI, STEFANO - University Of Californiaitem
                                            LUO, MINGCHENG - University Of Californiaitem
                                            MADISHETTY, KAVITHA - University Of Californiaitem
                                            SVENSSON, JAN - University Of Californiaitem
                                            MOSCOU, MATTHEW - University Of Californiaitem
                                            WANAMAKER, STEVE - University Of Californiaitem
                                            JIANG, TAO - University Of Californiaitem
                                            KLEINHOFS, ANDRIS - Washington State Universityitem
                                            MUEHLBAUER, GARY - University Of Minnesotaitem
                                            Wise, Rogeritem
                                            STEIN, NILS - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            MA, YAQIN - University Of Californiaitem
                                            RODRIGUEZ, EDMUNDO - University Of Californiaitem
                                            KUDRNA, DAVE - University Of Arizonaitem
                                            BARTOS, JAN - Institute Of Experimental Botanyitem
                                            BHAT, PRASANNA - University Of Californiaitem
                                            Chao, Shiaomanitem
                                            CONDAMINE, PASCAL - University Of Californiaitem
                                            HEINEN, SHANE - University Of Minnesotaitem
                                            RESNIK, JOSH - University Of Californiaitem
                                            WING, ROD - University Of Arizonaitem
                                            WITT, HEATHER - University Of Californiaitem
                                            ALPERT, MATTHEW - University Of Californiaitem
                                            BECCUTI, MARCO - University Of Californiaitem
                                            BOZDAG, SERDAR - University Of Californiaitem
                                            CORDERO, FRANCESCA - University Of Californiaitem
                                            MIREBRAHIM, HAMID - University Of Californiaitem
                                            OUNIT, RACHID - University Of Californiaitem
                                            WU, YONGHUI - University Of Californiaitem
                                            YOU, FRANK - US Department Of Agriculture (USDA)item
                                            ZHENG, JIE - University Of Californiaitem
                                            DOLEZEL, JAROSLAV - Institute Of Experimental Botanyitem
                                            GRIMWOOD, JANE - Department Of Energy Joint Genomeitem
                                            SCHMUTZ, JEREMY - Department Of Energy Joint Genomeitem
                                            DUMA, DENISA - University Of Californiaitem
                                            ALTSCHMIED, LOTHAR - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            BLAKE, TOM - Montana State Universityitem
                                            Bregitzer, Paulitem
                                            COOPER, LOL - Oregon State Universityitem
                                            DILBIRLIGI, MUHARREM - Washington State Universityitem
                                            FALK, ANDERS - Swedish University Of Agricultural Sciencesitem
                                            FEIZ, LEILA - Montana State Universityitem
                                            GRANER, ANDREAS - Leibniz Institute Of Plant Genetics And Crop Plant Researchitem
                                            GUSTAFSON, PERRY - Retired ARS Employeeitem
                                            HAYES, PATRICK - Oregon State Universityitem
                                            LEMAUX, PEGGY - University Of Californiaitem
                                            MAMMADOV, JAFAR - Virginia Techitem
                                            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 (http://harvest-web.org/hweb/utilmenu.wc) or through a new version of the Windows software HarvEST:Barley (download from harvest.ucr.edu). 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.


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