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

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