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


María Muñoz-Amatriaín 1,†, Stefano Lonardi 2,†, MingCheng Luo 3, Kavitha Madishetty 1, Jan T Svensson 1,4, Matthew J Moscou 1,5, Steve Wanamaker 1, Tao Jiang 2, Andris Kleinhofs 6, Gary J Muehlbauer 7, Roger P Wise 8, Nils Stein 9, Yaqin Ma 1,3
Edmundo Rodriguez 1,29, Dave Kudrna 10, Prasanna R Bhat 1,11, Shiaoman Chao 12, Pascal Condamine 1, Shane Heinen 7, Josh Resnik 1, Rod Wing 10, Heather N Witt 3, Matthew Alpert 2, Marco Beccuti 2,13, Serdar Bozdag 2,14, Francesca Cordero 2,13
Hamid Mirebrahim 2, Rachid Ounit 2, Yonghui Wu 2, Frank You 15, Jie Zheng 2,16, Hana Šimková 17, Jaroslav Doležel 17, Jane Grimwood 18, Jeremy Schmutz 18, Denisa Duma 2, Lothar Altschmied 9, Tom Blake 19, Phil Bregitzer 20, Laurel Cooper 21
Muharrem Dilbirligi 6,22, Anders Falk 23, Leila Feiz 19,24, Andreas Graner 9, Perry Gustafson 25, Patrick M Hayes 21, Peggy Lemaux 26, Jafar Mammadov 27,28 and Timothy J Close 1,*


Author Information

1 Department of Botany and Plant Sciences, University of California, Riverside, USA

2 Department of Computer Science, University of California, Riverside, USA

3 Department of Plant Sciences, University of California, Davis, USA

4 Nordic Genetic Resource Center, Alnarp, Sweden

5 The Sainsbury Laboratory, Norwich Research Park, Norwich, UK

6 Department of Crop and Soil Sciences, Washington State University, Pullman, USA

7 Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, USA

8 Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, USA

9 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

10 Arizona Genomics Institute, University of Arizona, Tucson, USA

11 Monsanto Research Center, Bangalore, India

12 USDA-ARS Biosciences Research Lab, Fargo, USA

13 Department of Computer Science, University of Turin, Turin, Italy

14 Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, USA

15 Agriculture and Agri-Food Canada, Morden, Manitoba, Canada

16 School of Computer Engineering, Nanyang Technological University, Singapore

17 Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic

18 US Department of Energy Joint Genome Institute, Walnut Creek, USA & Hudson Alpha Genome Sequencing Center, Huntsville, USA

19 Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, USA

20 USDA-ARS, Aberdeen, USA

21 Department of Crop and Soil Science, Oregon State University, Corvallis, USA

22 The Scientific and Technological Research Council of Turkey, International Cooperation Department, Ankara, Turkey

23 Swedish University of Agricultural Sciences, Uppsala, Sweden

24 Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA

25 USDA, University of Missouri, Columbia, USA

26 Department of Plant and Microbial Biology, University of California, Berkeley, USA

27 Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, USA

28 Dow AgroSciences LLC, Indianapolis, USA

29 Departamento de Ciencias Básicas, Universidad Autonóma Agraria Antonio Narro, México

†€ Equal contributors.

* Corresponding author: Timothy J. Close, Department of Botany and Plant Sciences, 2150 Batchelor Hall, 900 University Ave., Riverside, CA 92521 (USA). Phone: (951) 827-3318.Fax: (951) 827-4437. Email:


Keywords: Barley; Hordeum vulgare L; BAC sequencing; gene distribution; recombination frequency; synteny; centromere BACs; HarvEST:Barley; Aegilops tauschii


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 6,278 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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