Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome
Authors
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: timothy.close@ucr.edu.
Keywords: Barley; Hordeum vulgare L; BAC sequencing; gene distribution; recombination frequency; synteny; centromere BACs; HarvEST:Barley; Aegilops tauschii
Summary
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.
http://onlinelibrary.wiley.com/doi/10.1111/tpj.12959/abstract