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Open Access Research

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

Dina Raats1, Zeev Frenkel1, Tamar Krugman1, Itay Dodek1, Hanan Sela12, Hana Šimková3, Federica Magni4, Federica Cattonaro4, Sonia Vautrin5, Hélène Bergès5, Thomas Wicker6, Beat Keller6, Philippe Leroy7, Romain Philippe7, Etienne Paux7, Jaroslav Doležel3, Catherine Feuillet7, Abraham Korol1* and Tzion Fahima1*

Author Affiliations

1 Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel

2 The Institute for Cereal Crops Improvement, Tel-Aviv University, Tel Aviv, Israel

3 Haná Regional Center for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic

4 Instituto di Genomica Applicata, Udine, Italy

5 INRA-CNRGV, Plant Genomic Resource Center, Castanet Tolosan, France

6 Institute of Plant Biology, University of Zurich, Zurich, Switzerland

7 INRA Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France

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Genome Biology 2013, 14:R138  doi:10.1186/gb-2013-14-12-r138

Published: 20 December 2013

Abstract

Background

The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

Results

Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.

Conclusions

This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.