A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B Etienne Paux, et al. Science 322, 101 (2008); DOI: 10.1126/science.1161847 The following resources related to this article are available online at www.sciencemag.org (this information is current as of October 3, 2008 ): Updated information and services, including high-resolution figures, can be found in the online version of this article at: http://www.sciencemag.org/cgi/content/full/322/5898/101 Supporting Online Material can be found at: http://www.sciencemag.org/cgi/content/full/322/5898/101/DC1 A list of selected additional articles on the Science Web sites related to this article can be found at: This article cites 23 articles, 7 of which can be accessed for free: http://www.sciencemag.org/cgi/content/full/322/5898/101#otherarticles This article appears in the following subject collections: on October 3, 2008 Botany http://www.sciencemag.org/cgi/collection/botany Information about obtaining reprints of this article or about obtaining permission to reproduce this article in whole or in part can be found at: http://www.sciencemag.org/about/permissions.dtl www.sciencemag.org Downloaded from Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. Copyright 2008 by the American Association for the Advancement of Science; all rights reserved. The title Science is a registered trademark of AAAS. REPORTS 35. E. R. Wood, P. A. Dudchenko, H. Eichenbaum, Nature discussions and comments on this manuscript. This work Figs. S1 to S15 397, 613 (1999). was supported by NINDS (to I. Fried), Israel Science Table S1 36. C. M. Bird, N. Burgess, Nat. Rev. Neurosci. 9, 182 (2008). Foundation (to R. Malach), Binational United States– References 37. We thank the patients for their cooperation and Israel grant (to I. Fried and R. Malach), and Human Movies S1 and S2 participation in this study. We also thank E. Ho, B. Scott, Frontier Science Program Organization (HFSPO) E. Behnke, R. Kadivar, T. Fields, A. Postolova, K. Laird, fellowship (to R. Mukamel). C. Wilson, R. Quian-Quiroga, A. Kraskov, F. Mormann, 14 August 2008; accepted 28 August 2008 and M. Cerf for assistance with data acquisition; B. Salaz Supporting Online Material Published online 4 September 2008; and I. Wainwright for administrative help; and I. Kahn, www.sciencemag.org/cgi/content/full/1164685/DC1 10.1126/science.1164685 Y. Nir, G. Buzsáki, E. Pastalkova, and S. Gilaie-Dotan for Materials and Methods Include this information when citing this paper. physically mapping and ultimately sequencing a species for which this was unthinkable a few A Physical Map of the 1-Gigabase years ago. A physical map with 10-fold coverage of the Bread Wheat Chromosome 3B 17-Gb bread wheat genome would require more than 1.4 million BAC clones to be finger- Etienne Paux,1 Pierre Sourdille,1 Jérôme Salse,1 Cyrille Saintenac,1 Frédéric Choulet,1 printed, assembled into contigs, and anchored Philippe Leroy,1 Abraham Korol,2 Monika Michalak,3 Shahryar Kianian,3 Wolfgang Spielmeyer,4 to genetic maps. Although whole-genome BAC Evans Lagudah,4 Daryl Somers,5 Andrzej Kilian,6 Michael Alaux,7 Sonia Vautrin,8 libraries are available and fingerprinting mil- Hélène Bergès,8 Kellye Eversole,9 Rudi Appels,10 Jan Safar,11 Hana Simkova,11 lions of BAC clones is technically feasible with Jaroslav Dolezel,11 Michel Bernard,1 Catherine Feuillet1 high-information-content fingerprinting (HICF) (7), assembly to accurately depict individual chro- As the staple food for 35% of the world’s population, wheat is one of the most important crop mosomes and the anchoring of homoeologous species. To date, sequence-based tools to accelerate wheat improvement are lacking. BAC contigs onto genetic maps remains daunting. As part of the international effort to sequence the 17–billion–base-pair hexaploid bread wheat To address these issues, we used a chromosome- genome (2n =6x = 42 chromosomes), we constructed a bacterial artificial chromosome (BAC)– based approach (8) to construct a physical map on October 3, 2008 based integrated physical map of the largest chromosome, 3B, that alone is 995 megabases. A of the largest hexaploid wheat chromosome chromosome-specific BAC library was used to assemble 82% of the chromosome into 1036 contigs (3B) and, to compensate for the inherent limits that were anchored with 1443 molecular markers, providing a major resource for genetic and of the wheat genome (the lack of recombina- genomic studies. This physical map establishes a template for the remaining wheat chromosomes tion and polymorphism), we deployed a combi- and demonstrates the feasibility of constructing physical maps in large, complex, polyploid nation of genetic mapping strategies for anchoring genomes with a chromosome-based approach. the physical map. Fingerprinting and contig assembly were per- mong plants providing food for humans (2.6 Gb) is about the size of three wheat chro- formed with BAC clones originating from sorted and animals, one of the oldest and most mosomes (table S1). Further complicating the 3B wheat chromosomes of Chinese Spring (9), www.sciencemag.org Awidespread is wheat (Triticum aestivum challenge, bread wheat is a relatively recent hex- the reference cultivar chosen for genome se- L.). Despite its socioeconomic importance and aploid (2n = 6x = 42) containing three homoeol- quencing by the International Wheat Genome the challenges that agriculture is facing today ogous A, B, and D genomes of related progenitor Sequencing Consortium because of its previous (1), wheat genomics and its application to crop species, meiotic recombination is not distrib- use for cytogenetic studies and the availability improvement are lagging behind those of most uted homogeneously along the chromosomes, of a set of aneuploid lines (10). 67,968 3B BAC other important crops. The wheat genome has and intervarietal polymorphism is very low. clones were fingerprinted with a modified (11) always been viewed as impossible to sequence Genome sequencing is the foundation for HICF SNaPshot protocol (7), and a total of because of its large amount of repetitive se- understanding the molecular basis of pheno- 56,952 high-quality fingerprints (84%) was ob- Downloaded from quences (>80%) and its size of 17 Gb, which is typic variation, accelerating breeding, and im- tained. A first automated assembly (11)resulted five times larger than the human genome. The proving the exploitation of genetic diversity to in a final build of 1991 contigs with an aver- largest wheat chromosome (3B) alone is more develop new crop varieties with increased yield age size of 482 kb for a total length of 960 Mb than twice the size of the entire 370-Mb rice and improved resistance to biotic and abiotic (table S2). One hundred ninety-seven contigs genome (2), whereas the entire maize genome stresses. These new varieties will be critical were larger than 1 Mb; the largest was 3852 kb for meeting the challenges of the 21st century, in size. A minimal tiling path (MTP) consisting such as climatic changes, modifications of diets, of 7440 overlapping BAC clones was defined 1Institut National de la Recherche Agronomique, Université human population growth, and the increased for further analyses. After the preliminary auto- Blaise Pascal (INRA-UBP), UMR 1095, Genetics Diversity and demand for biofuels. Physical maps are essen- mated assembly, contigs were merged manually 2 Ecophysiology of Cereals, Clermont-Ferrand, France. Institute tial for high-quality sequence assembly re- (11), resulting in a final assembly of 1036 contigs of Evolution, University of Haifa, Haifa, Israel. 3Department of Plant Sciences, North Dakota State University, Fargo, ND, USA. gardless of the sequencing strategy used [such with an average size of 783 kb (table S2) cover- 4Commonwealth Scientific and Industrial Research Organiza- as bacterial artificial chromosome (BAC)–by– ing 811 Mb (~82%) of the estimated 995 Mb tion Plant Industry, Canberra, Australia. 5Agriculture and Agri- BAC or whole-genome shotgun strategies], and (12) constituting chromosome 3B. Food Canada, Cereal Research Centre, Winnipeg, Canada. they will remain pivotal for de novo sequenc- Contig assembly was validated through BAC 6Diversity Arrays Technology, Yarralumla, Canberra, Australia. 7INRA–Unité de Recherches en Génomique-Info, Versailles, ing even with the advent of short-read tech- library screening with markers derived from France. 8INRA–Centre National de Ressources Génomiques nologies (3). As the foundation for genome BAC-end sequences (BESs) (13) and by genetic Végétales, Toulouse, France. 9International Wheat Genome Se- sequencing, physical maps have been estab- mapping (11). Out of 421 markers derived from quencing Consortium, Eversole Associates, Bethesda, MD, USA. 10 lished for a dozen plants species so far, includ- BESs, 369 (88%) correctly identified the BAC Centre for Comparative Genomics, Murdoch University, – Perth, Australia. 11Laboratory of Molecular Cytogenetics and ing cereals such as maize, rice, and sorghum (4 6). clones belonging to computationally identified Cytometry, Institute of Experimental Botany, Olomouc, Czech Recently, the development of new genomic re- contigs. Conversely, 35 markers originating from Republic. sources for analyzing wheat paved the way for the same contigs mapped to the same genetic www.sciencemag.org SCIENCE VOL 322 3 OCTOBER 2008 101 REPORTS locus. The wheat genome has a high content 3B, 42% of the physical map length is repre- Further integration of the 3B physical map of long terminal repeat retrotransposons (> 67%) sented by only 2.2% of the genetic map length was achieved through meiotic mapping with a (13) and a large number of tandemly repeated in the centromeric regions) and the low level reference genetic map developed from an F2 sequences, which may result in the misassem- of polymorphism in the cultivated pool. population (CsRe) derived from a cross between bly of BAC clones.