The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome Glaucia Mendes Souza & Helene Berges & Stephanie Bocs & Rosanne Casu & Angelique D’Hont & João Eduardo Ferreira & Robert Henry & Ray Ming & Bernard Potier & Marie-Anne Van Sluys & Michel Vincentz & Andrew H. Paterson Received: 23 March 2011 /Accepted: 14 June 2011 /Published online: 30 June 2011 # Springer Science+Business Media, LLC 2011 Abstract Sugarcane cultivars derive from interspecific hybrids obtained by crossing Saccharum officinarum and Saccharum spontaneum and provide feedstock used world- wide for sugar and biofuel production. The importance of sugarcane as a bioenergy feedstock has increased interest in the generation of new cultivars optimised for energy production. Cultivar improvement has relied largely on traditional breeding methods, which may be limited by the complexity of inheritance in interspecific polyploid hybrids, and the time-consuming process of selection of plants with desired agronomic traits. In this sense, molecular genetics can assist in the process of developing improved cultivars by generating molecular markers that can be used in the breeding process or by introducing new genes into the sugarcane genome. For meeting each of these, and additional goals, biotechnologists would benefit from a Communicated by Paul Moore Helene Berges, Stephanie Bocs, Rosanne Casu, Angelique D’Hont, João Eduardo Ferreira, Robert Henry, Ray Ming, Bernard Potier, Marie-Anne Van Sluys and Michel Vincentz contributed equally to the work and have been listed in alphabetical order by last name. G. M. Souza Departamento de Bioquímica, Instituto de Química, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508–900, Brazil e-mail: glmsouza@iq.usp.br H. Berges INRA – CNRGV, Chemin de Borde Rouge, BP 52627, 31326 Castanet Tolosan, France e-mail: Helene.Berges@toulouse.inra.fr S. Bocs : A. D’Hont CIRAD, UMR AGAP, TAA108/03, Avenue Agropolis, 34398 Montpellier, France A. D’Hont e-mail: angelique.d’hont@cirad.fr R. Casu CSIRO Plant Industry, Queensland Bioscience Precinct 306 Carmody Road, St Lucia, QLD 4067, Australia e-mail: Rosanne.Casu@csiro.au J. E. Ferreira Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Rua do Matão, 1010, São Paulo, SP CEP 05508–090, Brazil e-mail: jef@ime.usp.br R. Henry Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Brisbane St Lucia, QLD 4072, Australia e-mail: robert.henry@uq.edu.au R. Ming Department of Plant Biology, University of Illinois at Urbana-Champaign 148 ERML, MC-051, 1201 W. Gregory Drive, Urbana, IL 61801, USA e-mail: rming@life.uiuc.edu Tropical Plant Biol. (2011) 4:145–156 DOI 10.1007/s12042-011-9079-0