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Tropical Plant Biology

, Volume 4, Issue 3–4, pp 145–156 | Cite as

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
Article

Abstract

Sugarcane cultivars derive from interspecific hybrids obtained by crossing Saccharum officinarum and Saccharum spontaneum and provide feedstock used worldwide 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 reference genome sequence of a sugarcane cultivar. The sugarcane genome poses challenges that have not been addressed in any prior sequencing project, due to its highly polyploid and aneuploid genome structure with a complete set of homeologous genes predicted to range from 10 to 12 copies (alleles) and to include representatives from each of two different species. Although sugarcane’s monoploid genome is about 1 Gb, its highly polymorphic nature represents another significant challenge for obtaining a genuine assembled monoploid genome. With a rich resource of expressed-sequence tag (EST) data in the public domain, the present article describes tools and strategies that may aid in the generation of a reference genome sequence.

Keywords

Sugarcane Genome Sequencing Sorghum 

Notes

Acknowledgements

The authors would like to thank Dr. Carol Hotton, Curator for plants of the GenBank taxonomy database, National Center for Biotechnology Information, USA for her valuable assistance in sugarcane nomenclature harmonization. The work of GMS, JEF, MAVS and MV is funded by Fundação de Amparo à Pesquisa do Estado de São Paulo. The work of AHP has been funded by the International Consortium for Sugarcane Biotechnology.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Glaucia Mendes Souza
    • 1
  • Helene Berges
    • 2
  • Stephanie Bocs
    • 3
  • Rosanne Casu
    • 4
  • Angelique D’Hont
    • 3
  • João Eduardo Ferreira
    • 5
  • Robert Henry
    • 6
  • Ray Ming
    • 7
  • Bernard Potier
    • 8
  • Marie-Anne Van Sluys
    • 9
  • Michel Vincentz
    • 10
  • Andrew H. Paterson
    • 11
  1. 1.Departamento de BioquímicaInstituto de QuímicaSão PauloBrazil
  2. 2.INRA – CNRGVCastanet TolosanFrance
  3. 3.CIRAD, UMR AGAP, TAA108/03MontpellierFrance
  4. 4.CSIRO Plant IndustrySt LuciaAustralia
  5. 5.Departamento de Ciências da ComputaçãoInstituto de Matemática e EstatísticaSão PauloBrazil
  6. 6.Queensland Alliance for Agriculture and Food Innovation (QAAFI)University of QueenslandBrisbane St LuciaAustralia
  7. 7.Department of Plant BiologyUniversity of Illinois at Urbana-Champaign 148 ERMLUrbanaUSA
  8. 8.Crop Biology Resource CentreSouth African Sugarcane Research InstituteMount EdgecombeSouth Africa
  9. 9.Instituto de Biociências, Departamento de BotânicaUniversidade de São PauloSão PauloBrazil
  10. 10.Instituto de Biologia, Departamento de Genética, Evolução e BioagentesUniversidade Estadual de CampinasCampinasBrazil
  11. 11.Plant Genome Mapping LaboratoryUniversity of GeorgiaAthensUSA

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