Open Access Highly Accessed Research article

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Alessandra C Palhares1, Taislene B Rodrigues-Morais1, Marie-Anne Van Sluys2, Douglas S Domingues23, Walter Maccheroni45, Hamilton Jordão45, Anete P Souza6, Thiago G Marconi6, Marcelo Mollinari1, Rodrigo Gazaffi1, Antonio Augusto F Garcia1 and Maria Lucia Carneiro Vieira1*

Author affiliations

1 Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil

2 Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil

3 Present address: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, 86047-902, Londrina, Brazil

4 CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil

5 Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil

6 Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil

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Citation and License

BMC Genetics 2012, 13:51  doi:10.1186/1471-2156-13-51

Published: 28 June 2012



The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily.


The mapping population parents (‘IAC66-6’ and ‘TUC71-7’) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.


Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Saccharum spp; AFLP; EST-SSR; Retrotransposon-based markers; Single-dose markers; Integrated genetic map; Marker distribution