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Open Access Research article

A reference linkage map for Eucalyptus

Corey J Hudson1*, Jules S Freeman12, Anand RK Kullan3, César D Petroli4, Carolina P Sansaloni4, Andrzej Kilian5, Frank Detering5, Dario Grattapaglia6, Brad M Potts1, Alexander A Myburg3 and René E Vaillancourt1

Author affiliations

1 School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia

2 CRN Research Fellow, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore, QLD, 4558, Australia

3 Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa

4 EMBRAPA Genetic Resources and Biotechnology - EPqB Final W5 Norte 70770–917 Brazilia DF and Dep. Cell Biology, Universidade de Brazilia – UnB, Brasilia, DF, Brazil

5 Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla, ACT, 2600, Australia

6 EMBRAPA Genetic Resources and Biotechnology - Parque Estação Biológica - PqEB - Av. W5 Norte (final), Brasília, DF - Brazil - 70770–917, Universidade Catolica de Brasília- SGAN, 916 modulo B, 70790-160, DF, Brasilia, Brazil

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Citation and License

BMC Genomics 2012, 13:240  doi:10.1186/1471-2164-13-240

Published: 15 June 2012

Abstract

Background

Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method.

Results

The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM.

Conclusion

The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.