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.