Genetic linkage maps are valuable resources which can be used to provide a framework for many genomic analyses. Linkage maps can be used to investigate the organisation and evolution of genomes through comparative mapping [1–3] and serve as a basis for investigating phenotypic traits of ecological and economic importance through the localisation of quantitative trait loci [QTL; [4–6]. Subsequently, QTL results may be used to help guide the selection of candidate genes for association studies or be applied in marker-assisted breeding programmes [7, 8]. Linkage maps can also be used to anchor physical maps and assist in the assembly of genome sequences [9–11]. The wide application of linkage maps in combination with their value to genetics research has led to numerous linkage mapping projects being undertaken in plants. Detailed linkage maps have been produced for all of the world’s staple cereal species , and in forest trees, linkage maps have been produced for many of the most widely-planted species due to their commercial importance as wood and fibre crops [1, 13, 14].
Grattapaglia and Sederoff  published the first genetic linkage map in the forest tree genus Eucalyptus in 1994. Subsequently, many mapping pedigrees have been established for the purpose of linkage map construction and associated QTL analyses. More than 20 eucalypt genetic linkage maps have been reported with most being produced in the main commercially grown species, or their hybrids, from the Eucalyptus subgenus Symphyomyrtus. Thus, the majority of linkage mapping projects have focussed on E. grandis
E. urophylla and E. globulus [reviewed in , while a smaller number of maps have also been produced for E. nitens, E. teriticornis[18, 19], E. camaldulensis and for species in the closely related genus Corymbia.
Many early eucalypt linkage maps were constructed using random amplification of polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) molecular markers [16, 22]. However, the anonymous nature of these dominant markers has limited the transfer of linkage information between studies [16, 23]. More informative, codominant markers such as isozyme and random fragment length polymorphism (RFLPs) have also been used in eucalypt linkage mapping, although, their low throughput, low inter-pedigree polymorphism and labour intensive genotyping requirements have limited their use [16, 23]. The more recent development of highly polymorphic microsatellite markers made available a large potential suite of markers that are transferrable between species and polymorphic in multiple pedigrees. This enabled linkage group synteny to be established between maps containing common microsatellite markers and the positions and stability of QTL across multiple species to be examined [e.g. [24–27]. The ability to establish linkage group synteny has also enabled moderate-density comparative mapping studies [23, 28].
Recent advances in molecular methods have led to high-throughput genotyping systems being developed [e.g. [29, 30]. These have made it possible to quickly generate many hundreds of markers in single mapping pedigrees and have helped facilitate the construction of high density linkage maps . Most recently in Eucalyptus, Diversity Arrays Technology [DArT;  has been used to generate large numbers of molecular markers for genetic linkage mapping in several mapping pedigrees [e.g. [11, 32, 33]. The eucalypt DArT markers are highly transferable across species from subgenus Symphyomyrtus and the high-throughput array-based genotyping system provides wide genome coverage . A key benefit of the Eucalyptus DArT markers is the public availability of the sequences of most of the 7680 markers contained on the genotyping array [GenBank accession numbers HR865291 - HR872186], thus making it possible to anchor DArT markers directly to the reference E. grandis genome sequence [v1.0 released January 2011; . However, while the DArT technology offers many advantages, the DArT markers do suffer some limitations due to their dominant nature. For example, the incomplete segregation information provided by those DArT markers segregating in a 3:1 ratio (intercross) results in an exponential increase of marker-ordering calculations compared to fully-informative co-dominant markers . Co-dominant markers also provide more complete information in QTL mapping studies [e.g. allowing estimation of additive and dominant allelic effects;  and are more useful in some genetic analyses, such as estimating population genetic parameters (e.g. inbreeding levels), relative to dominant marker types such as DArT. In addition, the DArT marker assay can be subject to cross-hybridization from duplicated loci in the genome, although most such artifacts can be excluded by preselecting markers exhibiting Mendelian segregation ratios in mapping pedigrees.
At present, DArT markers have been used to construct linkage maps in seven independent E. globulus and/or E. grandis × E. urophylla hybrid family mapping pedigrees [11, 32, 33]. All of these maps also contain a variable number of co-dominant microsatellite markers, which provide important links to many earlier eucalypt linkage maps. In the two largest mapping pedigrees (more than 500 individuals each), 1010  and 2229  DArT markers, were mapped at sub-centiMorgan marker densities and collectively more than 4000 DArT and microsatellite markers have been mapped in the seven pedigrees.
All DArT marker based linkage maps were constructed using the program JoinMap 4.0 . This program is one of the most commonly used linkage mapping programs and appears to be the only software available for building linkage maps using the combined segregation data from multiple populations [39–41]. However, it is presently not feasible to combine the segregation data contained within the seven eucalypt mapping families describe above (collectively 1950 individuals), and successfully order such large numbers of markers within linkage groups (up to ~ 500) due to computational limitations (Van Ooijen pers comm.). To circumvent the limitations of traditional segregation-based methods of linkage map construction, alternative marker-merging strategies have been developed. A so-called ‘composite map’ can be produced in which markers from individual component maps are merged into a single map based on their position relative to common anchor loci. For example, the ‘neighbours’ marker-merging approach of Cone et al.  and the marker-merging method implemented in the PhenoMap program (GeneFlow Inc. USA) have been used to successfully construct high density composite maps containing several thousand markers in a number of plant species; including Sorghum, barley [41, 44, 45] and maize [42, 46].
In this study, a marker-merging method was used to construct a high-density DArT and microsatellite marker composite linkage map from seven independently constructed maps. Recent comparative mapping analyses using 236 to 393 markers shared between three of the maps [see  showed that these linkage maps exhibited high synteny (> 93.4% markers occurring on the same linkage groups) and high colinearity (> 93.7% markers having the same order within linkage groups). This indicated that it would be possible to merge markers from several component maps into a single high quality map featuring robust marker-order together with very high marker density. It is expected that this composite map will facilitate marker and map information exchange and serve as a valuable reference for species in the subgenus Symphyomyrtus.