The pattern of variability in chloroplast DNA (cpDNA) of Eucalyptus globulus Labill. (Myrtaceae) was studied using 270 samples from southern Australia. Forty variable sequence characters were found, defining 105 haplotypes. Haplotypes were assigned to three major cpDNA clades based on their phylogeny. The pattern of cpDNA variation did not conform to subspecies boundaries; however, there was a strong geographic structure to the distribution of clades and haplotypes. One clade (JC) was geographically central and widespread and was found in 163 samples from Tasmania and continental Australia. Less-common clades occurred in more localised regions—southern (Js, 77 samples) and eastern (Jet, 12 samples). The distribution of the J et and Js clades coincides with hypothesised glacial refugia in Tasmania, suggesting limited seed-mediated dispersal since deglaciation.

Understanding genome differentiation is important to compare and transfer genomic information between taxa, such as from model to non-model organisms. Comparative genetic mapping can be used to assess genome differentiation by identifying similarities and differences in chromosome organisation. Following release of the assembled Eucalyptus grandis genome sequence (January 2011; http://www.phytozome.net/), a better understanding of genome differentiation between E. grandis and other commercially important species belonging to the subgenus Symphyomyrtus is required. In this study, comparative genetic mapping analyses were conducted between E. grandis, E. urophylla and E. globulus using high density linkage maps constructed from Diversity Array Technology and microsatellite molecular markers. There were 236 -393 common markers between maps, providing the highest resolution yet achieved for comparative mapping in Eucalyptus. In two intra-section comparisons (section Maidenaria -E. globulus and sectionLatoangulatae -E. grandis vs. E. urophylla), ~1% of common markers were non-syntenic and within chromosomes 4.7-6.8% of markers were non-colinear. Consistent with increasing taxonomic distance, lower synteny (6.6% non-syntenic markers) was observed in an inter-section comparison between E. globulus and E. grandis x E. urophylla consensus linkage maps. Two small chromosomal translocations, or duplications, were identified in this comparison representing possible genomic differences between E. globulus and section Latoangulatae species. Despite these differences, the overall high level of synteny and colinearity observed between section Maidenaria -Latoangulatae suggests that the genomes of these species are highly conserved indicating that sequence information from the E. grandis genome will be highly transferable to related Symphyomyrtus species.

· Eucalypts are one of the most planted tree genera worldwide, and there is increasing interest in marker-assisted selection for tree improvement. Implementation of marker-assisted selection requires a knowledge of the stability of quantitative trait loci (QTLs). This study aims to investigate the stability of QTLs for wood properties and growth across contrasting sites and multiple pedigrees of Eucalyptus globulus. · Saturated linkage maps were constructed using 663 genotypes from four separate families, grown at three widely separated sites, and were employed to construct a consensus map. This map was used for QTL analysis of growth, wood density and wood chemical traits, including pulp yield. · Ninety-eight QTLs were identified across families and sites: 87 for wood properties and 11 for growth. These QTLs mapped to 38 discrete regions, some of which co-located with candidate genes. Although 16% of QTLs were verified across different families, 24% of wood property QTLs and 38% of growth QTLs exhibited significant genotype-by-environment interaction. · This study provides the most detailed assessment of the effect of environment and pedigree on QTL detection in the genus. Despite markedly different environments and pedigrees, many QTLs were stable, providing promising targets for the application of marker-assisted selection.