Linkage disequilibrium (LD) mapping using natural populations results in higher resolution of markertrait associations compared to family-based quantitative trait locus (QTL) studies. Depending on the extent of LD, it is possible to identify alleles within candidate genes associated with a trait. Analysis of a natural mutant in Arabidopsis has shown that mutations in cinnamoyl CoA reductase (CCR), a key lignin gene, affect physical properties of the secondary cell wall such as stiffness and strength. Using this gene, we tested whether LD mapping could identify alleles associated with microfibril angle (MFA), a wood quality trait affecting stiffness and strength of wood. We identified 25 common single-nucleotide polymorphism (SNP) markers in the CCR gene in Eucalyptus nitens. Using single-marker and haplotype analyses in 290 trees from a E. nitens natural population, two haplotypes significantly associated with MFA were found. These results were confirmed in two full-sib families of E. nitens and Eucalyptus globulus. In an effort to understand the functional significance of the SNP markers, we sequenced the cDNA clones and identified an alternatively spliced variant from the significant haplotype region. This study demonstrates that LD mapping can be used to identify alleles associated with wood quality traits in natural populations of trees.

The neighbourhood model apportions offspring of individual mother plants to self-fertilization, outcrossing to males within a circumscribed area around the mother plant (the neighbourhood), and outcrossing to males outside the neighbourhood. Formerly the model was applied only to haploid pollen gametes in the offspring of conifers, but is extended so that it can be used with genotypic data from diploid offspring of both angiosperms and gymnosperms. In addition, it is shown that the mating parameters can be estimated without independent estimates of allele frequencies in the pollen pools outside the neighbourhood; thus the model might be applied effectively to natural populations exposed to unknown external pollen sources. Parameters of the neighbourhood mating model were estimated for a 10-year-old seed orchard population of the insect-pollinated tree, Eucalyptus regnans, in southeast Australia, which contained a mixture of two geographical provenances (Victoria and Tasmania). The mating patterns revealed were complex. Crosses between trees of the same provenance occurred three times more often than crosses between trees of different provenances. Levels of self-fertilization and patterns of mating within neighbourhoods were influenced by provenance origin, crop fecundity and orchard position (central vs. edge) of mother trees. Gene dispersal, however, was extensive, with approximately 50% of effective pollen gametes coming from males more than 40 m away from mother trees (average distance between neighbouring trees was 7.4 m). Thus, insect pollinators are efficient promoters of cross-fertilization in this orchard, with the result that the effective number of males mating with each female is large.

Summary In response to gravitational stresses, angiosperm trees form tension wood in the upper sides of branches and leaning stems in which cellulose content is higher, microfibrils are typically aligned closely with the fibre axis and the fibres often have a thick inner gelatinous cell wall layer (G‐layer). Gene expression was studied in Eucalyptus nitens branches oriented at 45° using microarrays containing 4900 xylem cDNAs, and wood fibre characteristics revealed by X‐ray diffraction, chemical and histochemical methods. Xylem fibres in tension wood (upper branch) had a low microfibril angle, contained few fibres with G‐layers and had higher cellulose and decreased Klason lignin compared with lower branch wood. Expression of two closely related fasciclin‐like arabinogalactan proteins and a β‐tubulin was inversely correlated with microfibril angle in upper and lower xylem from branches. Structural and chemical modifications throughout the secondary cell walls of fibres sufficient to resist tension forces in branches can occur in the absence of G‐layer enriched fibres and some important genes involved in responses to gravitational stress in eucalypt xylem are identified.

Four microsatellite loci have been characterised in Eucalyptus nitens Maiden and in six other eucalypt species. The dinucleotide repeats were identified by screening a Sau3AI genomic DNA library from E. nitens with (CA)n and (GA)n oligonucleotide probes and sequencing the positive clones. Genetic analysis of 20 unrelated individuals from five populations of E. nitens showed all loci to be highly polymorphic with an average of 9.5 alleles per locus and an average heterozygosity of 0.575. Analysis of four individuals from each of six species from three subgenera showed complete conservation of microsatellite loci between species within the same subgenus, Symphyomyrtus, and conservation of 50% of loci across species between the two main subgenera, Symphyomyrtus and Monocalyptus. None of the primers amplified microsatellite loci in Eucalyptus maculata from the subgenus Corymbia. All microsatellite loci that were detected were polymorphic. Highly polymorphic microsatellite loci that are conserved across species will be useful for mapping quantitative traits, fingerprinting breeding lines, and for within-population studies requiring fine-scale analysis of genetic variation.