Construction of microsatellite linkage maps for Corymbia

The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia's close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F 2 population (n = 90) created by crossing two unrelated Corymbia torelliana x C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog

The mountain yellow-legged frog Rana muscosa sensu lato, once abundant in the Sierra Nevada of California and Nevada, and the disjunct Transverse Ranges of southern California, has declined precipitously throughout its range, even though most of its habitat is protected. The species is now extinct in Nevada and reduced to tiny remnants in southern California, where as a distinct population segment, it is classified as Endangered. Introduced predators (trout), air pollution and an infectious disease (chytridiomycosis) threaten remaining populations. A Bayesian analysis of 1901 base pairs of mitochondrial DNA confirms the presence of two deeply divergent clades that come into near contact in the Sierra Nevada. Morphological studies of museum specimens and analysis of acoustic data show that the two major mtDNA clades are readily differentiated phenotypically. Accordingly, we recognize two species, Rana sierrae, in the northern and central Sierra Nevada, and R. muscosa, in the southern Sierra Nevada and southern California. Existing data indicate no range overlap. These results have important implications for the conservation of these two species as they illuminate a profound mismatch between the current delineation of the distinct population segments (southern California vs. Sierra Nevada) and actual species boundaries. For example, our study finds that remnant populations of R. muscosa exist in both the southern Sierra Nevada and the mountains of southern California, which may broaden options for management. In addition, despite the fact that only the southern California populations are listed as Endangered, surveys conducted since 1995 at 225 historic (1899-1994) localities from museum collections show that 93.3% (n=146) of R. sierrae populations and 95.2% (n=79) of R. muscosa populations are extinct. Evidence presented here underscores the need for revision of protected population status to include both species throughout their ranges.

Demographics, pollination syndrome and conservation status of Macrozamia platyrhachis (Zamiaceae), a geographically restricted Queensland cycad

To assess the International Union for Conservation of Nature (IUCN) status of Macrozamia platyrhachis F.M.Bailey, we surveyed this central Queensland cycad for its population abundance and health and its pollinator type and pollination syndrome (thermogenesis and volatile emissions). Plants are locally abundant within the 11 discrete populations surveyed, with an estimated population of 611 315 adult plants. Plants are highly restricted to a small area of occupancy, seed dispersal is nearly non-existent and extreme fires appear to have destroyed almost all seeds and seedlings and decimated the pollinators. Of known Macrozamia pollinators, only the thrips, Cycadothrips chadwicki Mound, were found on cones, and these were found in very low numbers. The pollination syndrome for this cycad appears to be unique, based on two cone traits. For one, thermogenesis peaks in early evening, a contrast with daytime peaks of other Cycadothrips-pollinated Macrozamia, but matches that of the Tranes weevil-pollinated Macrozamia machinii. In addition, cone volatiles include both previously unreported compounds as well as those reported exclusively on either Cycadothrips- or Tranes-pollinated species. Based on its small, fragmented area of occupancy, projected population declines and the unique pollination syndrome, we recommend that M. platyrhachis retain its current status as 'Endangered'. Habitat management plans should stipulate that controlled burns be avoided during cycad coning season and that wildfires be controlled to minimise damage to seedlings and pollinators.

Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis

Global amphibian decline by chytridiomycosis is a major environmental disaster that has been attributed to either recent fungal spread or environmental change that promotes disease. Here, we present a population genetic comparison of Batrachochytrium dendrobatidis isolates from an intensively studied region of frog decline, the Sierra Nevada of California. In support of a novel pathogen, we find low diversity, no amphibian-host specificity, little correlation between fungal genotype and geography, local frog extirpation by a single fungal genotype, and evidence of human-assisted fungus migration. In support of endemism, at a local scale, we find some diverse, recombining populations. Therefore neither epidemic spread nor endemism alone explains this particular amphibian decline. Recombination raises the possibility of resistant sporangia and a mechanism for rapid spread as well as persistence that could greatly complicate global control of the pathogen.

Genetic erosion and changes in distribution of sorghum (Sorghum bicolor L. (Moench)) landraces in north-eastern Ethiopia

Ethiopia is believed to be the centre of origin and domestication for sorghum, where sorghum remains one of the main staple crops. Loss of biodiversity is occurring at an alarming rate in Ethiopia and crops, including sorghum, have long been recognized as vulnerable to genetic erosion. A major collection of sorghum germplasm was made in 1973 by Gebrekidan and Ejeta from north-eastern Ethiopia. A new collection of landraces was made in 2003, and these were field evaluated at Sirinka in 2004 along with representative samples from the 1973 collection. Farmer surveys and soil and climate surveys were also performed. Preliminary analysis demonstrated that some important landraces have disappeared either locally or regionally in the past 30 years and many other landraces have become marginalized. Landraces which are less preferred in terms of agronomic value and end use, and introductions, have become increasingly important. Late maturing landraces were found to be particularly vulnerable, with a number disappearing altogether. Farmers have become more risk averse, and factors such as declining soil fertility, more frequent drought and unreliable rainfall, and increased pest infestation have contributed to a change in farmer landrace selection. Data are presented on the variability and unique characters of some of the Ethiopian landraces, and implications for conservation are discussed.

Genetics of heifer performance in 'wet' and 'dry' seasons and their relationships with steer performance in two tropical beef genotypes.

The genetics of heifer performance in tropical 'wet' and 'dry' seasons, and relationships with steer performance, were studied in Brahman (BRAH) and Tropical Composite (TCOMP) (50% Bos indicus, African Sanga or other tropically adapted Bos taurus; 50% non-tropically adapted Bos taurus) cattle of northern Australia. Data were from 2159 heifers (1027 BRAH, 1132 TCOMP), representing 54 BRAH and 51 TCOMP sires. Heifers were assessed after post-weaning 'wet' (ENDWET) and 'dry' (ENDDRY) seasons. Steers were assessed post-weaning, at feedlot entry, over a 70-day feed test, and after similar to 120-day finishing. Measures studied in both heifers and steers were liveweight (LWT), scanned rump fat, rib fat and M. longissimus area (SEMA), body condition score (CS), hip height (HH), serum insulin-like growth factor-I concentration (IGF-I), and average daily gains (ADG). Additional steer measures were scanned intra-muscular fat%, flight time, and daily (DFI) and residual feed intake (RFI). Uni- and bivariate analyses were conducted for combined genotypes and for individual genotypes. Genotype means were predicted for a subset of data involving 34 BRAH and 26 TCOMP sires. A meta-analysis of genetic correlation estimates examined how these were related to the difference between measurement environments for specific traits. There were genotype differences at the level of means, variances and genetic correlations. BRAH heifers were significantly (P < 0.05) faster-growing in the 'wet' season, slower-growing in the 'dry' season, lighter at ENDDRY, and taller and fatter with greater CS and IGF-I at both ENDWET and ENDDRY. Heritabilities were generally in the 20 to 60% range for both genotypes. Phenotypic and genetic variances, and genetic correlations, were commonly lower for BRAH. Differences were often explained by the long period of tropical adaptation of B. indicus. Genetic correlations were high between corresponding measures at ENDWET and ENDDRY, positive between fat and muscle measures in TCOMP but negative in BRAH (mean of 13 estimates 0.50 and -0.19, respectively), and approximately zero between steer feedlot ADG and heifer ADG in BRAH. Numerous genetic correlations between heifers and steers differed substantially from unity, especially in BRAH, suggesting there may be scope to select differently in the sexes where that would aid the differing roles of heifers and steers in production. Genetic correlations declined as measurement environments became more different, the rates of decline (environment sensitivity) sometimes differing with genotype. Similar measures (LWT, HH and ADG; IGF-I at ENDWET in TCOMP) were genetically correlated with steer DFI in heifers as in steers. Heifer SEMA was genetically correlated with steer feedlot RFI in BRAH (0.75 +/- 0.27 at ENDWET, 0.66 +/- 0.24 at ENDDRY). Selection to reduce steer RFI would reduce SEMA in BRAH heifers but otherwise have only small effects on heifers before their first joining.

Genetics of heifer puberty in two tropical beef genotypes in northern Australia and associations with heifer- and steer-production traits

A total of 2115 heifers from two tropical genotypes (1007 Brahman and 1108 Tropical Composite) raised in four locations in northern Australia were ovarian-scanned every 4-6 weeks to determine the age at the first-observed corpus luteum (CL) and this was used to de. ne the age at puberty for each heifer. Other traits recorded at each time of ovarian scanning were liveweight, fat depths and body condition score. Reproductive tract size was measured close to the start of the first joining period. Results showed significant effects of location and birth month on the age at first CL and associated puberty traits. Genotypes did not differ significantly for the age or weight at first CL; however, Brahman were fatter at first CL and had a small reproductive tract size compared with that of Tropical Composite. Genetic analyses estimated the age at first CL to be moderately to highly heritable for Brahman (0.57) and Tropical Composite (0.52). The associated traits were also moderately heritable, except for reproductive tract size in Brahmans (0.03) and for Tropical Composite, the presence of an observed CL on the scanning day closest to the start of joining (0.07). Genetic correlations among puberty traits were mostly moderate to high and generally larger in magnitude for Brahman than for Tropical Composite. Genetic correlations between the age at CL and heifer- and steer-production traits showed important genotype differences. For Tropical Composite, the age at CL was negatively correlated with the heifer growth rate in their first postweaning wet season (-0.40) and carcass marbling score (-0.49), but was positively correlated with carcass P8 fat depth (0.43). For Brahman, the age at CL was moderately negatively genetically correlated with heifer measures of bodyweight, fatness, body condition score and IGF-I, in both their first postweaning wet and second dry seasons, but was positively correlated with the dry-season growth rate. For Brahman, genetic correlations between the age at CL and steer traits showed possible antagonisms with feedlot residual feed intake (-0.60) and meat colour (0.73). Selection can be used to change the heifer age at puberty in both genotypes, with few major antagonisms with steer- and heifer- production traits.

Mitochondrial DNA supports the identification of two endangered river sharks (Glyphis glyphis and Glyphis garricki) across northern Australia

The river sharks (genus Glyphis) are a small group of poorly known sharks occurring in tropical rivers and estuarine waters across northern Australia, south-east Asia and the subcontinent. The taxonomy of the genus has long been unclear due to very few individuals having been caught and examined, resulting in a paucity of data regarding their distribution, biology and ecology. Only recently has attention focussed on the two Australian species, G. glyphis and G. garricki. This study is a result of a rare opportunity to collate the few samples that have been collected from these species and the bull shark Carcharhinus leucas, which shares an overlapping range. These samples were analysed using the DNA barcoding approach (cox1 mitochondrial gene), compared with six other species of carcharhinids and evaluated in light of the current taxonomic classification. Nine species-specific nucleotide differences were found between G. glyphis and G. garricki and no intra-specific variation provides strong support for the separation into distinct species. Significant differences were also observed at the inter-generic level, with Glyphis forming a distinct clade from Carcharhinus. This study provides the basis for future molecular studies required to better address conservation issues confronting G. glyphis and G. garricki in Australia.

Assessing the taxonomic status of dingoes Canis familiaris for conservation

1. The conservation status of the dingo Canis familiaris dingo is threatened by hybridization with the domestic dog C. familiaris familiaris. A practical method that can estimate the different levels of hybridization in the field is urgently required so that animals below a specific threshold of dingo ancestry (e.g. 1/4 or 1/2 dingoes) can reliably be identified and removed from dingo populations. 2. Skull morphology has been traditionally used to assess dingo purity, but this method does not discriminate between the different levels of dingo ancestry in hybrids. Furthermore, measurements can only be reliably taken from the skulls of dead animals. 3. Methods based on the analysis of variation in DNA are able to discriminate between the different levels of hybridization, but the validity of this method has been questioned because the materials currently used as a reference for dingoes are from captive animals of unproven genetic purity. The use of pre-European materials would improve the accuracy of this method, but suitable material has not been found in sufficient quantity to develop a reliable reference population. Furthermore, current methods based on DNA are impractical for the field-based discrimination of hybrids because samples require laboratory analysis. 4. Coat colour has also been used to estimate the extent of hybridization and is possibly the most practical method to apply in the field. However, this method may not be as powerful as genetic or morphological analyses because some hybrids (e.g. Australian cattle dog × dingo) are similar to dingoes in coat colour and body form. This problem may be alleviated by using additional visual characteristics such as the presence/absence of ticking and white markings.

Domestication for Conservation of an Endangered Species: The Case of the Wollemi Pine

A small population of tall slender conifers was discovered in 1994 in a deep rainforest canyon of the Wollemi National Park, New SouthWales, Australia. The living trees closely resembled fossils that were more than 65 million years old, and this ‘living fossil’ was recognised as a third extant genus in the Araucariaceae (Araucaria, Agathis and now Wollemia). The species was named the Wollemi pine (W. nobilis). Extensive searches uncovered very few populations, with the total number of adult trees being less than 100. Ex situ collections were quickly established in Sydney as part of the Wollemi Pine Recovery Plan. The majority of the ex situ population was later transferred to our custom-built facility in Queensland for commercial multiplication. Domestication has relied very heavily on the species’ amenability to vegetative propagation because seed collection from the natural populations is dangerous, expensive, and undesirable for conservation reasons. Early propagation success was poor, with only about 25% of cuttings producing roots. However, small increases in propagation success have a very large impact on a domestication program because plant production can be modelled on an exponential curve where each rooted cutting develops into a mother plant that, in turn, provides more rooted cuttings. An extensive research program elevated rooting percentages to greater than 80% and also provided in vitro methods for plant multiplication. These successes have enabled international release of the Wollemi pine as a new and attractive species for ornamental horticulture.

A comparison of alternative plant mixes for conservation bio-control by native beneficial arthropods in vegetable cropping systems in Queensland Australia.

Cucurbit crops host a range of serious sap-sucking insect pests, including silverleaf whitefly (SLW) and aphids, which potentially represent considerable risk to the Australian horticulture industry. These pests are extremely polyphagous with a wide host range. Chemical control is made difficult due to resistance and pollution, and other side-effects are associated with insecticide use. Consequently, there is much interest in maximising the role of biological control in the management of these sap-sucking insect pests. This study aimed to evaluate companion cropping alongside cucurbit crops in a tropical setting as a means to increase the populations of beneficial insects and spiders so as to control the major sap-sucking insect pests. The Population of beneficial and harmful insects, with a focus on SLW and aphids, and other invertebrates were sampled weekly oil four different crops which could be used for habitat manipulation: Goodbug Mix (GBM; a proprietary seed Mixture including self-sowing annual and perennial herbaceous flower species); lablab (Lablab purpureus L. Sweet); lucerne (Medicago sativa L.); and niger (Guizotia abyssinica (L.f.) Cass.). Lablab hosted the highest numbers of beneficial insects (larvae and adults of lacewing (Mallada signata (Schneider)), ladybird beetles (Coccinella transversalis Fabricius) and spiders) while GBM hosted the highest numbers of European bees (Apis mellifera Linnaeus) and spiders. Lucerne and niger showed little promise in hosting beneficial insects, but lucerne hosted significantly more spiders (double the numbers) than niger. Lucerne hosted significantly more of the harmful insect species of aphids (Aphis gossypii (Glover)) and Myzus persicae (Sulzer)) and heliothis (Heliothis armigera Hubner). Niger hosted significantly more vegetable weevils (Listroderes difficillis (Germar)) than the other three species. Therefore, lablab and GBM appear to be viable options to grow within cucurbits or as field boundary crops to attract and increase beneficial insects and spiders for the control of sap-sucking insect pests. Use of these bio-control strategies affords the opportunity to minimise pesticide usage and the risks associated with pollution.

Adaptation and management of Australian buffalograss cultivars for shade and water conservation

Soft-leaf buffalo grass is increasing in popularity as an amenity turfgrass in Australia. This project was instigated to assess the adaptation of and establish management guidelines for its use in Australias vast array of growing environments. There is an extensive selection of soft-leaf buffalo grass cultivars throughout Australia and with the countrys changing climates from temperate in the south to tropical in the north not all cultivars are going to be adapted to all regions. The project evaluated 19 buffalo grass cultivars along with other warm-season grasses including green couch, kikuyu and sweet smother grass. The soft-leaf buffalo grasses were evaluated for their growth and adaptation in a number of regions throughout Australia including Western Australia, Victoria, ACT, NSW and Queensland. The growth habit of the individual cultivars was examined along with their level of shade tolerance, water use, herbicide tolerance, resistance to wear, response to nitrogen applications and growth potential in highly alkaline (pH) soils. The growth habit of the various cultivars currently commercially available in Australia differs considerably from the more robust type that spreads quicker and is thicker in appearance (Sir Walter, Kings Pride, Ned Kelly and Jabiru) to the dwarf types that are shorter and thinner in appearance (AusTine and AusDwarf). Soft-leaf buffalo grass types tested do not differ in water use when compared to old-style common buffalo grass. Thus, soft-leaf buffalo grasses, like other warm-season turfgrass species, are efficient in water use. These grasses also recover after periods of low water availability. Individual cultivar differences were not discernible. In high pH soils (i.e. on alkaline-side) some elements essential for plant growth (e.g. iron and manganese) may be deficient causing turfgrass to appear pale green, and visually unacceptable. When 14 soft-leaf buffalo grass genotypes were grown on a highly alkaline soil (pH 7.5-7.9), cultivars differed in leaf iron, but not in leaf manganese, concentrations. Nitrogen is critical to the production of quality turf. The methods for applying this essential element can be manipulated to minimise the maintenance inputs (mowing) during the peak growing period (summer). By applying the greatest proportion of the turfs total nitrogen requirements in early spring, peak summer growth can be reduced resulting in a corresponding reduction in mowing requirements. Soft-leaf buffalo grass cultivars are more shade and wear tolerant than other warm-season turfgrasses being used by homeowners. There are differences between the individual buffalo grass varieties however. The majority of types currently available would be classified as having moderate levels of shade tolerance and wear reasonably well with good recovery rates. The impact of wear in a shaded environment was not tested and there is a need to investigate this as this is a typical growing environment for many homeowners. The use of herbicides is required to maintain quality soft-leaf buffalo grass turf. The development of softer herbicides for other turfgrasses has seen an increase in their popularity. The buffalo grass cultivars currently available have shown varying levels of susceptibility to the chemicals tested. The majority of the cultivars evaluated have demonstrated low levels of phytotoxicity to the herbicides chlorsulfuron (Glean) and fluroxypyr (Starane and Comet). In general, soft leaf buffalo grasses are varied in their makeup and have demonstrated varying levels of tolerance/susceptibility/adaptation to the conditions they are grown under. Consequently, there is a need to choose the cultivar most suited to the environment it is expected to perform in and the management style it will be exposed to. Future work is required to assess how the structure of the different cultivars impacts on their capacity to tolerate wear, varying shade levels, water use and herbicide tolerance. The development of a growth model may provide the solution.

Recognising the necessity for Indo-Pacific seagrass conservation.

Seagrass meadows are declining globally at an unprecedented rate, yet these valuable ecosystem service providers remain marginalized within many conservation agendas. In the Indo-Pacific, this is principally because marine conservation priorities do not recognize the economic and ecological value of the goods and services that seagrasses provide. Dependency on coastal marine resources in the Indo-Pacific for daily protein needs is high relative to other regions and has been found in some places to be up to 100%. Habitat loss therefore may have negative consequences for food security in the region. Whether seagrass resources comprise an important contribution to this dependency remains largely untested. Here, we assemble information sources from throughout the Indo-Pacific region that discuss shallow water fisheries, and examine the role of seagrass meadows in supporting production, both directly, and indirectly through process of habitat connectivity (e.g., nursery function and foraging areas). We find information to support the premise that seagrass meadows are important for fisheries production. They are important fishery areas, and they support the productivity and biodiversity of coral reefs. We argue the value of a different paradigm to the current consensus on marine conservation priorities within the Indo-Pacific that places seagrass conservation as a priority.

Resilience of a high-conservation-value, semi-arid grassland on fertile clay soils to burning, mowing and ploughing.

In grassland reserves, managed disturbance is often necessary to maintain plant species diversity. We carried out experiments to determine the impact of fire, kangaroo grazing, mowing and disc ploughing on grassland species richness and composition in a nature reserve in semi-arid eastern Australia. Vegetation response was influenced by winter-spring drought after establishment of the experiments, but moderate rainfall followed in late summer-autumn. Species composition varied greatly between sampling times, and the variability due to rainfall differences between seasons and years was greater than the effects of fire, kangaroo grazing, mowing or disc ploughing. In the fire experiment, species richness and composition recovered more rapidly after spring than autumn burning. Species richness and composition were similar to control sites within 12 months of burning and mowing, suggesting that removal of the dominant grass canopy is unnecessary to enhance plant diversity. Two fires (separated by 3 years) and post-fire kangaroo grazing had only minor influence on species richness and composition. Even disc ploughing caused only a small reduction in native richness. The minor impact of ploughing was explained by the small areas that were ploughed, the once-off nature of the treatment, and the high degree of natural movement and cracking in these shrink-swell soils. Recovery of the composition and richness of these grasslands was rapid because of the high proportion of perennial species that resprout vegetatively after fire and mowing. There appears to be little conservation benefit from fire, mowing or ploughing ungrazed areas, as we could identify no native plant species dependent on frequent disturbance for persistence in this grassland community. However, the ability of the Astrebla- and Dichanthium-dominated grasslands to recover quickly after disturbance, given favourable seasonal conditions, suggests that they are well adapted to natural disturbances (e.g. droughts, fire, flooding and native grazing).

Quantitative and molecular genetics of juvenile wood traits in radiata and slash/Caribbean pines.

The Juvenile Wood Initiative (JWI) project has been running successfully since July 2003 under a Research Agreement with FWPA and Letters of Association with the consortium partners STBA (Southern Tree Breeding Association), ArborGen and FPQ (Forestry Plantations Queensland). Over the last five and half years, JWI scientists in CSIRO, FPQ, and STBA have completed all 12 major milestones and 28 component milestones according to the project schedule. We have made benchmark progress in understanding the genetic control of wood formation and interrelationships among wood traits. The project has made 15 primary scientific findings and several results have been adopted by industry as summarized below. This progress was detailed in 10 technical reports to funding organizations and industry clients. Team scientists produced 16 scientific manuscripts (8 published, 1 in press, 2 submitted, and several others in the process of submission) and 15 conference papers or presentations. Primary Scientific Findings. The 15 major scientific findings related to wood science, inheritance and the genetic basis of juvenile wood traits are: 1. An optimal method to predict stiffness of standing trees in slash/Caribbean pine is to combine gravimetric basic density from 12 mm increment cores with a standing tree prediction of MoE using a time of flight acoustic tool. This was the most accurate and cheapest way to rank trees for breeding selection for slash/Caribbean hybrid pine. This method was also recommended for radiata pine. 2. Wood density breeding values were predicted for the first time in the STBA breeding population using a large sample of 7,078 trees (increment cores) and it was estimated that selection of the best 250 trees for deployment will produce wood density gains of 12.4%. 3. Large genetic variation for a suite of wood quality traits including density, MFA, spiral grain, shrinkage, acoustic and non-acoustic stiffness (MoE) for clear wood and standing trees were observed. Genetic gains of between 8 and 49% were predicted for these wood quality traits with selection intensity between 1 to 10% for radiata pine. 4. Site had a major effect on juvenile-mature wood transition age and the effect of selective breeding for a shorter juvenile wood formation phase was only moderate (about 10% genetic gain with 10% selection intensity, equivalent to about 2 years reduction of juvenile wood). 5. The study found no usable site by genotype interactions for the wood quality traits of density, MFA and MoE for both radiata and slash/Caribbean pines, suggesting that assessment of wood properties on one or two sites will provide reliable estimates of the genetic worth of individuals for use in future breeding. 6. There were significant and sizable genotype by environment interactions between the mainland and Tasmanian regions and within Tasmania for DBH and branch size. 7. Strong genetic correlations between rings for density, MFA and MoE for both radiata and slash/Caribbean pines were observed. This suggests that selection for improved wood properties in the innermost rings would also result in improvement of wood properties in the subsequent rings, as well as improved average performance of the entire core. 8. Strong genetic correlations between pure species and hybrid performance for each of the wood quality traits were observed in the hybrid pines. Parental performance can be used to identify the hybrid families which are most likely to have superior juvenile wood properties of the slash/Caribbean F1 hybrid in southeast Queensland. 9. Large unfavourable genetic correlations between growth and wood quality traits were a prominent feature in radiata pine, indicating that overcoming this unfavourable genetic correlation will be a major technical issue in progressing radiata pine breeding. 10. The project created the first radiata pine 18 k cDNA microarray and generated 5,952 radiata pine xylogenesis expressed sequence tags (ESTs) which assembled into 3,304 unigenes. 11. A total of 348 genes were identified as preferentially expressed genes in earlywood or latewood while a total of 168 genes were identified as preferentially expressed genes in either juvenile or mature wood. 12. Juvenile earlywood has a distinct transcriptome relative to other stages of wood development. 13. Discovered rapid decay of linkage disequilibrium (LD) in radiata pine with LD decaying to approximately 50% within 1,700 base pairs (within a typical gene). A total of 913 SNPS from sequencing 177,380 base pairs were identified for association genetic studies. 14. 149 SNPs from 44 genes and 255 SNPs from a further 51 genes (total 95 genes) were selected for association analysis with 62 wood traits, and 30 SNPs were shortlisted for their significant association with variation of wood quality traits (density, MFA and MoE) with individual significant SNPs accounting for between 1.9 and 9.7% of the total genetic variation in traits. 15. Index selection using breeding objectives was the most profitable selection method for radiata pine, but in the long term it may not be the most effective in dealing with negative genetic correlations between wood volume and quality traits. A combination of economic and biological approaches may be needed to deal with the strong adverse correlation.