The radiata pine tree improvement program in Australia estimates breeding values for selection criteria traits (SCTs) such as diameter at breast height and height, as measured in progeny trials. The data in each trial are standardised so that estimated breeding values (EBVs) are expressed in units of additive genetic standard deviations. EBVs for harvest-age breeding objective traits (BOTs), such as stand volume mean annual increment (VMAI), are predicted from the SCT EBVs and expressed in measurement units. BOTs are not routinely measured in progeny trials because it would prolong the generation interval. However, the slope of the relationship between VMAI and BOT EBV provides an estimate of the scale of VMAI EBVs. This slope was estimated using 26 block-plot realised-gain trials with stand total produced basal area (TPBA) measurements near age ten years and 11 trials with final VMAI measurements between 15 and 25 years extrapolated to a harvest age of 25. In all trials, EBVs were positively correlated with growth, demonstrating substantial realised genetic gains. At age ten years, on average, one standard deviation of BOT EBV corresponded to a realised gain in TPBA of 3.7 m(2) ha(-1) and an additive coefficient of variation (CVA) of 11.2%. At the harvest age of 25 years, one standard deviation in EBV corresponded on average to realised gains in VMAI of 4.2 m(3) ha(-1) y(-1) and a CVA of 15.0%. Methods for incorporating estimated genetic gains into growth and yield modelling and forest valuations are discussed.

Competition is a concern for tree breeding because of its potential to reduce the genetic gain. Competition, if not accounted for in the analytical model, can potentially introduce a source of bias in genetic parameter estimation and breeding value prediction. This study modelled competition between trees in 20 Swedish progeny trials of Norway spruce (Picea abies (L.) Karst.), Scots pine (Pinus sylvestris L.), and lodgepole pine (Pinus contorta Douglas ex Loudon). The competition model assumed a tree has a direct additive genetic effect, which affects the tree’s own phenotype, and an indirect additive effect, which affects the phenotypes of its neighbours. Genetic parameters were estimated via a factor analytic structure in which separate indirect effects were considered for each neighbour, or via a combined indirect effect approach. We analysed diameter, as it is the trait that can be expected to be affected most by competition. Competition at the genetic level was detected in 17 of the 20 trials analysed. In most cases, the ratio of indirect to direct additive variance was less than 20% and no major changes in ranking resulted. At this stage, there is little incentive to incorporate indirect effects into program-wide genetic evaluation models. The added complexity is not commensurate with the benefit that would be gained.

Productivity of forest tree plantations can be maximised by matching genetically improved planting stock to environments where it performs best. Radiata pine (Pinus radiata D. Don) breeding and deployment of genetically improved stock in Australia are currently based on the National Plantation Inventory (NPI) regions. These regions are not based on environmental drivers and biological patterns of genotype by environment interaction (G × E), so they may not deliver optimal genetic gains across plantation areas in Australia. This study used diameter at breast height data from trial sites with common parents to estimate site–site and age–age additive genetic correlations, and compile them into a database. A custom-built script in R was developed, which models the correlation estimates by minimising the weighted error sum of squares from the model to the estimates. First, parameters for the Lambeth’s age–age correlation model were derived to adjust for differences in age between sites. Second, estimates of average site–site additive genetic correlations between and within NPI regions were compared with currently assumed values. Third, to identify new breeding and deployment regions, sites were sequentially divided into groups based on critical values of climate and soil variables. Sites were first split into two clusters based on mean daily minimum temperature of wettest quarter, at a threshold of 9.0 °C, and then within the cool cluster, based on rainfall in March, at a threshold of 68 mm. Variances among breeding values were compared for different site classifications as a measure of potential genetic gain. The results from this study are currently being used to redefine the breeding and deployment regions for radiata pine grown in Australia.

In breeding forest trees, as for livestock, the goal is to capture as much genetic gain as possible for the breeding objective, while limiting long- and short-term inbreeding. The Southern Tree Breeding Association (STBA) is responsible for breeding Australia's two main commercial forest tree species and has adopted algorithms and methods commonly used in animal breeding to achieve this balance. Discrete generation breeding is the norm for most tree breeding programmes. However, the STBA uses an overlapping generation strategy, with a new stream of breeding initiated each year. A feature of the species bred by the STBA (Pinus radiata and Eucalyptus globulus) is the long interval (up to 7 years) between when an individual is mated and when its progeny is first assessed in field trials and performance data included in the national performance database. Mate selection methods must therefore recognize the large pool of unmeasured progeny generated over recent years of crossing. In addition, the substantial delay between when an individual is selected in a field trial and when it is clonally copied into a mating facility (breeding arboretum) means that selection and mating must occur as a two-step process. In this article, we describe modifications to preselection and mate selection algorithms that allow unmeasured progeny (juveniles) to be recognized. We also demonstrate that the addition of hypothetical new progeny to the juvenile pool is important for computing the increase in average co-ancestry in the population. Methods outlined in this article may have relevance to animal breeding programmes where between mating and progeny measurement, new rounds of mating are initiated.

In forest tree species with large natural ranges, there are usually several to many separate breeding populations, each designed to capture elite material suited to a particular geographic region. Separate test series are often dedicated to each population. Because the aim is to optimise gain in the meta-population, it is important to ensure that test series are linked so that individuals can be compared across test series as well as within. Computer simulation was used to determine the most efficient strategy for obtaining linkage. The average accuracy of a genetic value contrast between individuals in the same and in different test series was used as the criterion for assessing the optimal level of linkage. Accuracy is a function of the elements of the inverse coefficient matrix for a mixed linear model within a best linear unbiased prediction framework (BLUP). Material used to link test series was either common test families, common check-lots such as seed orchard bulks, or families generated by inter-crossing parents from different test series. Use of common test families was the most efficient strategy for the scenarios tested, which included having 50 parents crossed to produce 50 test families in each of three populations. For a low-heritability scenario, the amount of linkage material, relative to test material, needed to be 8 and 12 %, for progeny and parents, respectively, in order for a contrast between individuals in different test series to have equivalent accuracy as a contrast between individuals in the same test series. Other strategies were less efficient in terms of the amount of linkage material needed to obtain this equivalency.

Based on analyses using 20 genetically connected radiata pine trials and on the pattern of trial-trial genetic correlations, current regionalisation of breeding in southern Australia seems justified. However, relationships between environmental variables and genotype by environment interaction are complex.

The current benchmark for genetic value prediction is program-wide multivariate Best Linear Unbiased Prediction of measured traits, from which harvest age traits are predicted and then combined into economic indices. This is a very flexible framework, but is demanding to implement and not many programs have done so. Models for hybrid populations, calculation of standard errors for harvest traits and indices for genotypes, families and larger deployment units, economic models for risk traits, and integration of synthetic variables derived from markers information into evaluation are all in the process of operational adoption There are other advances, ranging from accounting for indirect genetic effects to integration of genome-wide molecular information for which there is still much work needed to allow them to be used on a program-wide scale. For operational implementation, both the computational systems and their supporting database systems need to be developed to store and process the increasing amounts of information used.

Mixed models incorporating the inverse of a numerator relationship matrix (NRM) are widely used to estimate genetic parameters and to predict breeding values in animal breeding. A simple and quick method to directly calculate the inverse of the NRM has been historically developed for diploid animal species. Mixed models are less used in plant breeding partly because the existing method for diploids is not applicable to autopolyploid species. This is because of the phenomenon of double reduction and the possibility that gametes carry alleles which are identical by descent. This paper generalises the NRM and its inverse for autopolyploid species, so it can be easily incorporated into their genetic analysis. The technique proposed is to first calculate the kinship coefficient matrix and its inverse as a precursor to calculating the NRM and its inverse. This allows the NRM to be calculated for populations containing individuals of mixed ploidy levels. This generalization can also accommodate uncertain parentage by generating the “average” relationship matrix. The possibility that non-inbred parents can produce inbred progeny (double reduction) is also discussed. Rules are outlined that are applicable for any level of ploidy. Examples of use of the matrix are provided using simulated pedigrees.

Genetic variation in drought damage in Eucalyptus globulus was studied in a sublined trial series across four neighbouring sites in Western Australia linked by ten common families. The trials included approximately 400 open-pollinated families, encompassing 51 native stand collection localities and 19 subraces from throughout the geographic range of the species. Data were analysed using mixed models, with spatial analysis used to better identify genetic effects. Significant subrace differences in drought damage were detected, with both broad-scale, regional and localised clines evident. The quantitative genetic differentiation between subraces as measured by Q ST (0.39 ± 0.091) was significantly greater than the F ST for neutral marker expectations and consistent with diversifying selection shaping the patterns of subrace divergence in drought susceptibility. This conclusion is supported by the significant association of subrace drought susceptibility with bioclimatic parameters, particularly those associated with temperature seasonality. Less drought damage was observed in subraces originating from areas with more temperature seasonality, but also less radiation and rainfall seasonality, less winter rainfall, higher radiation and higher temperatures in the warmest month. Significant additive genetic variation in drought damage was detected within subraces, with narrow-sense heritabilities ranging from 0.14 to 0.20. We argue that spatial genetic variation in drought susceptibility of E. globulus has been shaped by natural selection acting at multiple scales and discuss opportunities for exploiting this genetic variation in breeding and deployment programs.

Growth and form traits data were obtained from eight provenance trials of radiata pine (Pinus radiata D. Don) planted across the radiata pine plantation estate in southeast Australia. The genetic pool included 466 open-pollinated families collected from Año Nuevo, Monterey and Cambria provenances on the Californian mainland coast in the USA and from Guadalupe and Cedros islands off the coast of Baja California in Mexico. Early survival of all provenances was around 90%, except for Cedros (<60%). Monterey and Año Nuevo were the best performers at almost all sites. However, good growth performance of Cambria and good stem straightness of Guadalupe on some sites are important results, because the genetic base of the present Australian plantations evidently originated from only Monterey and Año Nuevo. The average estimated single-site heritability for diameter at breast height was 0.22 and 0.32 at juvenile and mature ages, respectively. Heritability estimates for stem straightness and branching ranged from 0.23 to 0.55. Genetic correlation estimates between diameter at breast height (DBH) at juvenile and rotation ages were all >0.80. Estimates of between-site genetic and provenance correlations for DBH were often low, indicating high genotype by environment interaction across trials, consistent with previous Australian studies. However, there was minimal G × E among trials on high-altitude high-rainfall sites and among trials on low-altitude, low-rainfall sites.

Eucalyptus nitens (Deane & Maiden) Maiden is widely planted in temperate regions of the southern hemisphere, principally for pulpwood production. Eucalyptus denticulata I.O. Cook & P.Y. Ladiges was previously recognised as an informal variant of E. nitens and, accordingly, was included in many ‘E. nitens’ field trials. We reviewed data from 85 E. nitens/E. denticulata field trials, located in Australia, Chile, China, Italy, Lesotho, New Zealand, South Africa and Zimbabwe and ranging in age from less than one year to 14 years, to investigate racial (among population groups) genetic variation in growth, wood-property, tree-architecture, fitness and morphological/developmental traits. Meta-analyses were undertaken on these data to gauge the significance of differences among races across trials. Race × rainfall zone interaction was also investigated by categorising field trials as summer-rainfall, winter-rainfall or nursery-based. Race × rainfall zone interaction was significant for growth traits only. In general, Central Victorian E. nitens populations outperformed New South Wales E. nitens populations in winter-rainfall zones, but this ranking was reversed in summer-rainfall zones. On average, E. denticulata grew less rapidly than the best-performing E. nitens races, particularly in winter-rainfall zones. Differences among races were detected in basic density, a commercially important trait, but these differences were small in magnitude. Significant differences among races were also evident in branch size and stem form (straightness). Eucalyptus denticulata races had significantly thinner branches than all E. nitens races except Southern Central Victorian, and Central Victorian E. nitens races generally had the straightest stems. The small number of trials represented for most traits limited the power of meta-analyses but significant differences among races detected in our study are likely to represent consistent and robust differences across a broad range of environments.

Pine needle blight, caused by Dothistroma septosporum (Dorog.) M. Morelet, is one of the most serious foliar diseases of Pinus spp. in Australia and New Zealand. In 16 Pinus radiata (D. Don.) progeny trials in northeastern Victoria, Australia, Dothistroma-caused defoliation varied widely among trials and assessment years, ranging from 5% to 65%. The estimated narrow sense heritability ranged from nonsignificant to as high as 0.69 with a median of 0.36. Spatial autocorrelation of residuals accounted for a significant proportion of residual variance, and that increased heritability estimates. Genetic correlation between defoliation scores at an early age and growth at a later age was negative with a median value of -0.39. Phenotypic correlation between defoliation and survival was low and negative with a median value of -0.11. Economic analyses indicated that at sites with a high risk of infection, the effect of reducing defoliation on profitability was comparable with that of increasing growth at sites free from infection. The genetic parameters and economic impacts of Dothistroma were used to derive selection indices and include resistance to defoliation into the current breeding objective for radiata pine.

Serial cutting propagation means that clones are produced in consecutive propagation cycles, where a new round of cuttings are taken from the previously rooted cuttings, etc. The objective of this study was to judge the importance of propagation cycle on height growth in field trials. In a field trial series with Norway spruce clones, comprising nine trials in four cutting propagation cycles, propagation cycle only had a minor effect on height growth compared to the site effect. For inter-site correlation models where all trials were included, the best fit was obtained by an unstructured model, while the most parsimonious model included constraints on the correlations depending on cycle structure. Model constraints based on grouping of the trials by site productivity did not improve the fit. Testing for generally good performers over a range of different site conditions appears to be a good approach, unless drivers of genotype by environment interaction can be identified.

Sustainable management of native forest gene pools requires an understanding of the levels and spatial patterns of genetic diversity in tree species. This diversity impacts on numerous management issues including seed transfer guidelines and in situ genetic resource conservation. Our long-term studies of Eucalyptus globulus (Tasmanian Blue Gum) have provided unprecedented insights into the complexity of the genetic variation that can exist in natural populations. We demonstrate that E. globulus comprises a fine-scale mosaic of family groups superimposed on a complex spatial pattern of local and broad-scale adaptive and non-adaptive genetic variation. The high level of genetic diversity observed within forest tree species such as E. globulus, coupled with their flexible breeding systems, provides the fundamental elements for adaptation to futureenvironmental challenges.

Genetic parameters were estimated for diameter at breast height (DBH), height and core basic density (CBD) from ten second-generation control-pollinated Eucalyptus globulus progeny trials in Australia. Using multi-site analysis we aimed, firstly, to determine a suitable linear model to fit to the data and, secondly, to determine the relative importance of additive and non-additive genetic effects. A model with heterogeneous additive and error variances was used for all traits. The individual site heritabilities averaged 0.12 for DBH, 0.11 for height and 0.44 for CBD. Over all sites, the ratios of SCA (specific combining ability) and subrace to additive genetic variance for DBH (0.25 and 0.5) and height (0.30 and 0.25) were significantly greater than zero, but not for CBD (0.08 and 1.00). Inter-site additive genetic correlations were 0.71 for DBH, 0.72 for height and 1.07 for CBD, and all were not significantly different from 1. This study suggests that, for early growth, levels of dominance are comparable to additive genetic effects in this breeding population and there are significant genetic differences between subraces. In contrast, for CBD most genetic variation was additive and significant differences between subraces could not be detected with the small sample.

A system where carbon sequestration was directly dependent upon biomass production in a plantation was modelled to assess whether economic breeding objectives for the genetic improvement of Eucalyptus globulus were sensitive to potential revenues from carbon sequestration. Carbon dioxide equivalent accumulation in the biomass (CO2e) of the Australian E. globulus plantation estate established between 2004 and 2012 was estimated. Total carbon dioxide equivalent (CO2e) accumulation was in the order of ∼146 t CO2e ha−1, of which 62 t CO2e ha−1 were tradable in 2012 (the 1st Kyoto Protocol commitment period) and a further 30 t CO2e ha−1 were tradable in 2016 (a hypothetical second Kyoto protocol commitment period). The correlated response of breeding objectives with and without carbon revenues (ΔcG h 1) never fell below 0.86 in sensitivity analysis, and the mean was 0.93. Where economic breeding objectives for the genetic improvement of Eucalyptus globulus for pulpwood plantations are based on maximizing net present value by increasing biomass production, the consideration of carbon revenues in economic breeding objectives will have no significant effect on the relative economic weights of the key economic traits, wood basic density and standing volume at harvest.