Expected benefit of genomic selection over forward selection in conifer breeding and deployment.

Genomic selection is a proven technology in animal and plant breeding to accelerate genetic gain, but as yet is to be fully realised in forest tree breeding. This paper examines, through stochastic simulation, the potential benefits of genomic selection (GS) over forward selection (FS) in a typical conifer breeding program. Methods of speeding the deployment of selected material were also considered, including top-grafting onto mature seed orchard ortets, using additional replicates of clones in archives for crossing, and embryogenesis and clonal propagation. Genetic gain per generation was found to increase considerably when the size of the training population was larger (800 c.f. 3000 clones), or when the heritability was higher (0.2 c.f. 0.5). The largest genetic gain, of 24% was achieved where large training populations (3000 clones) and high heritability traits (0.5) were combined. The accuracy of genomic breeding values (GEBVs) increased with the increase in the number of clones in the training population, the heritability of the trait and the density of the SNP markers. Calculated accuracies of simulated GEBVs and genetic gain per unit of time suggested that 2000 clones in the training population is the minimum size for effective genomic selection for conifers. Compared with forward selection, genomic selection with 2000 clones in the training population, and a 60K SNP panel, an increase of 1.58 mm per year in diameter-at-breast-height (DBH) and 2.44 kg/m3 per year for wood density can be expected. After one generation (9-years), this would be equivalent to 14.23 mm and 21.97 kg/m3 for DBH and wood density respectively. Deploying clones of the selected individuals always resulted in higher additional genetic gain than deploying progeny/seedlings. Deploying genetic material selected from genomic selection with top-grafting for early coning appeared to be the best option. Application of genomic selection to conifer breeding programs, combined with deployment tools such as top-grafting and embryogenesis are powerful tools to speed the delivery of genetic gain to the forest

Insect damage in eucalyptus: A review of plantations in Chile

Chile has more than 330 000 ha of eucalypt plantations, predominantly in the eighth to the tenth region (approximately 34 to 41°S). Eucalyptus globulus ssp. globulus is the principal eucalypt planted, but Eucalyptus nitens, Eucalyptus camaldulensis, Eucalyptus delegatensis and Eucalyptus viminalis are also grown. There are four main insect pests that have been detected attacking these eucalypts in Chile: the defoliator Gonipterus scutellatus, the bark borers Phoracantha semipunctata and Phoracantha recurva and the native wood borer Chilecomadia valdiviana. More recently, Thyrinteina arnobia and Ctenarytaina eucalypti have been detected. Gonipterus scutellatus and P. recurva have been discovered in Chile within the last 2 years and it is hoped they may still be eliminated using a combination of biological control and chemical control of local populations. Phoracantha recurva and P. semipunctata are not considered a problem because attack only occurs in areas of water deficit, away from current eucalypt plantations. Chilecomadia valdiviana can damage plantations of E. nitens but rarely attacks other eucalypts.◊Chilecomadia valdiviana may cause future problems through further host shifts. Thyrinteina arnobia has only been detected during quarantine surveillance in the port of Valparaiso. Ctenarytaina eucalypti, recently detected in August 1999, had an initial limited distribution in the first region. However, since then, this insect has expanded its distribution south up to the tenth region. None of the insects recorded on eucalypts in Chile to date currently presents a threat to the eucalypt industry. It is also essential that additional resources are made available for their continued monitoring and control, particularly given that the 44% of plantations are held by small to medium property owners that would otherwise be unable to control a serious outbreak because of economic restrictions

dataset for Dothistroma

Phenotypic observations for Dothistroma resistance with seven columns: trial ID, testedas (C: clone, F for full-sibs), tree ID, replicate, Setgroup, Dothistroma resistance in percentage and age of assessmen

dataset for diameter

Phenotypic observations for DBH with eight columns: trial ID, testedas (C: clone, F for full-sibs), tree ID, repicate, setgroup, row, DBH observation in millimeters and age of assessmen

pedigree file

This is pedigree file with three columns: Tree ID, Mother ID and Father I

dataset for height

Phenotypic observations for height with nine columns: trial ID, testedas (C: clone, F for full-sibs), tree ID, replicate, setgroup, row, block (Blk), age of assessment and height observation in meter

Genetic improvement of resistance to cyclaneusma needle cast in Pinus radiata

Progeny testing of resistance to needle loss caused by Cyclaneusma minus has been included in the needle disease resistance strategy of Pinus radiata in New Zealand since the late 1970s. Data on progeny trials, two in the North Island of New Zealand and one in Tasmania, Australia were available to estimate heritability, between trait genetic correlations and genotype by environment interaction. Resistance to cyclaneusma needle cast had moderate estimates of heritability (0.25 to 0.46) at all sites. Genetic correlations between the assessed traits indicated that selection for faster early growth, i.e. tree height at age four and diameter at breast height at age six favours trees that are prone to Cyclaneusma infection, whilst a favourable genetic association between resistance to cyclaneusma needle cast and productivity was evident at later assessment that was at age nine. No significant genotype by environment interaction was found for resistance to cyclaneusma needle cast, however, stability of genotypes across a wider range of environments and with a high genetic connectedness require more research. Considerable genetic improvement can be achieved for resistance to cyclaneusma needle cast and indirect selection for the trait should be pursued by selecting for productivity and culling susceptible genotypes from breeding.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Genetics of wood stiffness and its component traits in Pinus radiata

The potential for breeding Pinus radiata D. Don to improve wood stiffness (modulus of elasticity, MoE) was examined by obtaining pith-to-bark cores from trees at breast height in two independent genetic trials. The effectiveness of early selection for stiffness and indirect selection on the component traits, microfibril angle (MfA) and wood density, was determined as well as the age-related changes in the genetic variation of these traits. The first trial comprised 50 open-pollinated families in the central North Island, New Zealand. The second trial comprised 20 control-pollinated families in New South Wales, Australia. The genetic control of MfA, density, and MoE was found to be high in the corewood and moderate in the outerwood. Estimated genetic correlations suggested that early selection for most traits would be successful but could be carried out slightly earlier at the New Zealand site than at the Australian site. To maximize gain in the corewood, selection for MoE and MfA would be most effective around rings 4-8. There were no adverse correlations between MoE and MfA or density, implying that selection for MoE would also improve MfA and density

Simulation of hybrid forest tree breeding strategies

Computer simulation is the only realistic method of evaluating alternative methods of breeding hybrid forest trees. Empirical tests would be very long term and expensive. This paper describes the development of a simulation program, called XSIM, which generates two different but closely related outcrossing tree species. The genetic correlation between performance in each parental species and performance in the resulting hybrid can be set, in addition to the amounts and types of variances in each parental species. The breeding strategies available for testing include conventional reciprocal recurrent selection, reciprocal recurrent selection with forward selection, recurrent selection within each pure species, and the creation of a synthetic species. XSIM allows the strategies to be compared using the same base populations, equivalent selection intensities, and comparable mating patterns. Innovative best linear unbiased prediction procedures allow all ancestral and current progeny generation data, from both parental species and the hybrid, to be analysed together. The theoretical basis for the simulation is given, and genetic and statistical models are described. In summary, XSIM allows rigorous comparisons of the strategies in terms of genetic gain per time and provides useful insight into hybrid forest tree breeding