IUFRO Breeding theory and progeny testing

For the last four years the Southern Tree Breeding Association (STBA) of Australia has been using the TREEPLAN® system for an integrated genetic evaluation of all of the current and ancestral trees in its national breeding populations of Eucalyptus globulus and Pinus radiata. These evaluations have involved the simultaneous multivariate prediction of breeding values for each species of over 150,000 genotypes from 3 to 4 generations of breeding for more than 10 traits. The models used include all relevant design features and weight each trial by its heritability. Age to age, site to site and inter-trait correlations are all used and are incorporated in the trait definitions. These large multi-variate runs represent the most comprehensive breeding value calculations for tree breeding, but they run in less than 10 minutes on a standard computer. They are only possible because of an integrated data management system, some sophisticated programming from the Animal Genetics and Breeding Unit (AGBU) of the University of New England (Drs Bruce Tier and Richard Kerr), and some approaches to combining information across sites with heterogenous variances contributed by the Cooperative Research Centre for Sustainable Production Forestry (me and Dr Luis Apiolaza). TREEPLAN® is based on the BREEDPLAN® software that routinely predicts genetic values for 23 additive and 3 maternal traits in breeding populations of 1.2 million animals, so it is very efficient.

The STBA has now created a spin-off company called PLANTPLAN Genetics, to commercial its genetic evaluation services using its data management system and TREEPLAN®. I have taken the bold step of joining the company to get these products that I helped developed more widely used. I am proud of them, and I think that they can really help breeding programs boost their gain by effectively managing all of their data and information, and using it all in genetic evaluation. The system works within an intellectual framework developed by animal breeders to maximise economic gain in their comparatively unstructured breeding populations. When you look back at the efficiency of selection in previous generations, it can be as low as 30% of what could have been achieved with proper economic models and integrated analysis. So there’s plenty of scope for increased gain within this framework.
So far with the new service, the system has been used for breeding value prediction in one Eucalyptus nitens breeding program, and similar models have been used in two other Eucalyptus globulus programs. Two further projects, one in Eucalyptus nitens and the other in Pinus sylvestris are currently in progresss. The system works and is extremely flexible - we are developing proposals for kiwifruit and sugar cane breeding programs. Following a recent trip to Brazil, we are developing pilot studies for the mixed pure species and hybrid breeding programs for eucalypts typical of their programs.

With funding from the Forest and Wood Products Research and Development Corporation of Australia, there is also a $US 1 million project with STBA and AGBU to extend the system. New functionality will include the ability to integrate molecular information, spatial analysis and extend the model to predict total as well as additive genetic values.

An advertisement is probably not appropriate for an IUFRO working group newsletter, but I am certainly happy to talk with anyone who has a large and messy data set covering many trials across generations of breeding and who is at a loss as to how to manage its complexity and get the most out of it. For further literature you can go to the STBA web site www.stba.com.au or to the following references.

Kerr RJ, Tier B, McRae TA, Dutkowski GW, Apiolaza LA (2001). TREEPLANTM A genetic evaluation system for forest tree improvement. In 'Developing the Eucalypt of the Future'. 10-15 September, Valdivia, Chile. p. 74.

Kerr RJ, Dutkowski GW, Apiolaza LA, McRae TA, Tier B (2002). Developing a genetic evaluation system for forest tree improvement - the making of TREEPLAN®. In '7th World Congress on Genetics Applied to Livestock Production'. 19-23 August, Montpellier, France.

McRae TA, Dutkowski GW, Pilbeam DJ, Powell MB, Tier B (2004). Genetic Evaluation Using the TREEPLAN® System. In 'Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future'. Eds B Li and S McKeand. 1- 5 November 2004 Charleston, South Carolina. (North Carolina State University: Raleigh, North Carolina).

Graser HU, Tier B, Johnson DJ, Barwick SA (2005). Genetic evaluation for the beef industry in Australia. Australian Journal of Experimental Agriculture 45: 913-921.

Contact: Dr Greg Dutkowski, PLANTPLAN Genetics Pty Ltd, Australia.