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The Wood From The Trees - Issue Five - Molecular breeding to improve wood quality

Our association genetics project led by the Melbourne University molecular breeding group was featured in Edition 4 of our program newsletter.  You may remember that their approach is to search for different functional alleles (superior and inferior gene variants) in a number of candidate genes believed to contribute strongly to variation in economically important wood traits such as cellulose content and pulp yield, in an association population of over 400 unrelated Eucalyptus globulus (blue gum) trees.  Our ultimate aim is to routinely assay, at low cost, the allele patterns of many trees in breeding populations and combine this molecular information with standard quantitative data from breeding programs to accelerate genetic gain in breeding. The University of Melbourne research team is examining 20 carefully selected candidate genes known to be involved in determining wood quality, but of course there are about 30 000 genes in eucalypts, so there will be other genes that contribute.

Simulating the impact of molecular breeding

Greg Dutkowski has been running simulations for our CRC project to predict the impact of molecular information on blue gum breeding using his PPGSim breeding software, which can simulate all the stages of a breeding and deployment program.  Greg presented initial results at the recent Australasian Forest Genetics Conference held this April in Albany, WA.  His preliminary conclusion was that if molecular markers can account for 30% of the additive genetic variance in pulp yield in the breeding program, they could be used to accelerate breeding gain, by identifying at the seedling stage individuals with outstanding wood properties, enabling more rapid breeding of these outstanding trees.

Introducing Jules Freeman

Jules Freeman measuring trees in Victorian trial

Jules measuring trees in the Victorian trial

Jules Freeman, who has a PhD from UTas, is midway through his two-year UTas postdoctoral studies on molecular breeding for blue gum. Jules is studying a trial of three control-pollinated families of blue gum which the Southern Tree Breeding Association has planted at two locations, near Manjimup in Western Australia and near Hamilton in western Victoria.  With help from STBA’s David Pilbeam, Jules has extracted DNA from over 600 trees, and determined their wood properties from wood cores. Kraft pulp yield and cellulose were predicted by Geoff Downes and our Project 2.4 team using their near-infra-red calibrations. Quantitative genetic analysis showed there is wide variation in wood density, cellulose content and pulp yield among the individual trees in each family, and that families differed significantly in their mean performance, with family rankings stable across the two sites for most of the studied traits.

Now Jules is coming to the really interesting part of his project.  Luke McManus of Melbourne University is checking the DNA of the mother and father trees that are the parents of each of Jules’s families, to see if they carry the superior and inferior functional alleles (gene variants) of the candidate genes that Luke has identified in his research.  If they do, the progenies in Jules’s study families will segregate for superior and inferior versions of the genes, providing a further 'test bed' to validate the impact of these alleles in the STBA breeding population.   

DArT molecular markers (see http://www.diversityarrays.com/applicationsdart.html), which have been newly developed for eucalypts through the work of CRC’s Dr Dot Steane, will be used by Jules to 'dissect' overall genetic control of wood properties in the three blue gum families.  This is like the QTL (Quantitative Trait Loci) analysis approach used in previous CRCs, except that we now have over 2000 variable DArT loci across the genome—more than ten times the precision of previous QTL analyses.  This dissection will enable Jules to identify the regions of the blue gum genome which have the greatest control over important wood properties in his families. This will help us to assess the proportional contribution made by the gene variants that the Melbourne University team has discovered, to the total genetic control of wood properties.

Linking to the eucalypt genome sequencing project

An international collaborative project is currently well underway to sequence the genome of Eucalyptus grandis (http://eucalyptusdb.bi.up.ac.za). Each eucalypt DArT marker will also be sequenced, providing a direct link between DArT linkage maps and the eucalypt genome sequence.  As a result, QTL discovered using the fine-scale linkage maps based on DArT markers will allow us to interrogate the genome sequence to identify nearby candidate genes that may be contributing to control of the traits of interest.  Such candidate genes can then be tested in association studies. We hope this approach will help us get to the stage where we can account for much of the genetic control of wood properties and make molecular breeding a favoured tool for Australia’s eucalypt breeding programs.

Contacts

Jules Freeman
phone  03 6226 1828
jules.freeman@utas.edu.au

Luke McManus
phone 03 5321 4100
lmcmanus@unimelb.edu.au