Genomic mapping of growth and wood quality traits in Eucalyptus hybrids:   This project aims at dissecting the molecular basis of complex growth and wood property traits in trees.  High-throughput DNA genotyping technologies, as well as powerful statistical methods are utilised to develop genetic linkage maps that are used to associate growth and wood property phenotypes with underlying genotypes.  These associations enable us to identify specific genome regions (quantitative trait loci or QTLs) influencing economically important traits and identify markers that could be used to select desirable genotypes at these genomic locations.


Systems genetics analysis of wood formation in eucalypts:  All industrially important wood property traits impacting downstream applications such as processability are complex traits controlled by hundreds of genes and are influenced by multiple levels of regulation and feedback.  Biotechnological improvement of these traits for any downstream applicaiton will benefit from reverse engineering of secondary cell wall formation and biopolymer deposition during wood formation (xylogenesis).  We apply a systems genetics approach to modelling wood formation, by investigating genetic correlations of gene expression and metabolites such as sugars or phenolics in xylem, integrating this information with genome-wide genetics variation (QTLs).  Together, these data are utilised to model the molecular underpinnings of variation in component traits (e.g. gene expression and metabolite profiles) and derived complex traits (e.g. cellulose, xylan or lignin quantity and/or structure).  By understanding the genetic variation, the molecular components and their interactions underlying these traits, the limitations and potential targets for trait improvement can be identified and integrated into biotechnology applications.


Systems genetics analysis of disease resistance in eucalypts:  Plant disease resistance is essentially the manifestation of genetic variation segregating in the host and pathogen and therefore it is necessary to dissect plant defence mechanisms in Eucalyptus trees using a systems genetics approach, as described for wood formation.  The output of this approach is twofold:  it provides markers for selection of genetic loci contributing to disease resistance or tolerance, as well as biological insight into the molecular mechanisms that underlie the biological system.  Using the same segregating populations used for dissecting wood properties, we expect to identify regulatory pathways and groups of co-regulated genes which could be targeted to enhance disease tolerance using transgenic approaches.


Genome-wide SNP marker discovery and and genomic selection in Eucalyptus:  Marker-assisted selection of favourable trees in breeding populations requires high-throughput genotyping with dense, genome-wide marker panels.  In collaboration with the international Eucalyptus community, we are implementing a high-throughput, single nucleotide polymorphism (SNP) genotyping platform based on 60 000 markers. This has allowed us to generate genome-wide marker profiles for commercially important eucalypt species in South Africa.  These marker resources are being used to develop genomic selection for tree breeding populations and genome-wide association studies for growth and wood property traits.