Forest Genomics

Short bio My primary research interest is the genetic control of growth and development in trees with a focus on wood formation in Eucalyptus and pine species. Most commercially important phenotypes are quantitative in nature and affected by natural genetic variation in hundreds of genes throughout the genome, many of which interact with environmental signals. Genome-wide DNA marker analysis has proven to be a powerful tool for tracking this genetic variation and developing predictive models of the breeding values of individual trees. By adding molecular traits such as gene expression and metabolite variation, we can gain further biological insight into the molecular basis of complex trait variation. This forms the basis of systems genetics approaches combining the power of population genetics and systems biology (multi-level ‘omics) analyses to understand the nature of genetic variation affecting growth and wood formation in tree breeding populations. My group has successfully used this approach in an interspecific backcross population of E. grandis x E. urophylla to map key genomic regions affecting gene expression and metabolic profiles associated with variation in growth and wood chemistry. The systems genetics data is a rich source for identifying candidate genes and pathways to target for molecular breeding and genetic engineering. In the past three years, we embarked on an effort to engineer cell wall traits using new approaches such as CRISPR-Cas9 gene editing.Over the past four years we have successfully used a single nucleotide polymorphism (SNP) DNA marker chip with 60,000 DNA markers to genotype over 4000 Eucalyptus trees from E. grandis, E. dunnii, E. urophylla, E. nitens and E. grandis x E. urophylla and E. grandis x E. niens hybrids. This has provided us with unprecedented resolution to rapidly dissect complex traits in Eucalyptus and develop predictive models for genomic selection of growth and wood properties. We are working with industry partners to design the best approaches to validate and integrate these approaches into tree breeding programmes. With support from the Forestry Sector Innovation Fund (FSIF) we have expanded this work to other Eucalyptus and pine tree species and we have constructed the first version of a Genome Diversity Atlas (GDA) for Eucalyptus and pine species grown in South Africa. An outcome of this initiative is an international collaboration (Camcore, NC State University) aimed at generating a multi-species SNP genotyping chip for tropical pines that will be completed early in 2020. These resources will be useful for genetic resource management, gene conservation and molecular breeding of pines. The GDA project also lays the foundation for the emerging field of landscape genomics, which combines population genomics with analysis of interactions with environmental factors including biotic and abiotic stresses to predict tree genotypes that are best adapted to such environments, or that can be deployed to combat new biotic challenges such as pests and diseases. This part year we made excellent progress towards the first phase of a landscape genomics study of Eucalyptus grandis in its natural range in Australia and we have also surveyed three (E. grandis) breeding populations in South Africa to assess genomic patterns of artificial selection and interspecific introgression that have occurred over the past 100 years of selective breeding. Finally, we have started an effort to sequence the genomes of elite Eucalyptus parental genotypes in an effort to understand genome sequence and structural variation that underlie hybrid combining ability and hybrid superiority.