Fundamental Genomic Research

We study the genetic architecture of transcript level variation, and partition of additive, dominance, epistatic, and non-genetic sources of variation that affect transcriptional regulation. These studies define sites that regulate the level of transcripts for individual genes, which can be the location of the gene coding sequence (cis-regulation), or its trans-regulator.

Applied Genomic Research

We use classical approaches (QTL analysis and association genetics) to identify genetic loci associated with quantitative traits. These approaches are complemented by integrating other levels of genomic information (transcriptome and metabolome), creating a powerful platform for identification of specific genes that control quantitative variation. The rationale is that a significant component of the quantitative variation arises as a consequence of quantifiable variation at  the transcription and metabolic level. By integrating information from different genomic platforms we have identified specific genes, as well as regulatory and physiological networks implicated in variation in growth and wood quality in forest tree species.

Technology and Genomic Tool Development

We work on the development of methods for discovering SNPs from EST databases and other sources. For genotyping we use two microarray platforms (NimbleGen and Combimatrix, which allow high flexibility in probe design). We develop hybridization methods for genomic DNA hybridization to genotyping arrays of some of the most complex plant genomes, including the pine megagenome (~ 21,000 Mbp) and maize.    

The Quantitative Genomics Laboratory has a number of collaborative projects in these and related areas with research groups working on maize, Eucalyptus, Pine and other forestry and agronomic crops in the USA (Buckler’s Lab at Cornell University; Jerry Tuskan’s DOE’s Oak Ridge National Laboratory), South America (Dario Grattapaglia’s Lab at EMBRAPA), and Africa (Zander’s Myburg Lab at the University of Pretoria in South Africa).