Updated: August 2013
I. Evolutionary Biology of Genome Structure (Polyploidy)
Research in our lab addresses fundamental questions about genome structure and its role in plant evolution. Plant genomes are remarkably dynamic and structural change is tolerated in plants much more readily than in animals. One of the most frequent structural changes in plant genomes involves the duplication of the entire chromosome complement leading to a state known as polyploidy. Two types of polyploids are distinguished: allopolyploids (hybrids with duplicated genomes of two different species) and autopolyploids (duplicated genomes of one species). See http://www.polyploidy.org for details. Because polyploid genomes carry more loci of every gene than diploids do, it has been suggested that they are more adaptive to their environment and are superior to diploids in their ability to evolve.
Using the model genus Arabidopsis we study molecular mechanisms in polyploidy that could lead to speciation, adaptation, and genome evolution. Specifically, we have studied the role of epigenetics in transcriptional change (Madlung et al. 2002), and particularly with respect to conditionally mobile sequences in the genome called transposons (Madlung et al. 2005).
More recently we have used cytogenetics to address the question of genome stability in newly-formed as compared to established polyploids. We find that somatic cells in Arabidopsis allopolyploids are mosaic for varying degrees of aneuploidy (loss or gain of individual chromosomes, not entire sets) (Wright et al. 2009) and that higher levels of polyploidy lead to increased levels of aneuploidy. In an experimental population of Arabidopsis allohexaploids that we produced by cross-pollination of the parents and subsequent inbreeding for seven generations we were able to show a correlation between increasing phenotypic diversity and cytogenetic variation (Matsushita et al. 2012). This study was featured as the cover story in the June 2012 issue of Genetics. We continue to study the question to what degree allopolyploidy functions as a mechanism for rapid diversification and speciation.
II. Floral reversion
A second related project aims to understand a peculiar process called floral reversion. Plants that undergo floral reversion abort the normally terminal developmental process of flowering. Instead of producing flowers and setting seed, reverting branches produce new inflorescences, and in some species new leaves, out of fully developed flowers. We have begun to analyze the molecular mechanisms for this phenomenon in polyploids of Arabidopsis suecica (McCullough et al., 2010) and are interested in finding out if genome duplication plays a role in this novel phenotype. We currently use genomic tools, such as microarray analysis and in situ hybridization to find out which genes are involved in the process and where candidate genes are expressed in reverting flowers. We use genetic screening to identify possible genetic enhancers or repressors, and we continue to define the mutation better using scanning electron and light microscopy. This project is funded by a grant from the National Science Foundation.
III. Molecular genetics of signal transduction in eukaryotic cells
Throughout development, signal transduction plays an important role in determining cell fate and establishing a developmental program so that a single cell can develop into a multicellular organism. Signal transduction uses signaling pathways, which are circuits that convey messages between cells and their environment. The response to external signals is context dependent, meaning the output depends not only upon the cell type, in which signals are transduced, but also upon the stage of development of the organism, other interacting signaling molecules, and outside environmental signals.
Our lab uses genetic model organisms to study signal transduction networks. Knowledge gained from models can ultimately help us to understand signaling networks in more complex organisms. Arabidopsis and tomato are excellent models to study environmental effects on development and reproduction. Among others, important regulators of development are light and hormones. We concentrate on the interaction between light perception and the cross-regulation between hormones, as they implement the perceived signals and translate them into developmental patterning of the organism. Techniques used to study these questions include microarray analysis, quantitative real time PCR, RNAi-mediated gene knock-down, gene cloning, reporter gene (GUS-) constructs, double- and triple mutant analysis, and physiological experimentation on whole organisms.
All projects in our lab lend themselves well to independent research. If you are interested in genetics, molecular biology, cell biology, or whole organism physiology and would like to learn more about specific projects, or how you could fit into our lab within any of the current projects, please contact me. In the meantime you can read about our work in these selected publications.