Erica Bakker
|
Assistant Professor, Horticulture |
|||||||||||||
 |
|
||||||||||||
Education
Ph.D. 2001 Wageningen UniversityResearch
My interests are in understanding the evolution of disease resistance in plants. One form of plant defense is called gene-for-gene resistance in which a plant resistance (R) protein can perceive the presence or action of a corresonding avirulence (avr) protein from the pathogen. A large subset of R genes in plants encode nucleotide binding sites (NBS) and a leucine-rich repeat (LRR) region. This latter domain functions in protein-protein interactions and is assumed to mediate recognition of pathogen-derived ligands. Only a small number of the NBS-LRR class R genes have been functionally characterized, and of the subset subjected to molecular population genetic analysis, balancing selection appears to be the predominant force acting to maintain both resistance and susceptibility alleles. This is surprising because the coevolutionary arms-race dynamics expected in a ‘gene-for-gene interaction’ should result in a high rate of turnover for R gene alleles, and thus generate loci with few, relatively young alleles with extended haplotypes.Tests to detect selection have traditionally used predictions from the theory of neutrally evolving sites as a null hypothesis. Departures from equilibrium expectations can indicate the presence of natural selection acting either at one or more of the sites under investigation or at a tightly linked site. However, recent surveys of genome-wide polymorphism in Arabidopsis thaliana show that the data do not fit standard neutral models in several ways. The inability to model these observations, i.e., generate a plausible null hypothesis, argues for substituting an empirical distribution of genome-wide polymorphism for a theoretical distribution as baseline against which to identify unusual features of R gene polymorphism.
My research involves high-throughput genomics and bioinformatics in order to study polymorphisms in the LRR region for all 149 NBS-LRR class R genes that are present in the Col-0 genome. Polymorphism patterns exhibited by these R genes can be viewed as many independent snapshots of possible states of the evolutionary process, and is expected to reveal features of the breadth and distribution of evolutionary outcomes for this group of loci. Comparison with the empirical distribution of polymorphism in 876 randomly distributed genomic regions will allow us to minimize sampling artifacts while testing for selection. This will allow us to explore the prevalence of directional and balancing selection in a class of genes that are expected to be under continual selection for alleles that allow the plant to detect attack by pathogens.