Natural genetic variation in Arabidopsis thaliana (Weigel)
A key question in biology is how organisms adapt to their environment, which eventually leads to the invention of new structures or organs. Many developmental biologists are trying to answer this question by comparing complex structures between distantly related taxa. The difficulties inherent in such an approach were already apparent to Darwin: “To suppose that the eye with all its inimitable contrivances … could have been formed by natural selection, seems, I freely confess, absurd to the highest degree.” An alternative to the study of macroevolutionary events is to investigate variation that occurs within a species or between sister species that can still interbreed. One of the models that is used in the department to address such questions is the flowering behaviour of different strains of Arabidopsis thaliana. The geographical distribution of Arabidopsis includes much of the Northern hemisphere, especially the temperate and subarctic latitudes as well as mountainous regions. Since plants have to flower during the right season to reproduce successfully, one can expect that strains of different geographical origin are differentially adapted in their flowering behaviours. Environmental factors known to affect flowering include day length (photoperiod) and transient exposure to winter-like cold temperatures (vernalisation) as well as ambient temperature.
Extensive variation in the time to flowering has been found by surveying a collection of over a hundred wild strains for their response to the aforementioned three environmental variables (Lempe et al., 2005). Several strains have rather unusual behaviours, and the molecular basis for some of these, such as insensitivity to vernalization, has already been identified by extreme mapping using DNA hybridization to Affymetrix expression arrays, comparative expression profiling, mapping and candidate gene analysis (e.g., Balasubramanian et al., 2006).
To enable the more rapid discovery of functionally relevant variation, we recently concluded a collaboration with Perlegen Sciences to discover a large fraction of SNPs in 19 wild strains of Arabidopsis thaliana, using array-based whole-genome variation scans. More than 1 million unique SNPs were identified at moderate false discovery rates, with many of them causing non-synonymous substitutions or even premature stops (Clark et al., 2007). In one next step, we will integrate these resources with expression profiles and large-scale mapping, to discover alleles involved in the regulation of a suite of adaptive plant traits. As a tool to enable such studies, we have developed a web interface for selecting markers that distinguish any arbitrary groups of wild strains. Another avenue is the more extensive re-sequencing using Illumina's Solexa technology. An instrument has been recently (June 2007) installed at the institute, and we have already analyzed the genomes of several A. thaliana strains with this technology.
Finally, we have recently discovered multiple cases of gene-flow barriers between wild strains of Arabidopsis thaliana. Fertilization, hybrid zygote formation and germination of F1 plants are normal at either 16°C or 23°C. At 23°C, F1 hybrid seedlings continue to develop normally, but at 16°C they progressively suffer severe growth defects and are infertile. Our results show that this is caused by dominant interaction of gene products from two unlinked loci, with each parent contributing one incompatible allele at one of the loci. This conforms to predictions of the Bateson-Dobzhansky-Muller model for evolution of post-zygotic isolation. The underlying mechanism is autoimmunity, in which another genome is mistaken as pathogenic (Bomblies et al., 2007).
Key publications
Personnel
- Dr. Kirsten Bomblies
- Postdoctoral fellow
- Dr. Jun Cao
- Postdoctoral fellow
- Dr. Eunyoung Chae
- Postdoctoral fellow
- Dr. Richard Clark
- Postdoctoral fellow
- Dr. Vojislava Grbic
- Visiting scientist
- Dr. Yalong Guo
- Postdoctoral fellow
- Dr. Sang-tae Kim
- Postdoctoral fellow
- Dr. Yasushi Kobayashi
- Postdoctoral fellow
- Dr. Roosa Laitinen
- Postdoctoral fellow
- Stephan Ossowski
- PhD. student (also Small RNA group)
- Dr. Patrice Salome
- Postdoctoral fellow
- Dr. Lisa Smith
- Postdoctoral fellow (also Small RNA group)
- Korbinian Schneeberger
- Ph.D. student
- Gabriele Schweikert
- Ph.D. student (with G. Rätsch, FML)
- Marco Todesco
- Ph.D. student (also Small RNA group)
- Norman Warthmann
- Ph.D. student
- Georg Zeller
- Ph.D. student (with B. Schölkopf, MPI for Biological Cybernetics, and G. Rätsch, FML)
- Dr. Detlef Weigel
- Director
Collaborators
- Dr. Justin Borevitz
- University of Chicago, US
- Dr. Joanne Chory
- Salk Institute, California, US
- Dr. Joe Ecker
- Salk Institute, California, US
- Dr. Daniel Huson
- University Tübingen
- Dr. Magnus Nordborg
- University of South California, US
- Dr. Gunnar Rätsch
- Friedrich Miescher Laboratory, Tübingen
- Dr. Bernhard Schölkopf
- Max Planck Institute for Biological Cybernetics, Tübingen