Genomics

A long-term focus of our laboratory has been to build genetic resources and tools in Arabidopsis thaliana. In collaboration with the Nordborg lab, we have established that A. thaliana has patterns of linkage disequilibrium well suited for GWAS mapping and have genotyped sets of accessions to allow mapping by members of the community.

We have made extensive collections of A. thaliana accessions, and made these available as well. We are currently collaborating on the 1001 Genome Project to sequence ~1100 A. thaliana accessions. These efforts have provided many opportunities to address questions in plant genomics and population structure.

Ongoing Projects

Molecular Evolution of the Complex R-gene

Why is there such an abundance of molecular variation in nature, and how are regions of high molecular variation generated? Even in the predominantly selfing species Arabidopsis thaliana, plant NB-LRR resistance (R-) genes provide some of the most extreme examples of polymorphism in eukaryotic genomes. Most R-genes exist as tandem arrays and many segregate for copy number polymorphism; studies of complex, duplicated R-gene loci lag behind those of simple R-loci, as assembly of duplicated genes is challenging for current next-generation sequencing methodologies. Here we applied the Sanger method to sequence 48 Rpp8 homologs from 31 accessions of A. thaliana and 12 Rpp8 homologs from A. lyrata.

Epigenetics of Trans-generational Defense Induction


A. thaliana plant displaying brown, necrotic lesions caused by P. viridiflava infection.

One of the most fascinating discoveries in recent years is that stress-induced changes in parent phenotypes can be epigenetically transmitted to offspring, altering offspring interactions with their own environments. Evolutionary ecologists now face the task of rigorously incorporating this mode of individual variation into our understanding of ecological interactions and evolutionary change. To do so, we must first understand how epigenetic variation interacts with ecologically realistic environments and with natural genetic variants in the production of phenotypic diversity. This project addresses this critical issue by examining heritable effects of bacterial infection on genome-wide DNA methylation states, at single-base resolution, in a diverse natural sample of the evolutionary model plant Arabidopsis thaliana.

Selected publications:

Wang, M., Roux, F., Bartoli, C., Huard-Chauveau, C., Meyer, C., Lee, H., Roby, D., McPeek, M. S. and J. Bergelson (2018) Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes. Proceedings of the National Academy of Sciences, 115 (24): E5440–49. https://doi.org/10.1073/pnas.1710980115
Here, we present a method to simultaneously perform GWA mapping on two interacting species. We applied our approach to the Arabidopsis thaliana–Xanthomonas arboricola pathosystem and identified candidate genes conferring host–pathogen specificity, as well as genes more consistently involved in resistance.

1001 Genomes Consortium. 2016. 1135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481-491. https://doi.org/10.1016/j.cell.2016.05.063
We present a detailed map of variation in 1135 high-quality re-sequenced natural accessions of A. thaliana from the native Eurasian and African ranges, as well as North American, and find relict populations that continue to inhabit ancestral habitats, primarily in the Iberian peninsula. Insights into the history and fine scale genetic structure of the species provides the basis to exploit A. thaliana natural variation through integrations of genomes and epigenomes with molecular and non-molecular phenotypes.

Atwell, S., Huang, Y., Vilhkálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A., Hu, T. T., Jiang, R., Muliyati, N. W., Zhang, X., Amer, M. A., Baxter, I., Brachi, B., Chory, J., Dean, C., Debieu, M., de Meaux, J., Ecker, J. R., Faure, N., Kniskern, J. M., Jones, J. D. G., Michael, T., Nemri, A., Roux, F., Salt, D. E., Tang, C., Todesco, M., Traw, M. B., Weigel, D., Marjoram, P., Borevitz, J. O., Bergelson, J. and M. Nordborg (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature, 465 (7298): 627-631. https://doi.org/10.1038/nature08800
This is the first major GWAS study to demonstrate the feasibility of GWAS approaches outside of human biology. Our results on A. thaliana are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, although interpretation is also harder due to confounding by population structure. A-priori candidates are significantly over-represented among these associations, making many of them excellent candidates for follow-up experiments.

University of Chicago, Dept. of Ecology & Evolution