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Evolutionary and population genomic of Arabidopsis

Chris Toomajian

Adaptation and natural genetic variation in Arabidopsis thaliana:

The model plant A. thaliana occurs throughout the Northern Hemisphere in a wide range of environments, and shows considerable variation for many ecologically relevant traits. My work on discovering and analyzing natural genetic variation in A. thaliana has had several related goals. One, as part of a larger effort led by Magnus Nordborg at USC, is the development of resources (genetic markers, genotyped, inbred population samples, and methodologies) for the whole-genome association mapping of ecologically important traits back to the genome that promises a much higher resolution than standard QTL studies. An important problem addressed by this work is the proper interpretation of associations in structured populations when both phenotypes and genotypes follow a geographic gradient. A second has been the genome-wide search for molecular genetic patterns consistent with recent selective events in individual or multiple populations, with the prospect of de novo identification of genes that are currently playing a role in adaptation to local environments and ecological conditions. Finally, I have studied genetic polymorphism throughout the genome in order to understand how several forces, including mutation, recombination, genetic drift, demography, and natural selection, combine to produce the observed levels and patterns of polymorphism.

Speciation and comparative genomics in Arabidopsis:

In conjunction with studying patterns of genetic variation within A. thaliana, I am using whole-genome sequence divergence from A. lyrata to investigate patterns of selection along these lineages. Within approximately five million years, these lineages have diverged with respect to their mating system (selfer versus obligate outcrosser), genome size (almost a two-fold difference), and life history (A. thaliana is predominantly a weedy and opportunistic species, compared to the more stable populations of A. lyrata). By documenting sequence divergence and gene family expansion and contraction between the related species, we can infer patterns of selection among related groups. I am especially interested in investigating what the range of divergence levels across genes can tell us about the speciation process and potential introgression events that carried a selective advantage. Given the major changes in genome size and organization between these closely related species, I am also interested in determining which genome rearrangements, such as translocations and inversions, occurred at the time of speciation (and potentially played important roles in the speciation process) and which occurred subsequently.

Relevant publications:

Bakker, EG, MB Traw, C Toomajian, M Kreitman & J Bergelson. Low levels of polymorphism in genes that control the activation of defense response in Arabidopsis thaliana. Genetics 178: 2031-2043 (2008); published online 1 February 2008 (doi:10.1534/genetics.107.083279).

Zhao, K, MJ Aranzana, S Kim, C Lister, C Shindo, C Tang, C Toomajian, H Zheng, C Dean, P Marjoram & M Nordborg. An Arabidopsis example of association mapping in structured samples. PLoS Genet 3: e4 (2007); published online 22 November 2006 (doi:10.1371/journal.pgen.0030004).

Bakker, EG, C Toomajian, M Kreitman & J Bergelson. A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell 18: 1803-1818 (2006); published online 23 June 2006 (doi:10.1105/ tpc.106.042614).

Toomajian C, TT Hu, MJ Aranzana, C Lister, C Tang, H Zheng, K Zhao, P Calabrese, C Dean & M Nordborg. A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome. PLoS Biol 4: e137 (2006); published online 25 April 2006 (doi:10.1371/journal.pbio.0040137).

Aranzana, MJ, S Kim, K Zhao, E Bakker, M Horton, K Jakob, C Lister, J Molitor, C Shindo, C Tang, C Toomajian, B Traw, H Zheng, J Bergelson, C Dean, P Marjoram & M Nordborg. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1: e60 (2005); published online 10 October 2005 (doi:10.1371/ journal.pgen.0010060).