Genetical Genomics - Genetic regulation of environmental responses in Arabidopsis

Genetic variation in natural populations of Arabidopsis thaliana has allowed the species to adapt to a wide range of environmental conditions. The identification of natural alleles affecting important traits can be used to enhance our understanding of the molecular mechanisms deployed by Arabidopsis to respond to the environment. These responses are generally controlled by multiple genes contributing quantitatively to the observed phenotypic traits. The molecular dissection of quantitative traits has been aided by the availability of RILs and genetic maps allowing the linkage of traits to genotypes by QTL analysis. The concept of genetical genomics was based on the idea that natural variation not only affects phenotypic traits, but also the variation in gene expression that can be measured on a genome-wide scale. In this thesis it was shown that the quantitative analyses of genome-wide gene expression in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) RIL population revealed heritable expression patterns for which thousands of eQTLs could be mapped. Local regulation was as prevalent as distant regulation. Loci were detected though, that harbor distant eQTLs for a large number of genes, which possibly point to master regulators. The possibility to dissect gene regulatory networks using eQTL data is based on the assumption that the expression of target genes correlates with the expression of the regulator gene. We successfully applied this principle to construct regulatory networks for genes known to be involved in flowering time and to genes downstream of the master regulator ERECTA. The two genetical genomics experiments described in this thesis allowed an initial comparison which gave an impression of plasticity in gene expression regulation. About 1000, predominantly locally regulated, linkages were identified in both experiments. The majority of eQTLs, however, was specific for each experiment, and enriched for distant eQTLs. We explored the added value of the genetical genomics in the analysis of the response of Arabidopsis to the virulent bacterial strain Pseudomonas syringae pv tomato (Pst) and to treatment with low light in the Ler/Cvi RILs respectively, in search for new factors in the regulation of these stress responses. The higher susceptibility of Cvi compared to Ler could be mapped to several disease susceptibility QTLs in the Ler/Cvi RILs. The major QTL had large impact on the transcriptional response to jasmonic acid during infection. The genetical genomics data allowed the identification of NUDT8, a Nudix hydrolase co-expressed with JA biosynthesis genes. Further studies are needed to analyze the role of NUDT8 in susceptibility of Arabidopsis to Pst infection. The low light treatment is known to induce the shade avoidance syndrome for which Ler and Cvi showed considerable natural variation. A major HTR affected the expression of components of the circadian clock, a ROS-activated signaling cascade and auxin- and sterol homeostasis. A common feature linking these processes could be the regulation of protein ubiquitination. The local regulation of CSN5A by the HTR could indicate a role for the CSN in the HTR-mediated processes. These results demonstrate the added value of genetical genomics in the dissection of quantitative traits.