Transcript Profiling of Different Arabidopsis thaliana Ecotypes in Response to Tobacco etch potyvirus Infection

The use of high-throughput transcript profiling techniques has opened the possibility of identifying, in a single experiment, multiple host mRNAs whose levels of accumulation are altered in response to virus infection. Several studies have used this approach to analyze the response of Arabidopsis thaliana to the infection by different RNA and DNA viruses. However, the possible differences in response of genetically heterogeneous ecotypes of the plant to the same virus have never been addressed before. Here we have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to A. thaliana ecotype Ler-0 and a set of seven plant ecotypes to tackle this question. Each ecotype was inoculated with the same amount of the virus and the outcome of infection characterized phenotypically (i.e., virus infectivity, accumulation, and symptoms development). Using commercial microarrays containing probes for more than 43,000 A. thaliana transcripts, we explored the effect of viral infection on the plant transcriptome. In general, we found that ecotypes differ in the way they perceive and respond to the virus. Some ecotypes developed strong symptoms and accumulated large amounts of viral genomes, while others only developed mild symptoms and accumulated less virus. At the transcriptomic level, ecotypes could be classified into two groups according to the particular genes whose expression was altered upon infection. Moreover, a functional enrichment analyses showed that the two groups differed in the nature of the altered biological processes. For the group constituted by ecotypes developing milder symptoms and allowing for lower virus accumulation, genes involved in abiotic stresses and in the construction of new tissues tend to be up-regulated. For those ecotypes in which infection was more severe and productive, defense genes tend to be up-regulated, deviating the necessary resources from building new tissues.