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Spatial Analysis of Arabidopsis thaliana Gene Expression in Response to Turnip mosaic virus Infection

April 2007 , Volume 20 , Number  4
Pages  358 - 370

Chunling Yang , 1 Rong Guo , 2 Fei Jie , 2 Dan Nettleton , 2 Jiqing Peng , 3 Tyrell Carr , 1 Joanne M. Yeakley , 4 Jian-Bing Fan , 4 and Steven A. Whitham 1

1Department of Plant Pathology, 2Department of Statistics, and 3GeneChip Facility, Iowa State University, Ames 50011 U.S.A.; 4Illumina, Incorporated, 9885 Towne Centre Drive, San Diego, CA 92121, U.S.A.


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Accepted 27 October 2006.

Virus-infected leaf tissues comprise a heterogeneous mixture of cells at different stages of infection. The spatial and temporal relationships between sites of virus accumulation and the accompanying host responses, such as altered host gene expression, are not well defined. To address this issue, we utilized Turnip mosaic virus (TuMV) tagged with the green fluorescent protein to guide the dissection of infection foci into four distinct zones. The abundance of Arabidopsis thaliana mRNA transcripts in each of the four zones then was assayed using the Arabidopsis ATH1 GeneChip oligonucleotide microarray (Affymetrix). mRNA transcripts with significantly altered expression profiles were determined across gradients of virus accumulation spanning groups of cells in and around foci at different stages of infection. The extent to which TuMV-responsive genes were up- or downregulated primarily correlated with the amount of virus accumulation regardless of gene function. The spatial analysis also allowed new suites of coordinately regulated genes to be identified that are associated with chloroplast functions (decreased), sulfate assimilation (decreased), cell wall extensibility (decreased), and protein synthesis and turnover (induced). The functions of these downregulated genes are consistent with viral symptoms, such as chlorosis and stunted growth, providing new insight into mechanisms of pathogenesis.


Additional keywords: Potyvirus, ribosomal protein.

© 2007 The American Phytopathological Society