Identification of NPR1-dependent and independent genes early induced by salicylic acid treatment in Arabidopsis Francisca Blanco 1,3 , Virginia Garreto´n 1,4 , Nicolas Frey 1 , Calixto Dominguez 2 , Toma´s Pe´ rez-Acle 2 , Dominique Van der Straeten 3 , Xavier Jordana 1 and Loreto Holuigue 1, * 1 Departamento de Gene´tica Molecular y Microbiologı´a, Facultad de Ciencias Biolo ´gicas, Pontificia Universidad Cato ´lica de Chile, P.O. Box 114-D, Santiago, Chile (*author for correspondence; e-mail lholuig@bio.puc.cl); 2 Centro de Geno ´mica y Bioinforma ´tica, Facultad de Ciencias Biolo ´gicas, Pontificia Universidad Cato ´lica de Chile, P.O. Box 114-D, Santiago, Chile; 3 Department of Molecular Genetics, Unit Plant Hormone Signaling and Bio-imaging, Ghent University, Ledeganckstraat 35, B-9000, Gent, Belgium; 4 AustralBiotech SA., San Sebastian 2952, piso 5. Las Condes., Santiago, Chile Received 31 March 2005; accepted in revised form 17 August 2005 Key words: as-1, cDNA-AFLP, cell protection to stress, early activated genes, NPR1, salicylic acid Abstract Salicylic acid (SA) plays a crucial role in stress resistance in plants by modifying the expression of a battery of genes. In this paper, we report the identification of a group of early SA-regulated genes of Arabidopsis (activated between 0.5–2.5 h), using the cDNA-amplified fragment length polymorphism technique (cDNA- AFLP). Using 128 different primer combinations, we identified several genes based on their differential expression during SA treatment. Among these, we identified 12 genes up-regulated by SA whose patterns of induction were confirmed by Northern analysis. The identified genes can be grouped into two functional groups: Group 1: genes involved in cell protection (i.e. glycosyltransferases, glutathion S-transferases), and Group 2: genes involved in signal transduction (protein kinases and transcription factors). We also eval- uated NPR1 requirement for the induction of the 12 up-regulated genes, and found that only those belonging to Group 2 require this co-activator for their expression. In silico analysis of the promoter sequences of the up-regulated genes, allowed us to identify putative cis-elements over-represented in these genes. Interestingly, as-1-like elements, previously characterized as SA-responsive elements, were specifi- cally over-represented in Group 1 genes. The identification of early SA-regulated genes is an important step towards understanding the complex role of this hormone in plant stress resistance. Abbreviations: AFLP-TP, amplified fragment length polymorphism-based transcript profiling; as-1, activation sequence-1; GST, glutathione S-transferase; GT, glycosyltransferase; HR, hypersensitive response; IEGT, immediate early glycosyltransferase gene; JA, jasmonic acid; NPR1, nonexpressor of PR genes 1; PR, pathogenesis-related proteins; ROS, reactive oxygen species; SA, salicylic acid; SAR, systemic acquired resistance; TDF, transcript derived fragments; TGAs, family of bZip transcription factors recognizing TGACG motif; WT, wild type Introduction Salicylic acid (SA) accumulation in plants is essential to establish effective defense responses against several kinds of environmental stresses such as pathogen attacks, UV irradiation, osmotic stress or ozone exposure (Gaffney et al., 1993; Yalpani et al., 1994; Borsani et al., 2001). The relevance of SA in these defense responses has been clearly demonstrated by studying the effect of Plant Molecular Biology (2005) 59:927–944 Ó Springer 2005 DOI 10.1007/s11103-005-2227-x