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First published online April 7, 2006; 10.1104/pp.105.072645 Plant Physiology 141:257-270 (2006) © 2006 American Society of Plant Biologists Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants1,[W]Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (J.T.S., T.J.C.); Consiglio per la Ricerca e la Sperimentazione in Agricoltura Centro per le Ricerche Genomiche, 29017 Fiorenzuola d'Arda, Italy (C. Crosatti, C. Campoli, A.M.S., L.C.); and Dipartimento Scientifico e Tecnologico, Università di Verona, 37134 Verona, Italy (C. Campoli, R.B.)
Previously, we have shown that barley (Hordeum vulgare) plants carrying a mutation preventing chloroplast development are completely frost susceptible as well as impaired in the expression of several cold-regulated genes. Here we investigated the transcriptome of barley albina and xantha mutants and the corresponding wild type to assess the effect of the chloroplast on expression of cold-regulated genes. First, by comparing control wild type against cold-hardened wild-type plants 2,735 probe sets with statistically significant changes (P = 0.05;
1 This work was supported by the GENEFUN (functional genetics) program, the Fondo Investimenti Ricerca di Base programs (nos. RBNE01LACT [plant stress] and RBAU01E3CX), and the U.S. Department of Agriculture/Cooperative State Research, Education and Extension Service/Initiative for Future Agriculture and Food Systems (2001–52100–11346). 2 These authors contributed equally to the paper. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Luigi Cattivelli (luigi.cattivelli{at}entecra.it). [W] The online version of this article contains Web-only data. Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.072645. * Corresponding author; e-mail luigi.cattivelli{at}entecra.it; fax 390523983750. Received October 7, 2005; returned for revision March 27, 2006; accepted March 27, 2006. Related articles in Plant Physiol.:
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2-fold change) were identified. Expression of these wild-type cold-regulated genes was then analyzed in control and cold-hardened mutants. Only about 11% of the genes cold regulated in wild type were regulated to a similar extent in all genotypes (chloroplast-independent cold-regulated genes); this class includes many genes known to be under C-repeat binding factor control. C-repeat binding factor genes were also equally induced in mutants and wild-type plants. About 67% of wild-type cold-regulated genes were not regulated by cold in any mutant (chloroplast-dependent cold-regulated genes). We found that the lack of cold regulation in the mutants is due to the presence of signaling pathway(s) normally cold activated in wild type but constitutively active in the mutants, as well as to the disruption of low-temperature signaling pathway(s) due to the absence of active chloroplasts. We also found that photooxidative stress signaling pathway is constitutively active in the mutants. These results demonstrate the major role of the chloroplast in the control of the molecular adaptation to cold. 
