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Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

Anita Zamboni1, Laura Zanin2, Nicola Tomasi2, Mario Pezzotti1, Roberto Pinton2, Zeno Varanini1* and Stefano Cesco3

Author Affiliations

1 Department of Biotechnology, University of Verona, via delle Grazie 15, 37134 Verona, Italy

2 Department of Agriculture and Environmental Sciences, University of Udine, via delle Scienze 208, 33100 Udine, Italy

3 Faculty of Science and Technology, Free University of Bolzano, piazza Università 5, 39100 Bolzano, Italy

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BMC Genomics 2012, 13:101  doi:10.1186/1471-2164-13-101

Published: 20 March 2012



Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far.


A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism.


The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.