Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 R E S E A R C H A R T I C L E Open Access Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis Stephanus J Ferreira1, Melanie Senning1, Sophia Sonnewald1, Petra-Maria Keßling2, Ralf Goldstein3, Uwe Sonnewald1* Abstract Background: Even though the process of potato tuber starch biosynthesis is well understood, mechanisms regulating biosynthesis are still unclear. Transcriptome analysis provides valuable information as to how genes are regulated. Therefore, this work aimed at investigating transcriptional regulation of starch biosynthetic genes in leaves and tubers of potato plants under various conditions. More specifically we looked at gene expression diurnally in leaves and tubers, during tuber induction and in tubers growing at different velocities. To determine velocity of potato tuber growth a new method based on X-ray Computed Tomography (X-ray CT) was established. Results: Comparative transcriptome analysis between leaves and tubers revealed striking similarities with the same genes being differentially expressed in both tissues. In tubers, oscillation of granule bound starch synthase (GBSS) expression) was observed which could be linked to sucrose supply from source leaves. X-ray CT was used to determine time-dependent changes in tuber volume and the growth velocity was calculated. Although there is not a linear correlation between growth velocity and expression of starch biosynthetic genes, there are significant differences between growing and non-growing tubers. Co-expression analysis was used to identify transcription factors positively correlating with starch biosynthetic genes possibly regulating starch biosynthesis. Conclusion: Most starch biosynthetic enzymes are encoded by gene families. Co-expression analysis revealed that the same members of these gene families are co-regulated in leaves and tubers. This suggests that regulation of transitory and storage starch biosynthesis in leaves and tubers, respectively, is surprisingly similar. X-ray CT can be used to monitor growth and development of belowground organs and allows to link tuber growth to changes in gene expression. Comparative transcriptome analysis provides a useful tool to identify transcription factors possibly involved in the regulation of starch biosynthesis. Background Starch is not only the most important carbohydrate source to the human diet, but has major industrial applications. It consists of two major fractions, amylose and amylopectin. Amylose is essentially a linear polymer of glucose units linked with alpha (1,4) bonds whilst amylopectin has a higher percentage of branched alpha (1,6) bonds. Due to its importance, crop plants * Correspondence: usonne@biologie.uni-erlangen.de 1Friedrich-Alexander-University Erlangen-Nuremberg, Department of Biology, Staudtstrasse 5, 91058 Erlangen, Germany producing starch in large quantities have been exten- sively researched. The fourth most important crop in the world in terms of total biomass produced is potato and this is due to its starchy tuber which can store up to 80% of its dry weight as starch [1]. In potato starch is either accumulated transiently in leaves or as storage starch in tubers. In leaves starch is synthesised in the chloroplast from triose-phosphates produced during photosynthesis. After several inter- mediate steps, glucose 6-phosphate is converted to glu- cose 1-phosphate by the enzyme phosphoglucomutase (PGM). Glucose 1-phosphate, along with ATP serves as © 2010 Ferreira et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.