Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 7 of 17 Figure 5 Expression of genes known to be involved in starch biosynthesis during tuber induction. A) Import of glucose 6-phosphate and ATP into the plastid and the conversion thereof to ADP-Glucose. GPT1 (light blue), GPT2 (dark blue), PGM (orange), NTT1 (brown), AGPase LS (light green), AGPase SS (dark green). B) Starch synthases and branching enzymes. SSII (dark grey), SSIII (light grey), GBSS (blue), SSIV (black), SBEA (light purple), SBEB (dark purple), ISA1 (dark red) and ISA2 (pink). C) Sucrose cleavage and phosphorylation. Cw-Inv (Black), FK (blue), Susy (gold), HK1 (Dark yellow) and HK2 (green). Values are the mean of two replicates. has been provided that DPE2 might be present inside the plastid [38], which questions the role of MEX1. If the expression data is compared to that of Arabidopsis, indications are there that a similar pathway for starch degradation probably occurs in potato leaves, except that isoamylase 3 was not differentially expressed. The other genes mentioned were all differentially co- expressed in leaves, and expression patterns followed that of starch accumulation in the leaf (Figure 7). The entire microarray dataset for both the diurnal leaf experiment and the tuber induction experiment have been deposited on ArrayExpress (accession numbers E- MEXP-2481 Ferreira et al. Potato diurnal leaf time- course and E-MEXP-2482 Ferreira et al. Potato tuber induction). POCI sequence and annotation data are available through the POCI online tool http://pgrc.ipk- gatersleben.de/poci. Diurnal oscillation of GBSS in potato tubers can be linked to differences in sucrose supply It is known that starch biosynthetic genes are diurnally regulated by several factors, with sucrose and the circa- dian clock seemingly being the most important. Bläsing et al. [39] showed that between 30-50% of genes in Ara- bidopsis rosettes show diurnal changes in their tran- scripts and that this was especially true for genes involved in redox regulation, nutrient acquisition and assimilation, and starch and sucrose metabolism. Com- parative analysis of nutrient feeding and diurnal tran- scription profiles indicate that sugars make a major contribution to diurnal regulation. Furthermore, Osuna et al. [40] analysed gene expression in carbon-deprived Arabidopsis seedlings after the addition of sucrose. Genes involved in central carbon metabolism, and more specifically starch biosynthesis, showed a response to sucrose and this did lead to an increase in starch con- tent. A second major regulator of diurnal gene expres- sion seems to be the circadian clock. Bläsing et al. [39] identified a subset of 373 genes known to be circadian regulated [41]. The gene set was used in a principle component analysis which showed that sucrose and the circadian clock are the predominant factors in regulating diurnal gene expression and that light, nitrogen and water deficiency makes a smaller contribution. Starch degradation related genes also have a strong diurnal