Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 10 of 17 Figure 8 GBSS relative expression and stolon sucrose content at different time-points of the day. A) Diurnal expression of GBSS in tubers. B) GBSS expression at the 24 hour time-point from plant grown in light/dark cycle and from plants kept in twenty four hours of darkness. C) Stolon sucrose content at different time-points of the day (dark grey bars) and at the same time-points from plant kept in darkness from 0 hours onward (dark grey bars). Two values were not determined (n.d.). Error bars represent standard deviation (n = 3-7). Figure 10A illustrate that potato tubers were clearly dis- tinguishable from the surrounding soil, and a histogram demonstrated that segmentation of tuber material was possible. The software used for segmentation also allowed for manual correction of possible mistakes made during the automatic segmentation process. Tuber growth velocities were calculated for seventeen tubers. To validate the method, calculated tuber volumes were compared to measured tuber volumes after harvest. X- ray CT calculated volumes showed a correlation coeffi- cient with experimental volume measurements of 0.986 showing that X-ray CT calculated volumes were accu- rate (Figure 10B). Six tubers with different growth velocities (Figure 11) were selected for microarray hybridisation and the gene expression patterns were analysed. Interestingly no lin- ear correlation between the expression of starch biosyn- thetic genes and growth velocity could be observed. The expression of genes involved in starch biosynthesis is shown in figure 12. The expression of these genes, and also other genes involved in starch biosynthesis, did not show large differences in expression levels between tubers that were still growing, albeit at very different velocities. Starch biosynthetic gene expression was however much lower in tubers that have virtually stopped growing and it seems as though the relationship between growth velocity and starch biosynthetic gene expression is qualitative rather than quantitative. This was especially true for Susy, a major determinant of tuber sink strength [11]. These data indicate that tubers that look visually simi- lar have large differences in gene expression depending on their growth stage. Moreover, transcription profiles reveal many genes that are differentially expressed between growing and non-growing tubers which provide important information towards the identification of fac- tors determining tuber growth. The entire microarray dataset for the tuber growth velocity experiment has been deposited on ArrayExpress (accession number E- MEXP-2484 Ferreira et al. tuber growth velocity). Comparative analysis of transcription profiles reveals genes possibly regulating starch biosynthesis The similarities observed in terms of starch biosynthetic gene expression between leaves and tubers suggests that the same regulators might be involved in both processes. In an attempt to identify these regulators, comparative analyses of various transcription profiles were con- ducted. Firstly, features differentially expressed between