Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 4 of 17 Figure 1 Proposed pathway of starch metabolism in photosynthetic and non-photosynthetic tissue. has made it possible to do similar types of analysis in potato. The POCI microarray was designed from the largest collection of ESTs from potato yet [29] and can be used to study all aspects of the potato transcriptome, which include starch biosynthesis. Due to the abundance of transcriptome data available, co-expression analysis has become a common method to identify new genes involved in specific metabolic pathways. The principle of the technique is that genes involved in similar processes would be expressed or inhibited at the same time point or under similar conditions. This would not only include structural genes, but possibly also regulatory genes like transcription factors. They are able to bind to specific sequences of various targets and thus have the ability to regulate entire metabolic pathways [30]. Moreover, over- expression of two transcription factors in tomato led to the over-expression of the entire anthocyanin synthesis pathway, producing purple anthocyanin rich tomatoes [31]. These results show that by manipulating transcrip- tion factors entire biosynthetic pathways can be influenced. The aim of this work was to investigate the transcrip- tional regulation of starch biosynthesis in potato under various conditions. More specifically we looked at simi- larities between gene expression in leaves and tubers. Furthermore we established a new technique using X- ray computed tomography to determine tuber growth velocity in vivo and used it to analyse gene expression in tubers growing at different velocities. Finally com- parative analysis of transcription profiles were used to identify transcription factors possibly regulating starch biosynthesis. Results and discussion Starch biosynthesis in potato leaves follow carbohydrate accumulation and show similarities to tuber starch biosynthesis Leaf samples for starch and RNA extractions were taken from potato plants grown under a 14 hour light and 10 hour dark cycle. The light conditions were chosen to ensure diurnal turnover of transitory starch. As was expected, starch levels were the lowest at the start of the light period and accumulated during the day to a high at the end of the light period (Figure 2A). The same pattern was observed for sucrose although the accumulation and decline was more rapid (Figure 2B). The levels of starch and sucrose compared well to what was previously measured in potato leaves [4]. After confirming that there was a turnover of transient starch under the specific light conditions used, gene expression at different times of the day was analysed by microarray. To investigate how much similarity there is between leaf and tuber starch biosynthesis, the expres- sion of genes known to be important for tuber starch biosynthesis was investigated in leaves. Starch biosyn- thetic genes had a strong diurnal rhythm of expression.