Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 12 of 17 Figure 11 Estimated growth velocity of tubers in cubic centimetre volume increase per day. Tubers chosen for microarray hybridisation are marked by arrow heads amiR-white-1(MIR172a) knockout [52]. The construct targets the GUN4 allele which is important for plastid to nucleus signalling and when this is interrupted it affects plastidic expression of several nuclear encoded genes. Furthermore, the expression of GPT2, plastidial PGM, GBSS and SBEB was also significantly down in these plants. This, along with the fact that these tran- scription factors were co-expressed in the same clusters as starch biosynthetic genes, indicate that they might be important in regulating starch accumulation. Conclusion Comparative transcriptome analysis between leaves and tubers indicate that transient and storage starch biosynthesis might not be all that different with the same isoforms being differentially expressed in both tis- sues. There was also a diurnal rhythm of GBSS expres- sion in tubers which could be correlated to sucrose supply from the leaves. This provided evidence not only of the diurnal regulation of starch biosynthetic gene expression in tubers, but also showed the importance of sucrose supply in regulating gene expression in tubers. Since tuber initiation and growth is not synchronised, it was important to determine the growth velocity of individual tubers. To this end X-ray CT was used to determine the volume of individual tubers at different time points and calculate the growth velocity. This was the first time that the growth velocities of tubers were Figure 12 Relative expression of starch biosynthetic genes in tubers growing at different velocities. GPT1 (pink), GPT2 (yellow), ISA2 (orange), AGPase LS (purple), AGPase SS (brown) and Susy4 (green). Values are the mean of two replicates.