Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 3 of 17 the synthesis of amylose and a potato mutant lacking any activity produce amylose free starch [21]. Starch synthase IV seems to be important for starch granule initiation and mutants lacking this isoform do not only show changes in diurnal starch accumulation, but also have fewer, and bigger, starch granules [22,23]. Despite the many isoforms of branching enzyme, they can be grouped in starch branching enzyme A (SBEA) and B (SBEB). The majority of branching enzyme activity can be attributed to SBEB [24], but silencing of only SBEB did not lead to a change in starch structure. Simulta- neous silencing of SBEA and SBEB, however, lead to production of high amylose potato starch [25]. Table 1 contains all the genes involved in starch metabolism which will be further discussed in this paper. The path- ways in which these enzymes are involved are shown in figure 1. One of the major problems with potato tuber research is the fact that tuber growth and induction rates are not synchronised. Although tuber developmental stages are well defined [26], this does not mean that tubers in the same stage have similar growth- or biochemical charac- teristics. Adding to this, tubers are underground organs making in vivo analysis without damaging the plant almost impossible. To date no study has determined the in vivo growth velocity of individual tubers. X-ray com- puted tomography (X-ray CT) provides the opportunity to determine the velocity of tubers without physically damaging the plant. It has been used to study under- ground plant organs [27], but to date no study has determined tuber growth velocity using this method. Even though the pathway of starch biosynthesis is well understood, mechanisms regulating biosynthesis are still unclear. Smith et al. [28] did an extensive study on tran- scriptional regulation of starch metabolism in Arabidop- sis leaves over a 24 hour diurnal period. This study was very useful elucidating the regulating machinery of starch metabolism. The design of a custom microarray Table 1 List of genes involved in starch metabolism discussed in this paper. Name Plastocyanin Chlorophyll a/b binding Ribulose 1,5 bisphosphate carboxylase oxygenase Triose phosphate translocator 1 Glucose 6-phosphate translocator 1 Glucose 6-phosphate translocator 2 Plastidial phosphoglucomutase ATP/ADP translocator 1 ADP-glucose pyrophosphorylase large subunit ADP-glucose pyrophosphorylase small subunit Starch synthase II Starch synthase III Granule bound starch synthase Starch synthase IV Starch branching enzyme A Starch branching enzyme B Isoamylase 1 Isoamylase 2 Glucan, water dikinase Isoamylase 3 PCT-Beta-amylase Maltose transporter Alpha-amylase Disproportionating enzyme 1 Disproportionating enzyme 2 SEX4 phosphoglucan phosphatase Cell wall invertase Fructokinase Sucrose synthase 4 Hexokinase 1 Hexokinase 2 Abbreviated name Plastocyanin CAB Rubisco TPT GPT1 GPT2 PGM NTT1 AGPase LS AGPase SS SSII SSIII GBSS SSIV SBEA SBEB ISA1 ISA2 GWD ISA3 PCT-BMY MEX1 AAMY DPE1 DPE2 SEX4 Cw-Inv FK Susy4 HK1 HK2 POCI identifier Micro.4322.c1 Micro.4163.c1 Micro.4165.c3 Micro.3160.c1 Micro.4029.c2 Micro.1076.c1 Micro.1743.c2 Micro.1831.c2 Micro.2198.c1 Micro.367.c1 Micro.1850.c2 Micro.1658.c1 Micro.920.c2 Micro.16059.c1 Micro.16220.c1 Micro.1689.c1 Micro.7513.c1 Micro.13258.c1 Micro.3453.c1 Micro.10651.c1 Micro.13823.c2 Micro.10450.c1 Micro.10377.c1 Micro.1834.c1 Micro.6841.c1 Micro.1811.c1 Micro.4223.c2 Bf_suspxxxx_0040h09.t3m.scf Micro.196.c8 Micro.5594.c1 Micro.4130.c1