Zhang et al. BMC Genomics 2011, 12:63 http://www.biomedcentral.com/1471-2164/12/63 Page 9 of 20 Figure 6 Pathways regulating the floral transition in Arabidopsis [68,69]. Long photoperiod and gibberellic acids (GAs) promote the floral transition by activating the floral pathway integrators. The enabling pathways regulate floral competence of the meristems by regulating floral repressor activity such as the FLC. Arrows indicate activation and short lines ending with a dot indicate repression. The data underlying the model and the corresponding homologs in citrus are presented in Table 1. A plus sign (+) indicates up-regulation and a minus sign (-) indicates down-regulation in precocious trifoliate orange. Genes in red type were not found by MPSS. citrus are presented in Table 3. For example, we found some putative homologs for floral integrator or identity gene such as FT, SOC1, FLC, CO, and AP1. Most genes of the Arabidopsis photoperiodic pathway were found in 36,523 nonredundant unigenes. We found several genes encoding putative photoreceptor apoproteins including Phytochrome A-C, Cryptochrome 1-3, ZEITLUPE (ZTL), and FLAVIN BINDING KELCH REPEAT F-BOX 1 (FKF1) (Table 3). In addition to genes of the photoperiodic pathway, homologs for both known sequences belonging to light quality pathways, PHYTOCHROME AND FLOWERING TIME 1 (PFT1) and RELATIVE OF EARLY FLOWERING 6 (REF6), were found. Of the central circadian clock genes, homologs of LATE ELONGATED HYPOCOTYL (LHY) and TIMING OF CAB 1 (TOC1) were also present in the two libraries (Table 3), but CCA1 was lacking. Furthermore, we found seven citrus unigenes that showed significant similarity to the Arabidopsis CO; these sequences were initially organized in six clusters. Among the regulators of CO transcription and protein stability, GIGANTEA (GI) was identified in the two libraries (Table 3). For the vernalization pathway, we were not able to find MAF-like sequences (MAF1-MAF5: MADS AFFECTING FLOWERING1-5) from our libraries by BLAST searches (Table 3). However, we identified