Ectopic expression of a Flowering Locus T (CiFT) from Citrus confers an early flowering phenotype on trifoliate orange (Poncirus trifoliata L. Raf.). To profile transcriptional effects of CiFT, mRNA extracted from the shoots of the transgenic trifoliate orange was subjected to genetic analysis using a 22-K oligo DNA microarray. Microarray results and reverse transcription polymerase chain reaction analysis indicated that genes relating to transcription, cell wall modification and defense responses were expressed at higher levels in the transgenic shoots than in the control wild-type shoots. Of the genes showing ectopic mRNA accumulation, two SEPALLATA (SEP) and one FRUITFULL (FUL) homologues (CuSEP1, CuSEP3 or CuFUL) were introduced to Arabidopsis thaliana. Constitutive expression of each gene caused early flowering in transgenic Arabidopsis, suggesting that these genes could function as regulators of flowering time.