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Background  In citrus the transition from juvenility to mature phase is marked by the capability of a tree to flower and fruit consistently. The long period of juvenility in citrus severely impedes the use of genetic based strategies to improve fruit quality, disease resistance, and responses to abiotic environmental factors. One of the genes whose expression signals flower development in many plant species is  FLOWERING LOCUS T (FT) .    Results  In this study, gene expression levels of flowering genes  CiFT1, CiFT2 and CiFT3  were determined using reverse-transcription quantitative real-time PCR in citrus trees over a 1 year period in Florida. Distinct genotypes of citrus trees of different ages were used. In mature trees of pummelo ( Citrus grandis  Osbeck) and ‘Pineapple’ sweet orange ( Citrus sinensis  (L.) Osbeck) the expression of all three  CiFT  genes was coordinated and significantly higher in April, after flowering was over, regardless of whether they were in the greenhouse or in the field. Interestingly, immature ‘Pineapple’ seedlings showed significantly high levels of  CiFT3  expression in April and June, while  CiFT1  and  CiFT2  were highest in June, and hence their expression induction was not simultaneous as in mature plants.    Conclusions  In mature citrus trees the induction of  CiFTs  expression in leaves occurs at the end of spring and after flowering has taken place suggesting it is not associated with dormancy interruption and further flower bud development but is probably involved with shoot apex differentiation and flower bud determination.  CiFTs  were also seasonally induced in immature seedlings, indicating that additional factors must be suppressing flowering induction and their expression has other functions.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1094-3) contains supplementary material, which is available to authorized users.

Expression patterns of flowering genes in leaves of ‘Pineapple’ sweet orange [Citrus sinensis (L.) Osbeck] and pummelo (Citrus grandis Osbeck)