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Background  Carotenoid compounds play essential roles in plants such as protecting the photosynthetic apparatus and in hormone signalling. Coloured carotenoids provide yellow, orange and red colour to plant tissues, as well as offering nutritional benefit to humans and animals. The enzyme phytoene synthase (PSY) catalyses the first committed step of the carotenoid biosynthetic pathway and has been associated with control of pathway flux. We characterised four  PSY  genes found in the apple genome to further understand their involvement in fruit carotenoid accumulation.    Results  The apple PSY gene family, containing six members, was predicted to have three functional members, PSY1, PSY2, and PSY4, based on translation of the predicted gene sequences and/or corresponding cDNAs. However, only PSY1 and PSY2 showed activity in a complementation assay. Protein localisation experiments revealed differential localization of the PSY proteins in chloroplasts; PSY1 and PSY2 localized to the thylakoid membranes, while PSY4 localized to plastoglobuli. Transcript levels in ‘Granny Smith’ and ‘Royal Gala’ apple cultivars showed  PSY2  was most highly expressed in fruit and other vegetative tissues. We tested the transient activation of the apple  PSY1  and  PSY2  promoters and identified potential and differential regulation by AP2/ERF transcription factors, which suggested that the  PSY  genes are controlled by different transcriptional mechanisms.    Conclusion  The first committed carotenoid pathway step in apple is controlled by  MdPSY1  and  MdPSY2 , while  MdPSY4  play little or no role in this respect. This has implications for apple breeding programmes where carotenoid enhancement is a target and would allow co-segregation with phenotypes to be tested during the development of new cultivars.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0573-7) contains supplementary material, which is available to authorized users.

The Phytoene synthase gene family of apple (Malus x domestica) and its role in controlling fruit carotenoid content