Zhang et al. BMC Genomics 2011, 12:63 http://www.biomedcentral.com/1471-2164/12/63 R E S E A R C H A R T I C L E Open Access Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing Jin-Zhi Zhang1, Xiao-Yan Ai1, Lei-Ming Sun1, Dong-Liang Zhang, Wen-Wu Guo1,2, Xiu-Xin Deng1,2, Chun-Gen Hu1* Abstract Background: After several years in the juvenile phase, trees undergo flowering transition to become mature (florally competent) trees. This transition depends on the balanced expression of a complex network of genes that is regulated by both endogenous and environmental factors. However, relatively little is known about the molecular processes regulating flowering transition in woody plants compared with herbaceous plants. Results: Comparative transcript profiling of spring shoots after self-pruning was performed on a spontaneously early flowering trifoliate orange mutant (precocious trifoliate orange, Poncirus trifoliata) with a short juvenile phase and the wild-type (WT) tree by using massively parallel signature sequencing (MPSS). A total of 16,564,500 and 16,235,952 high quality reads were obtained for the WT and the mutant (MT), respectively. Interpretation of the MPSS signatures revealed that the total number of transcribed genes in the MT (31,468) was larger than in the WT (29,864), suggesting that newly initiated transcription occurs in the MT. Further comparison of the transcripts revealed that 2735 genes had more than twofold expression difference in the MT compared with the WT. In addition, we identified 110 citrus flowering-time genes homologous with known elements of flowering-time pathways through sequencing and bioinformatics analysis. These genes are highly conserved in citrus and other species, suggesting that the functions of the related proteins in controlling reproductive development may be conserved as well. Conclusion: Our results provide a foundation for comparative gene expression studies between WT and precocious trifoliate orange. Additionally, a number of candidate genes required for the early flowering process of precocious trifoliate orange were identified. These results provide new insight into the molecular processes regulating flowering time in citrus. Background Flowering is one of the most important aspects of devel- opment in plants to ensure successful reproduction and eventual adaptation to surrounding environments. Plants have evolved mechanisms to integrate various environ- mental signals, including photoperiod and vernalization, * Correspondence: chungen@mail.hzau.edu.cn 1Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, PR China Full list of author information is available at the end of the article to enable flowering under conditions that optimize seed production [1,2]. In recent years, molecular and genetic regulation of flower development has been extensively investigated in herbaceous plants, particularly in Arabi- dopsis [3-5]. A number of different pathways have been described in Arabidopsis that induce the floral transi- tion, including vernalization, photoperiod, autonomous, and gibberellin (GA) pathways that form a regulatory network [6,7]. Genes involved in controlling the timing of floral transition have been identified through muta- genesis and analysis of natural variation. These four © 2011 Zhang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.