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Background   Jatropha curcas , whose seed content is approximately 30–40% oil, is an ideal feedstock for producing biodiesel and bio-jet fuels. However,  Jatropha  plants have a low number of female flowers, which results in low seed yield that cannot meet the needs of the biofuel industry. Thus, increasing the number of female flowers is critical for the improvement of  Jatropha  seed yield. Our previous findings showed that cytokinin treatment can increase the flower number and female to male ratio and also induce bisexual flowers in  Jatropha . The mechanisms underlying the influence of cytokinin on  Jatropha  flower development and sex determination, however, have not been clarified.    Results  This study examined the transcriptional levels of genes involved in the response to cytokinin in  Jatropha  inflorescence meristems at different time points after cytokinin treatment by 454 sequencing, which gave rise to a total of 294.6 Mb of transcript sequences. Up-regulated and down-regulated annotated and novel genes were identified, and the expression levels of the genes of interest were confirmed by qRT-PCR. The identified transcripts include those encoding genes involved in the biosynthesis, metabolism, and signaling of cytokinin and other plant hormones, flower development and cell division, which may be related to phenotypic changes of  Jatropha  in response to cytokinin treatment. Our analysis indicated that  Jatropha  orthologs of the floral organ identity genes known as ABCE model genes,  JcAP1,2, JcPI ,  JcAG , and  JcSEP1,2,3 , were all significantly repressed, with an exception of one B-function gene  JcAP3  that was shown to be up-regulated by BA treatment, indicating different mechanisms to be involved in the floral organ development of unisexual flowers of  Jatropha  and bisexual flowers of  Arabidopsis . Several cell division-related genes, including  JcCycA3;2 ,  JcCycD3;1 ,  JcCycD3;2  and  JcTSO1 , were up-regulated, which may contribute to the increased flower number after cytokinin treatment.    Conclusions  This study presents the first report of global expression patterns of cytokinin-regulated transcripts in  Jatropha  inflorescence meristems. This report laid the foundation for further mechanistic studies on  Jatropha  and other non-model plants responding to cytokinin. Moreover, the identification of functional candidate genes will be useful for generating superior varieties of high-yielding transgenic  Jatropha .    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-974) contains supplementary material, which is available to authorized users.

Transcriptome of the inflorescence meristems of the biofuel plant Jatropha curcas treated with cytokinin