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Background  Oriental hybrid lily ‘Sorbonne’, a very important cut flower for lily, is enjoyed great popularity in the world, but it must experience a period of low winter temperature to initiate or accelerate the flowering process. To gain a better understanding of the temperature signaling pathway and the molecular metabolic reactions involved in the vernalization response, a genome-wide transcriptional analysis using RNA-Seq was performed.    Results  188,447,956 sequencing reads was assembled into 66,327 unigenes and showed similarity to known proteins in the Swiss-Prot protein database, and 2,893, 30,406 and 60,737 unigenes aligned to existing sequences in the KEGG, COG, and GO databases. Based on qRT-PCR results, we studied the expression of three signal regulation pathways genes–the plant hormones signal transduction ( LoAP2 ,  LoIAA1 ,  LoARF10 ), the DNA methylation ( LoCMT ,  LoFLD ), and vernalizatin pathway ( LoFLC ,  LoVRN1 ,  LoVRN2 ,  LoFT ,  LoSOC1 ,  LoLFY ,  LoSVP ) in the immature flower buds of Oriental hybrid lily. In addition, we identified two vernalizaiton–related genes ( LoSVP  and  LoVRN1 ) from the cDNA library, which appear to be promising candidates for playing key roles in the development and response of flowering in Oriental lily plants, and  LoSVP  had a function in delaying flowering but  LoVRN1 could promote flowering early.    Conclusions  We collected a sample for transcriptome sequencing and comparison when the bulb’s apical meristem was in the time of floral transition when the apical meristem had not converted into the morphological differentiation process, which helped to obtain more genes playing key roles in the floral induction pathways. The upstream and downstream relationship between different genes were forecasted by the analysis of genes’ expression levels in a wide range of time. Future research that is targeted towards how genes interact on each other, which will promote establishing and perfecting the molecular mechanisms of floral induction pathway by vernalization.

Transcriptome comparison reveals key candidate genes in response to vernalization of Oriental lily