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Open Access Highly Accessed Research article

Transcriptome profiling of the cold response and signaling pathways in Lilium lancifolium

Jingmao Wang1, Yang Yang2, Xiaohua Liu1, Jie Huang1, Qing Wang1, Jiahui Gu1 and Yingmin Lu1*

Author Affiliations

1 College of Landscape Architecture & China National Engineering Research Center for Floriculture, Beijing Forestry University, No.35 Qinghua East Road Haidian District, Beijing 100083, China

2 College of soil and water conservation, Beijing Forestry University, No.35 Qinghua East Road Haidian District, Beijing 100083, China

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BMC Genomics 2014, 15:203  doi:10.1186/1471-2164-15-203

Published: 17 March 2014



Lilium lancifolium, a very important cold-resistant wild flower for lily cold resistance breeding, is widely distributed in southwestern and northeastern China. To gain a better understanding of the cold signaling pathway and the molecular metabolic reactions involved in the cold response, we performed a genome-wide transcriptional analysis using RNA-Seq.


Approximately 104,703 million clean 90- bp paired-end reads were obtained from three libraries (CK 0 h, Cold-treated 2 h and 16 h at 4°C); 18,736 unigenes showed similarity to known proteins in the Swiss-Prot protein database, and 15,898, 13,705 and 1849 unigenes aligned to existing sequences in the KEGG and COG databases (comprising 25 COG categories) and formed 12 SOM clusters, respectively. Based on qRT-PCR results, we studied three signal regulation pathways —the Ca2+ and ABA independent/dependent pathways —that conduct cold signals to signal transduction genes such as LlICE and LlCDPK and transcription factor genes such as LlDREB1/CBF, LlAP2/EREBP, LlNAC1, LlR2R3-MYB and LlBZIP, which were expressed highly in bulb. LlFAD3, Llβ-amylase, LlP5CS and LlCLS responded to cold and enhanced adaptation processes that involve changes in the expression of transcripts related to cellular osmoprotectants and carbohydrate metabolism during cold stress.


Our study of differentially expressed genes involved in cold-related metabolic pathways and transcription factors facilitated the discovery of cold-resistance genes and the cold signal transcriptional networks, and identified potential key components in the regulation of the cold response in L lancifolium, which will be most beneficial for further research and in-depth exploration of cold-resistance breeding candidate genes in lily.

Lilium lancifolium; RNA-Seq; Transcriptome; Cold response; Signaling pathway; Biochemical mechanism