To cite this paper: Xian, M., T. Luo, M.N. Khan, L. Hu and Z. Xu, 2017. Identifying differentially expressed genes associated with tolerance against low temperature stress in Brassica napus through transcriptome analysis. Abstract Under direct-seeding method of sowing, seedling survival is adversely affected due to low temperature. The purpose of this study was to understand the morphological, physiological and molecular response of rapeseed resistance to low temperature stress at seedling

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... lishment. Two varieties Qinyou No.7 (resistant biotype) and Fengyou 730 (sensitive biotype) were used for morphological and physiological experiments under low temperature stress and the resistant variety was used for transcriptome analysis based on the Illumina HiSeq 2000 platform. Results showed resistant variety initiated osmotic regulation system firstly and then triggered the antioxidant enzyme system when exposed to low temperature stress for long duration. The MDA content firstly tended to increase and then decreased in resistant variety, but it continued to increase in sensitive variety. Through transcriptome analysis of Qinyou No. 7 under low temperature for 0 h, 24 h, 48 h and 96 h, 2254 differentially expressed unigenes clustering in 7 expression patterns were participated in low temperature stress. Proteinserine/threonine kinases, myo-inositol-1-phosphate synthases and calmodulins, as the members of ABA and IP3/Ca2+ signal transduction pathway, played an important role in the low temperature stress. Different expressed genes dataset provides useful candidate genes for functional analysis of rapeseed resistance to low temperature.