Transcriptome Characterization and Sequencing Based Identification of Cold Responsive Genes in Cabbage

Cabbage (Brassica oleracea) is one of the most important vegetable crops in the world. Yet, its sensitivity to cold stress, especially at the seedling stage, could limit the production. Until now, only, few studies about heritably durable cold tolerance were carried out in cabbage. Hence this study was done to characterize the transcriptome profiles of two cabbage genotypes with contrasting responses to cold stress using Illumina Hiseq 2000 short read (paired-end) sequencing technology. Using the mRNAs of control (22˚C) and cold-treated (0˚C) seedlings ∼198 million short reads were generated and further processed into 124,199 unigene sequences with a high depth of coverage. A total of 58,094 unigenes were obtained by de novo assembly and were assigned with Nr annotations. Functional classification revealed the involvement of unigenes in various biological processes, highly accounted with cellular process and metabolic process. In total, 12,578 unique cold-responsive candidate genes were identified with significantly differential expression. Of which, 5,792 unique genes were up-regulated while 6,786 were down-regulated. Results in reverse transcription- polymerase chain reaction (RT-PCR) and real-time PCR analyses, verified the changes in expression levels of 19 up and down-regulated unigenes. The transcriptome of B. oleracea will provide valuable gene resources for future application in crop improvement. In addition, this study sets a good example for large-scale identification of cold-responsive genes in non-model organisms using the sequencing-based approach.