Transcriptome analysis of rosette and folding leaves in Chinese cabbage using high-throughput RNA sequencing

• DOI: 10.1016/j.ygeno.2012.02.005
• Publication Date: 2012-02-23T21:18:11Z
• Authors: Fengde Wang; Libin Li; Huayin Li; Lifeng Liu; Yihui Zhang; Jianwei Gao; Xiaowu Wang
• Keywords: 2. Zero hunger; 0303 health sciences; Reverse Transcriptase Polymerase Chain Reaction; Gene Expression Profiling; Brassica rapa; High-Throughput Nucleotide Sequencing; Rosette leaves; Chinese cabbage; Polymorphism, Single Nucleotide; High-throughput RNA sequencing; Plant Leaves; Alternative Splicing; 03 medical and health sciences; Gene Expression Regulation, Plant; Genetics; Folding leaves; Transcriptome; Gene Library

In this study, we report the first use of RNA-sequencing to gain insight into the wide range of transcriptional events that are associated with leafy head development in Chinese cabbage. We generated 53.5 million sequence reads (90 bp in length) from the rosette and heading leaves. The sequence reads were aligned to the recently sequenced Chiifu genome and were analyzed to measure the gene expression levels, to detect alternative splicing events and novel transcripts, to determine the expression of single nucleotide polymorphisms, and to refine the annotated gene structures. The analysis of the global gene expression pattern suggests two important concepts, which govern leafy head formation. Firstly, some stimuli, such as carbohydrate levels, light intensity and endogenous hormones might play a critical role in regulating the leafy head formation. Secondly, the regulation of transcription factors, protein kinases and calcium may also be involved in this developmental process.