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Transcriptome Analysis of the Chinese Cabbage (Brassica rapa Ssp. Pekinensis) Petal Using RNA-Seq

Liu Chang, Liu Zhiyong, Ye Xueling, Wang Yiheng, Meng Qian and Feng Hui

Flowers are the most complex and attractive organ in flowering plants that play an important role in the angiosperm reproductive process. In this study, we employed next-generation high-throughput sequencing (RNA-Seq) to gain insight into the wide range of transcriptional events that are associated with petal development in the Chinese cabbage (Brassica rapa ssp. pekinensis). We isolated RNA sequences from the vegetative mass at the four-leaf stage and petals in their full-bloom. The sequences were aligned to a reference genome and analyzed to measure gene expression levels and to detect Differentially Expressed Genes (DEGs). A total of 11,079 DEGs were obtained, of which 3,900 DEGs were up-regulated in the petal sample, and 7,179 were down-regulated. In 1,595 Specifically Expressed Genes (SEGs); 303 SEGs exhibited up-regulation with 1,292 down-regulations. Gene Ontology (GO) analysis was further used to recognize the main biological functions of DEGs. Subsequently, using KEGG enrichment analysis, we found that DEGs were involved in 125 pathways. Finally, quantitative real-time PCR (qRT-PCR) was used to verify the expression pattern of partial DEGs against the sequencing data. Importantly, all partially known genes (which were specifically expressed in petals) were reflected in the attained DEGs, including; PISTILLATA, APETALA3, SEPALLATA2, SEPALLATA1. Moreover, we found multiple genes that gave high levels of expression differences but whose functions were unknown. Further functional analysis of the differentially expressed genes set will help us to elucidate the mechanism of petal development and may significantly facilitate the breeding practices at the molecular level.