Gene Expression Analysis Of Pak Choi In Response To Vernalization

Pak choi (Brassica rapa ssp. chinensis) is a seed vernalization-type plant and it will bolting and flowering after a period of vernalization. It likely undergoes early bolting during production due to low temperatures in the Spring, leading to decline in commercial quality and causing economic losses. Therefore, it is critical to study the vernalization mechanism in pak choi. The vernalization mechanism of the Arabidopsis thaliana, Chinese cabbage and wheat has been studied deeply. However, the mechanism in pak choi is currently undear, and need futher research. In this study, using the Chinese cabbage genome as a reference, the gene expression profiles were analyzed in shoot apex the pak choi after cold treatment and before flower bud differentiation using RNA-Seq technology. By comparing the sequencing results and analyse the GO annotation to screen the differentially expressed genes related to vernalization between vernalizated and control plant during two stages. The vernalization genes were discovered and lay the foundation of vernalization mechanism of pak choi by analyze the function annotation of different expressed genes. The main conclusion are as follows:1) The 4 libraries of vernalized and control plant after cold treatment and before flower bud differentiation acquired 9.68?11.25?11.06 and 10.16 M total reads,493.43?573.82?564.03 and 517.85 M total nucleeotide,11111314,11268910,11072438 and 10169936 total reads respectively, of which 82.94%, 84.80%,85.08% and 84.77% reads can be annotated by the reference genome.2) A total of 1664 DEGs were identified between vernalized and control plant after cold treatment, of which 747 were upregulated and 917 were downregulated; a total of 1192 DEGs before flower bud differentiation were identified between vernalized and control plant, of which 533 were upregulated and 659 were downregulated; a total of 242 genes showed expression difference at both stages.3) 4 known vernalization genes in Chinese Cabbage including 2 FLC,1 VIN3 and 1 VRN1 have been discover by comparative analysis with Chinese Cabbage genome; 4 unknown vernalization genes in Chinese Cabbage including Bra030284, Bra041170, Bra024351 and Bra0131622 have been discovered by comparative analysis with Chinese Cabbage and Arabidopsis thaliana genome. Moreover,9 genes including Bra014527, Bra020445 and Bra000393 are predicted to paricipate in the vernalization of pak choi by gene ontology (GO) annotation and analysis to the DEGs. They need futher functional verification and expression analysis.4) Further KEGG pathway enrichment analysis showed tryptophan metabolism play role of resist the cold stress during the vernalization of pak choi. Morever, the pathway of flavonoid, glucosinolate and phenylpropanoids metabolic were enriched after vernalization and predicted these secondary compounds were crucial in the vernalization of pak choi.5) FLC (Bra028599) of pak choi was selected to conduct exopession analysis by real-time PCR. The results showed that expression gradually reduced during the vernalization and increased slowly after stage 1, with the lowest expression level at stage 1. This result indicated that the hibiting function of FLC to flowering happened before flower bud differentiation in pak choi.