there is protocol published in nature protocols.." A robust plant RNA isolation method suitable for Affymetrix Genechip analysis and Quantitative real- time RT-PCR by Damla D Bilgin.. you can try with this...
Check the protocol by Ghawana et al., 2011. An RNA isolation system for plant tissues rich in secondary metabolites. BMC Research Notes 2011, 4:85
The method is very simple and robust. You can isolate RNA in 45 min. We are using RNA isolated by this protocol for various applications including transcriptome analysis.
I have isolated the total RNA from leaves and flowers sample using SpectrumTM Plant total RNA isolation Kit. It give good quality of total RNA. So you can use this kit for better results.