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.

Good luck..

I have used QIAGEAN RNAESY Mini plant EVEN FOR Affymetrix Genechip analysis and it was well worked with the good quality 260/280 between 1.8 and 2