If you mix RNA from both leaf and root together, you cannot distinguish the expression levels of a (specific) gene in leaf vs. root.

Yes, see attached paper below from the Liu's group. Gene expression levels were studied after plants subjected to PEG-induced stress. They used leaves. But genes in different organs (leaves or roots) could response to a stress differently. So, it depends on your research goal. If necessary, you may need to do 2 sets of experiments.

"Identification of Differentially Expressed Genes in Leaf of Reaumuria soongorica under PEG-Induced Drought Stress by Digital Gene Expression Profiling (2014)"

Thank you so much. I try both leaf and  root.

Dear Bushra,

May I ask what the aim of the study is? Do you want to identify genes which alter in expression as a plant loses water? If so, there are  many studies of this type. However what is unclear is how gene expression is related to cellular/nuclear conditions as the water content, water potential and  osmotic potential decrease and the concentrations of ions, metabolites etc change. It has become rather standard to assume that a change (generally  increased expression) of in gene expression indicates a response which is part of a drought adaptation mechanism. However, there is also the possibility that the changes are part of an unbalanced cellular regulatory system, and without particular significance for adaptation. To analyse the response of gene expression to cellular water loss requires a rather more detailed analysis of cell physiology than is often done. Here I must say that  Yuan-Yeu Yau's work, which is cited in his response, seems to lack any  detail about the physiological conditions and just using a single PEG concentration of unspecified osmotic potential does not provide adequate information.  

Perhaps reading:

D Z. Habash (2014) Systems Responses to Progressive Water Stress in Durum Wheat PLOSone: September 29, 2014

and literature given there will help.

As Yuan-Yew Yau says clearly, I also do not see what value there is in treating roots and leaves as if their responses are the same. What will be learned?

Best regards

David  

Dear Bushra,

I fully agree with the comments by David: looking at gene expressions response to drought or other abiotic stress, a detailed information about the physiological conditions (i.e., tissue water potential, osmotic potential or relative water content) should be provided in the first hand. Otherwise all comparisons made at the molecular level are not really meaningful.

Best Regards,

Fulai

Thank you so much @ Sir David W. Lawlor & Sir Fulai Liu for your suggestions. I surely read literature, hope so my problem solve.

 Hello Bushra,

I agree with the valuable comments that provided by David and Liu. During abiotic stress plants go through a noteworthy modification in their cellular and molecular level to cope with that stress condition. I don't know aim of your research. But I can tell you, drought study with PEG and drought study in soil, plant's response are not similar. Even though numerous publication's are available based on PEG based drought. Measure the physiological responses under certain stress and capture the responsive gene responsible for that stress is more fruitful approach.

Mixing roots and shoots RNA mixing together are not very insightful. As, every tissue acts differently during stressful environment and you can't differentiate the tissue specific responses.

Thank you!

Regards,

Rokebul

My aim is find out MYB genes response during abiotic stress, in order to know which genes give response to stress, I am not going to check stress effect on root, leaf etc so in this case can I use whole seedling and extract RNA from whole seedling??

Hello Bushra

A couple of points

-  perhaps consider the value of  information  you will get, because without a measure of the conditions in the plant/organ the changes in MYB genes will be of little value in my view. Try measuring relative water content at least (for a drought study) and use a range of PEG concentrations

-  Use of PEG: I have used PEG for drought studies extensively where a more specific control of plant water status over a longer period  is needed than can be easily obtained in small pot experiments.Despite Rokbul's view, PEG simulates soil drying quite well.  PEG should not be regarded as providing the same conditions as a field experiment  but it does provide a way of rapidly achieving a more-or-less constant water content/potential which is useful for hysiological/biochemical/genomic studies, such as you intend.  

Hope the comments help

Regards

David

Hello Bushra, maybe you can read two of papers from my PhD thesis. The first study was physiologic response on drought stress during flowering time on blackcurrants. At the same time we did experiment on molecular response from leaf samples. Taking samples from root is so difficult. Finally, it was wonderful when we connected our gene expression results with physiological response to drought. Both papers are published and can see it on my profile. Hope can help. Kind regards, Natasa

Thanks alot Rokebul Anower & Natasa Cerekovic for your suggestions. It is very informative.