I want to check expression of genes induced by spider mites infestation. Since disease has effect on whole plant and hypersensitive response against infection leads to activation of genes and subsequently achievement of Systemic acquired resistance. All these changes are occurring at whole plant level and not just at the infection site. So i thought it won't matter if i take leaves showing no visible symptoms. Because in case of control plants i have already taken innermost fresh new leaves but in diseased plants these leaves have no visible symptoms. What should i do? What is recommended for genes expression analysis of diseased plants
You just need to replicate your control plant to make it really comparable. If the expression is systemic, and as you said it would not matter, so take the same tissue from both of the plant to avoid the effect of the origin of the tissue.
However, I would say the expression could be significantly different in the leaves with and without the visible symptoms.
There are some studies that have mentioned significant difference in the affected and the systemic leaf. So I suggest if your plants sets are of the same age you can refer to BBCH scale (Lancashire et al., 1991, Annals of applied Biology 119(3): 561-601.) to identify the same leaf in your control set plants as on the plants with spider mite infection.
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