Is it necessary to keep a blank even when we keep a negative control in PCR?

The answer is yes. Let me explain why. Sometimes we assume a gene to be transgenic and may be it is true. But a similar kind of cisgene may be there which is phylogenetically related to it. For example: Suppose we have a DREB gene from a crop which is more responsive to drought than the given crop in which we need to impart resistance. After introducing the trans DREB gene suppose we went for PCR with a DREB gene specific marker then there are chances you get a same sized band in the negative also. Sometimes when both the related genes are of different sizes then it is also possible that in a transgenic plant you get 2 bands; one for the transgene and the other for the cisgene and in negative you may get only one band corresponding to the cisgene. This is why we keep the DNA of any non-transgenic plant of the same variety or line as negative control for PCR. But the purpose of keeping a Blank (All the PCR components except template) is quite different. A blank can show positive only when there is template contamination from a positive sample or from the positive control in anyone of the PCR components or more than one PCR components. Thus keeping a blank in PCR always helps us to avoid false positives and also helps us to find out whether the components are safe or contaminated.

L:Ladder (100 bp), P: Positive Control (Plasmid) and B: Blank. The figure shows the PCR confirmation of Nos promotor gene (Whether present or not in the plasmid ). The empty B (Blank) Lane assures us that there is no contamination in any of the PCR components used and the result we are getting in the positives are true positives. Amplicon size is nearly 240 bp. Agarose gel electrophoresis done in 1.2% Agarose gel.