First of all: the running buffer has mostly a pH of 8.9 or even higher. The most performed mistake in SDS PAGE has been to titrate the buffer to pH 8.3, which causes very slow SDS PAGE runs and blurred pattern. Never add an acid to the running buffer!

Second: the stacking gel buffer has a pH of 6.8, because this is close to the pI  of glycine (the trailing ion), which causes a low mobility of glycine. Please read Standard literature and learn about "isotachophoresis".

When the glycine has overtaken the protein stack after passing the Interface beteen stacking and resolving gel (pH 8.8), it becomes highly charged and behind the chloride ion front you have suddenly only Tris/glycine , which has a pH 9.5 due to the  pK value ot the basic buffer group of glycine.

I wouldn't mess up with buffer composition. The recipe for SDS gels (Lämmli) was originally derived from the multiphasic buffer system of Ornstein and Davies. The different buffer composition and pH means that upon setting up a voltage gradient across the gel, a sharp boundary forms between the electrode buffer and the stacking gel buffer. Proteins will migrate faster in the top buffer and slower in the lower buffer, so that they get concentrated at the boundary. As the boundary moves down and reaches the separating gel, the proteins are retarded and migrate according to their size, while the boundary migrates ahead of them. Thus, by altering the recipe for buffers, you risk loosing the benefit of stacking and get fuzzy bands.

Thnks Pierre for the response. I know about the importance of stacking gel and resloving gel in a SDS PAGE. My query is not about altering the pH but I wish to know why there is a pH difference in running buffer (pH 8.3) and stacking gel buffer (pH8.8)? What will happen if we raise the pH of running buffer equal to resolving gel buffer?

Secondly, How the operating pH goes upto 9.5 for resolving gel during electrophoresis?

First of all: the running buffer has mostly a pH of 8.9 or even higher. The most performed mistake in SDS PAGE has been to titrate the buffer to pH 8.3, which causes very slow SDS PAGE runs and blurred pattern. Never add an acid to the running buffer!

Second: the stacking gel buffer has a pH of 6.8, because this is close to the pI  of glycine (the trailing ion), which causes a low mobility of glycine. Please read Standard literature and learn about "isotachophoresis".

When the glycine has overtaken the protein stack after passing the Interface beteen stacking and resolving gel (pH 8.8), it becomes highly charged and behind the chloride ion front you have suddenly only Tris/glycine , which has a pH 9.5 due to the  pK value ot the basic buffer group of glycine.

Again: the pH value of the running  buffer is irrelevant, it has nothing to say. See my answer above.

You cannot polymerize a stacking gel with pH 8.8.: this is too far from the polymerization optimum, the solution will not polymerize, but stay liquid.

If you skip the stacking gel, you will lose the stacking effect (see isotachophoresis). a part of the proteins will aggregate and precipitate at the bottom of the sample pocket, because the starting conditions will be too harsh due to the high charges of the Proteins at this pH value.

And now you have to allow me this question: Why do you think do thousands of electrophoresis users take the pains and follow the relative work-intensive standard Laemmli procedure and polymerizing a stacking gel short bevor sample application??: because it gives the best results according to the theory and due to more than 40 years of practical experiences!

Of course, you can also apply other gel and buffer conditions for SDS PAGE, like the Weber and Osborne technique. But with much less good results

Thank you Reiner for the explanation. I am trying to understand the effect of pH on SDS-PAGE gel. I find the question interesting regarding operating temperature and your explanation seems logical.

Thaks a lot. 

Note that the pH is temperature dependent, you need different buffer systems at RT and 4 °C. It is also possible to design buffer systems for different pH-values, Jovin's group has done a systematic study on this (1973). Unfortunately, their internet buffer calculator has gone offline, it was a valuable resource. But you really should read, mark and inwardly digest the original Ornstein paper on discontinuous electrophoresis (doi:10.1111/j.1749-6632.1964.tb14207.x).