We had this problem once in our lab. We solved the problem by cloning the whole genomic sequence of the protein of interest (including the introns) instead of the CDS. Since the Agros will not splice the sequence, you should be safe.

Thank you. But the purpose of this experiment is to do it on CDS, due to some mutations splicing could not work well. I was thinking if there exist some tolerant strain or other possible way.

So are you planning to perform the BiFC experiment in the agrobacteria? If not, and you want to transform this to another, higher, organism, splicing should still be fine. Which system you want to transform?

Recheck your transformation procedure. If it is via electroporation, check the fitness of electrocompetent cells or you can reprepare it. Also vector DNA should have minimum concentration of salts or TE. Prepare dissolve the pDNA in water.