If you are going to do this once, I suppose you could add your own attributes to your GFF file to indicate these relationships, and this could be as simple as adding a term (i.e., ortholog_of:somegene). However, I'd try something that was created for this purpose rather than trying to come up with a new format and then figuring out how to parse it. The OrthoXML format was developed for storing these relationships, so I would have a look at the documentation for the OrthoXML format and try to get your hands on some orthoxml files to study. Also, OrthoXML is supported in BioPerl so you should be able to read/write these files without too much work.