Sounds like an interesting project you’ve go there!

You’ve been given a flying start by those Open Helix people…
http://www.openhelix.com/blog/?p=388

The gramene database has some good tutorials if you fancy tinkering yourself (with a crash course in bioinformatics, thrown in for free)
http://www.gramene.org/tutorials/

The sequence viewer linked to by the mary at
http://gramene.org/Zea_mays/cytoview?l=5:1-6365100;h=umc1766

is based on a browser called “ensembl” for which there are also good tutorials.

http://www.ebi.ac.uk/~bert/presentations/genomes_to_systems/
http://www.google.co.uk/search?q=ensembl+tutorial

Needless to say, this would be a lot easier (and perhaps less fun!) if it was genetic “defect” in humans, mice, e.coli or any other better understood model organism… (rather than pesky tetraploid corn)