genetics - Why was it so hard to decode the corn genome?

Why was decoding the genome so significant?
Because decoding the genome gives us a complete picture of the genetic makeup of an organism.

What made it so difficult?
The repetitive sequences as mentioned by other people is a main problem. Imaging you are trying to complete a big puzzle with millions of pieces. Each piece represents a sequencing reads that we get from the experiment. If there are repetitive sequences in the genome, basically the pieces that representing these regions would look very similar (or even entirely identical). Undoubtedly, this would make the puzzle very difficult to finish. To give a scale, the maize genome is ~2.3 billion base pairs and each sequencing reads is <1,000 base pairs.