The wealth of sequence data from many flowering plant species offer unique opportunities for us to understand the dynamic genomic changes that have occurred in many plant lineages. Such changes are evident through comparisons from both within the same genome and across multiple related genomes. I have developed improved methodology to identify and interpret synteny patterns that are more suitable for comparing plant genomes. The novel computational tool helps to infer ancient whole genome duplications in both the eudicot and monocot lineages and also provides clearer correspondences between representative taxa across the two divergent lineages. In the second part of my dissertation, I fine mapped the sorghum grain shattering (seed dispersal) locus Sh1, which was previously mapped to a ~1Mb genomic region by linkage study. In order to associate the shattering trait with specific DNA polymorphisms, I carried out extensive resequencing in the region using a diversity panel consisting of shattering and non-shattering sorghum individuals. The second study suggests a few candidate DNA changes for further functional confirmations, among which might underlie a key genetic transition from wild to domesticated sorghum.