Segmental duplications are prevalent in both plant and animal genomes, and have played important roles in genome evolution. The focus of my project is to understand the transposition-mediated mechanisms that lead to the formation of segmental duplications, and the immediate impact of recently generated large (up to 14.6 Mb) tandem duplications in maize. We applied a variety of genetic, molecular, statistical and bioinformatics approaches, including genetic screening, PCR, Southern blotting, qRT-PCR, microarray, mRNA-sequencing, small RNA-sequencing, and a self-developed program (STRAND: Search for Transposon-Induced Tandem Direct Duplications) to study these questions. We discovered new genome rearrangement mechanisms, including transposition of paired DNA transposon termini that can generate tandem direct duplications (TDD) and novel structures termed Composite Insertions. Genomic study revealed that these mechanisms have played an important role in generating TDD in 8 of 22 examined plant genomes. We also found a significant dosage-dependent effect of a 14.6 Mb duplication on phenotypic variation, and expression of mRNA and small RNA transcripts. This work expands our current knowledge of how DNA transposons contribute to rapid genome expansion, extends our understanding of the significance of DNA transposons in altering genome structure, and provides new insight into the transcriptional expression and phenotypic effect of a specific and recent maize duplication.