Approximately 80% of ~2,500 Mbp maize genome consists of highly repetitive sequences. Initial sequencing efforts have targeted the gene-rich regions of this genome. A new open reading frame (ORF) selecting vector (pORF-Rescue) was developed to efficiently distinguish between the coding and non-coding fractions of this complex genome. pORF-Rescue can enrich ORFs by ~15 fold and non-transposon coding sequences by ~3.6 fold. This vector can also be applied for rapid gene discovery from maize BAC DNA and to establish peptide/expression libraries;Methylation filtration (MF) and high-Cot (HC) sequencing strategies have also proven successful in maize gene-enrichment. To best utilize MF and HC genome survey sequences (GSSs), these GSS data were first examined by identifying types and frequencies of sequencing errors and then assembled into maize assembled genomic islands (MAGIs). Computational and biological quality assessments indicate that a very high percentage of the MAGIs accurately reflect the structure of the maize genome. In addition, we estimate that this assembly of the maize gene space has "tagged" >6,900 expressed genes that previously lacked evidence of transcription and that almost 350 of these expressed genes are "orphans"; i.e., they do not exhibit similarity to genes in other species;To construct a sequence-based maize genetic map using large-scale genic sequence data and intermated B73xMo17 recombinant inbred lines (IRILs) as mapping population will facilitate the map-based genome sequencing project, QTL and eQTL studies, and candidate gene cloning experiments. The observations that two segregation distortion regions overlap with maize flowering time QTLs suggest that the altered allele frequencies were a consequence of inadvertent selection during the development of the IBM IRILs. Detection of inter-chromosomal two-locus gamete disequilibrium suggests another means to discover potential functional relationships (e.g. epistasis) of different chromosome regions using well-characterized plant RILs.*;*This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Adobe Acrobat; Microsoft Office.