Plants are the basis for the survival of all "higher" organisms on Earth. Development of molecular genetics tools has allowed analysis of the structure, evolution, and function of whole plant genomes, rather than individual genes. DNA-based markers were instrumental in constructing detailed genetic maps of model plants and all major crop species. These molecular maps were the basis of physical maps and the first plant whole genome sequences. Comparative analysis based on genetic, cytogenetic, and physical maps and DNA sequence information provided new insights into the evolution of plant nuclear and organellar genomes. Mapping factors controlling Mendelian and quantitative traits made possible the cloning and functional characterization of novel genes, which function in plant development, adaptation to biotic and abiotic stress, or in the formation of other agronomic characters. The parallel analysis of all transcripts, proteins, and metabolites present in plant cells or tissues has generated information that may lead to a better integrated understanding of genome function. Postfunctional analysis of natural variation of gene function and its effects on phenotype is envisaged to provide new diagnostic and therapeutic molecular tools for applications in plant breeding, adaptation, and ecology.