Allelic diversity is the "raw material" for natural selection. Consequently mechanisms that modulate allelic diversity should play and important evolutionary role, and these mechanisms should themselves be subject to stringent natural selection. Maize alleles are remarkably polymorphic, and much of the diversity can be attributed to transposable element activity. Transposons remain resident in many alleles, proven to confer novel regulatory properties in some cases. Insertion-deletion mutations in allele comparisons are similar in size to the footprints created by transposon insertion-deletion events. Because transposons cause mutations, most of which are predicted to be deleterious, their activities are regulated at the cellular, organismal, and populational levels. Retrotransposons comprise the majority of the maize genome; these elements can insert but never excise. Today, these retroelements are restricted mainly to intergenic regions; sporadic amplification of specific retroelements distinguish closely related grass genomes, but few retroelement are active today. In contrast, DNA transposons are active in a few individuals in every population, and they show preferential insertion into transcription units. Such insertions often create null alleles in host genes, but a wide spectrum of functional alleles can be generated after transposon excision. Some transposons generate both somatic and germinal excision alleles (Ac/Ds, Spm/dSpm in maize), while others generate primarily somatic diversity (MuDR/Mu elements in maize). MuDR/Mu elements are the most aggressive known in terms of forward mutation, and these elements are under stringent developmental regulation. Somatic excisions are restricted to the terminal cell divisions of organ development, resulting in a fine mosaic of diverse revertant alleles. Germinal revertants are rare, although the MuDR/Mu elements proliferate during meiosis and in the gametophyte. Because plants have an alternation of generations in which genetic "quality" is tested in the gametophyte, individuals carrying deleterious or lethal mutations are eliminated in the haploid phase.

Key words: genome structure, mutation, transposons