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The following HTML text is provided to enhance online readability. Many aspects of typography translate only awkwardly to HTML. Please use the page image as the authoritative form to ensure accuracy. incorrigible irregularity” (7). What follows is a brilliant analysis of “freak ears” containing large sectors in which the unstable P allele has either further mutated or reverted. Emerson was able to capture the behavior of unstable mutations in the Mendelian paradigm by postulating that variegation commenced with the temporary association of some type of inhibitor with a locus required for pigmentation. Emerson's suggestion was that normal pigmentation was restored upon loss of the inhibitor. Several prominent geneticists, among them Correns and Goldschmidt, dismissed unstable mutations as a special category of “diseased genes ” (10,11). It was their view that little could be learned from the study of such mutations that was relevant to the study of conventional genes. But the drosophilist Demerec and the maize geneticist Rhoades shared Emerson's view that there was no difference in principle between stable and unstable mutations. Indeed, the Rhoades mutation cited in Stebbin's volume illustrates the important point that instability is conditional. Rhoades' experiments had revealed that a standard recessive allele of the maize A1 locus, isolated decades earlier and in wide use as a stable null allele, could become unstable in a different genetic background. The key ingredient of the destabilizing background was the presence of the Dt locus, which caused reversion of the a1 allele to wild type both somatically and germinally (12,13). In the late 1930s, McClintock had begun to work with broken chromosomes and by the early 1940s she had devised a method for producing deletion mutations commencing with parental plants, each of which contributed a broken chromosome 9 lacking a terminal segment and the telomere. Searching for mutants in the progeny of such crosses, she observed a high frequency of variegating mutants of all kinds (14). She noted that although reports of the appearance of new mutable genes were relatively rare in the maize literature, she already had isolated 14 new cases of such instability and observed more. She chose to follow the behavior of a locus, which she called Dissociation (Ds), for its propensity to cause the dissociation of the short arm of chromosome 9 at a position close to the centromere, although she soon appreciated that chromosome dissociation required the presence of another unlinked locus, which she designated the Activator (Ac) locus (14,15). By 1948, she had gained sufficient confidence that the Ds locus moves to report: “It is now known that the Ds locus may change its position in the chromosome” (11,16). The relationship between the chromosome-breaking Ds locus and variegation emerged as McClintock analyzed the progeny of a new variegating mutation of the C locus required for kernel pigmentation. She carried out an extraordinary series of painstakingly detailed cytological and genetic experiments on this new mutation, c-m1, whose instability was conditional and depended on the presence of the Ac locus (11,16,17). She showed that the origin of the unstable mutation coincided with the transposition of Ds from its original position near the centromere on chromosome 9 to a new site at the C locus and that when it reverted to a stable wild-type allele, Ds disappeared from the locus. Having established that Ds could transpose into and out of the C locus germinally, she inferred that somatic variegation reflects the frequent transposition of Ds during development. Transposition explained both Emerson's and Rhoades' earlier observations. McClintock and Rhoades were good friends, of course, and it is evident from their correspondence that McClintock immediately saw the parallels between the behavior of the c-m1 mutation and Rhoades' a1 mutation (Lee Kass, personal communication). The Ac and Ds elements are transposition-competent and transposition-defective members of a single transposon family. In the ensuing years, McClintock identified and studied a second transposon family, called Suppressor-mutator (Spm) (18,19). Her studies on these element families were purely genetic, and she was able to make extraordinary progress in understanding the transposition mechanism because she studied the interactions between a single transposition-competent element and one or a small number of genes with insertions of cognate transposition-defective elements (20). Two points about this early history of transposition merit emphasis. First, the active elements were denumerable and manageable as genetic entities, despite their propensity to move. Second, the number of different transposon families and family members uncovered genetically was (and still is) small. Hence the genetic impact of transposable elements was limited. McClintock recognized that the high frequency of new variegating mutations in her cultures was linked to the genetic perturbations associated with the presence of broken chromosomes (14,21). Her inference, extraordinarily prescient, was that transposons are regular inhabitants of the genome, but genetically silent. Plant Transposons in the Age of GenomicsWith the cloning of the maize transposons, first the Ac element in my laboratory and later the cognate En and Spm elements in Heinz Saedler's and my laboratories, the picture began to change (22 –24). To begin with, it became obvious immediately that the maize genome contains more copies of a given transposon than there are genetically identifiable elements. Although most of these sequences are not complete transposons, there are nonetheless more complete transposons than can be perceived genetically (25). Importantly, it was clear almost immediately that a genetically active transposon could be distinguished from one that was genetically silent by its methylation pattern (25,26). Both of these observations bear on the genetic visibility of transposons. As maize genes and genome segments began to be cloned and sequenced, the discovery of new transposons accelerated. Although the transposons that McClintock identified and studied were DNA transposons, both gypsy-like and copia-like retrotransposons were soon identified in the maize genome and subsequently in many other plant genomes (27 –32). It has also become evident that non-long terminal repeat (LTR) retrotransposons are abundant in maize, as well as other plant genomes (33,34). Many additional maize transposon families have been identified through their sequence organization and their presence in or near genes (35 –40). We now know that transposons and retrotransposons comprise half or more of the maize genome (41). What Do Transposons Do?Commencing with McClintock's elegant analyses of transposonassociated chromosomal rearrangements and extending into the literature of today, the range of transposon-associated genetic changes has continued to expand (18). Insertion of plant transposons, like almost all known transposons, is accompanied by the duplication of a short flanking sequence of a few base pairs (42). Plant transposons excise imprecisely, generally leaving part of the duplication at the former insertion site (42). The consequences of insertion and excision of a transposon therefore depend on the location within the coding sequence and excision of an insertion from an exon commonly results in either an altered gene product or a frame-shift mutation. Transposon insertions can alter transcription and transcript processing, and there are cases in which transposons are processed out of transcripts by virtue of the presence of splice donor and acceptor sequences (43 –45). Transposons also can promote the movement of large segments of DNA either by transposition or by illegitimate recombination (46,47). The ParadoxOne might think that given their abundance, transposable elements would rapidly randomize genome order. Yet the results of a decade of comparative plant genome studies has revealed that
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