These questions have weighed on me since my laboratory published a series of papers, with the first appearing in PNAS in 1985, on the structure of spontaneous mutations at the maize waxy gene (1). This and subsequent studies revealed the predominance of two classes of mutations: long-terminal repeat (LTR) retrotransposons (2) and complex deletions (3). Members of the same LTR retrotransposon families found among waxy mutants were also found as causative agents of spontaneous mutation at other maize loci. In all cases, the insertions contained members of LTR retrotransposon families, with fewer than 10 copies genome-wide. In contrast, the availability of an increasing amount of maize genome sequence revealed that 75% was derived from LTR retrotransposons, largely families with thousands, even tens of thousands, of copies (4). Despite comprising the vast majority of the maize genome, LTR retrotransposon activity—that is, the movement of elements in real time—had not been convincingly demonstrated in the 35 y since their discovery in spontaneous mutants. The paper in PNAS by Dooner et al. (5) reports that the mechanism to activate LTR retrotransposons in maize has been hiding in plain sight in the fields of geneticists and breeders. The authors couple their mastery of maize genetic resources with modern genomic and computational analyses to produce a large collection of spontaneous mutations, both at targeted genetic loci and throughout the genome. They demonstrate that low-copy retrotransposons are likely responsible for virtually all observed spontaneous mutations, including the unusual deletions. Furthermore, they determine that genetic backgrounds differ in the spectrum of activated retrotransposon families, with some elements moving in only one background and no elements moving in others. Most important is the finding that mutations only occur during pollen development; no mutations could be isolated through the female lineage of any tested line. This latter finding provides a convincing rationale for the failure of prior studies to detect spontaneous mutations, as virtually all followed the pioneering crossing strategy of Stadler (6) who used female rows with dominant markers open-pollinated with plants containing several recessive markers.
Dooner et al. (5) begin with a simple question: What is the frequency of spontaneous mutation at the Bzlocus? To this end, they set up reciprocal crosses of two Bz stocks with bz testers where rare spontaneous mutations could be easily identified as bronze kernels in a purple-kernel background. For each of the four crosses, they screened at least 400,000 kernels (∼1,000 ears). To identify the molecular lesions, putative mutant bz kernels were planted and DNA was isolated from leaf tissue for PCR amplification with Bz primers. This straightforward experimental design produced several surprising results. First, bz mutants were only detected when the dominant Bz alleles were in the male parent. Second, for the two structurally distinct dominant alleles tested (Bz-B73 and Bz-McC), the frequency of mutation was unexpectedly high (4.3 and 3.6 per 100,000 gametes, respectively). This is over an order of magnitude greater than estimates by Stadler (6) of spontaneous mutation frequencies at six maize genes. Third, the majority of new mutants contained low-copy LTR retrotransposons or deletions that were reminiscent of the waxy mutations reported decades earlier. For example, several insertions of members of the Magellan and Hopscotch families of LTR retrotransposons were among the new bz and previously characterized wx mutants. Taken together, these results suggested that low-copy LTR retrotransposons were mobile during pollen (male), but not female gamete, development. However, a striking difference in the spectrum of LTR retrotransposons inserted in the two Bz alleles was noted. Insertions in Bz-B73 included six Magellan and 12 Bs2 LTR retrotransposons, while insertions in Bz-McC included two Hopscotch LTR retrotransposons and four soloLTRs (sLTRs), presumably derived by internal deletion, from previously undescribed LTR retrotransposons.