Origin of spontaneous mutations in maize has been hiding in plain sight

Abstract

Spontaneous mutations are the raw material of evolutionary change. Given their importance, it is surprising that so little is known about their origin, frequency, or molecular structure. 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 … [↵][1]1Email: susan.wessler{at}ucr.edu. [1]: #xref-corresp-1-1