Spontaneous mutations in maize pollen are frequent in some lines and arise mainly from retrotranspositions and deletions.

While studying spontaneous mutations at the maize () locus, we made the unexpected discovery that specific low-copy number retrotransposons are mobile in the pollen of some maize lines, but not of others. We conducted large-scale genetic experiments to isolate new mutations from several stocks and recovered spontaneous stable mutations only in the pollen parent in reciprocal crosses. Most of the new stable mutations resulted from either insertions of low-copy number long terminal repeat (LTR) retrotransposons or deletions, the same two classes of mutations that predominated in a collection of spontaneous mutations [Wessler S (1997) , pp 385-386]. Similar mutations were recovered at the closely linked locus. These events occurred with a frequency of 2-4 × 10 in two lines derived from W22 and in 4Co63, but not at all in B73 or Mo17, two inbreds widely represented in Corn Belt hybrids. Surprisingly, the mutagenic LTR retrotransposons differed in the active lines, suggesting differences in the autonomous element make-up of the lines studied. Some active retrotransposons, like , , and , a variant, were described previously; others, like and in 4Co63, were not. By high-throughput sequencing of retrotransposon junctions, we established that retrotranposition of , , and occurs genome-wide in the pollen of active lines, but not in the female germline or in somatic tissues. We discuss here the implications of these results, which shed light on the source, frequency, and nature of spontaneous mutations in maize.