Fig. 4: Small RNA size distributions differ among tissues and inbreds.

a Size distributions of sRNAs were calculated in each tissue of each inbred line (CPM, count per million mapped reads). Maize and teosinte inbreds have similar size distributions in coleoptilar nodes (CN), but differ in other tissues. In pollen, more 24nt sRNA (orange) accumulates in B73 relative to other inbreds, while in ears TIL11 has reduced levels of 24nt and increased levels of 21nt sRNAs (red). In root tips and endosperm, NC350 has reduced levels of 24nt siRNAs. Error bars are standard error between two biological replicates. b Whole-genome browsers of 21, 22 and 24nt siRNAs expressed in pollen and coleoptilar node (CN) in each inbred, highlighting the presence of hairpins producing high levels of 22 and 24nt sRNAs in pollen and only 22nt in CN. Each track is scaled to its maximum CPM. At this scale the 21nt sRNAs mostly show expression of the most highly expressed microRNAs. c Secondary structure of a representative pollen-specific hairpin made with RNAfold¹¹². 50 bp of the 3 kb stem is shown at the bottom. d Browser screenshots of a representative pollen-specific hairpin (same as in c), present in W22, B73 and TIL11, producing high levels of stranded 22nt sRNAs, as well as 21 and 24nt sRNAs in all pollen inbreds in a very similar pattern. The gray boxes represent the two repeated halves of the hairpin.