Identification and characterization of a novel hybrid upregulated long non-protein coding RNA in maize seedling roots

Previous studies have shown that heterosis is associated with differential gene expression between hybrids and their parents, but the responsible molecular mechanisms have not been determined. Long non-protein coding RNAs (npcRNAs) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNAs and siRNAs. Here, a novel npcRNA up-regulated in maize seedling roots of hybrid Zong3/87-1 was identified and named ZmUHR, which comprised multiple members arranged in clusters of 1–4 copies throughout the maize draft genome. Consistent with its preferential expression in young and vigorous growth tissues, promoter sequences of this gene possesses about 10 motifs related to meristem specific activation. Most notably, 41 of 47 siRNAs matched to ZmUHR mRNA were specifically expressed in hybrid and 20 out of 25 (80%) were validated by real-time PCR, which exhibited a good correlation with the up-regulation of ZmUHR gene in hybrid. Collectively, it can be concluded that differential accumulation of some siRNAs may be controlled by transcript levels of the precursor produced, which provide new insights into maize npcRNA biology and the potential roles of this gene in heterosis.