longistaminata, providing a rich resource for the further elucidation of small RNA functions in rice. Many miRNAs display temporal or tissue-specific expression patterns [33]. Some miRNAs were expressed exclusively in ASs and rhizomes of O. longistaminata, indicating their possible regulatory roles in tissue development. We identified 19 miRNAs,

including osa-miR319a-3p and osa-miR529a, Trametinib chemical structure which were highly and exclusively expressed in the rhizome, and four predicted target genes for osa-miR319a-3p were characterized as encoding the Alg9-like mannosyltransferase protein, dihydrodipicolinate reductase, LSD ONE LIKE 3 (LOL3), and a retrotransposon protein ( Table S4). LOL3 is a zinc finger that may be involved in programmed cell death and defense responses [34]. While the targets for osa-miR529a were predicted to encode a carboxyl-terminal proteinase, a phytosulfokine receptor, a conserved hypothetical protein, and a transposon protein ( Table S4), their detailed functions in rhizome development need further investigation. Comparative analysis of miRNAs differentially expressed between ASs and rhizomes could promote understanding of miRNA functions in rhizome growth regulation and development. In this study, 117 known rice miRNAs, including several important miRNA families, were found to be differentially expressed in rhizomes relative to ASs. Ten

members of the osa-miR156 Clomifene family, whose LDE225 chemical structure target genes are TGA1, SBP TFs, and SPL TFs, which were previously reported to be related to growth and development in plants [35], [36] and [37], had significantly lower expression levels in rhizomes than in ASs. Seven members of the osa-miR444 family, whose predicted target genes included several MADS-box TFs and SNF2 TF, which were found to be involved in cellular processes, also had lower expression levels in rhizomes [38] and [39]. In contrast, osa-miR319b, whose target genes are two TCP TFs, which have been reported to control the morphology of shoot lateral

organs [40], was highly enriched in the rhizome. These results revealed that the identified differentially expressed miRNAs, correlated with their respective target genes, could function in the regulation of rhizome formation. miRNAs bind to target sequences in mRNAs, typically resulting in repressed gene expression, and targets can also reciprocally control the level and function of miRNAs [41]. In the present study, expression antagonism was observed for several miRNAs and their corresponding target genes, including osa-miR156a and two TGA1s. However, a correlative antagonistic expression pattern could not be detected for osa-miR319b and its target TCP gene, indicating their co-expression in specific tissues, a finding consistent with previous reports [42] and [43].