Identification Of MicroRNA Genes And Their Targets Involved In The Early Development Of Brace Root In Zea Mays L.

Maize (Zea mays L.) is one of the most significant cereal crops cultivated around theworld. It has brace roots, which contribute significantly to lodging resistance, water andnutrient uptake, and most importantly, normal grain yield under soil flooding andwater-limited conditions. MicroRNAs (miRNAs) are a class of small non-coding regulatoryRNAs that play essential regulatory roles in plant growth, development, and stress responses.However, miRNAs concerning the initiation or early development of brace roots arecompletely unkown.In order to characterize the miRNAs that contribute to the development of brace root inmaize (Zea mays L.), Solexa high-throughput sequencing of three small RNA librariesderived from tissues of node (N), nodes with just-emerged brace roots (NR), and nodes withjust-emerged brace roots after IAA treatment (NRI) was performed. Total of511,617and462known miRNA-matched sequences were obtained out of650,793,957,303and1,082,948unique reads in N, NR and NRI libraries, respectively. Further analysis confirmed theauthenticity of137known miRNAs belong to26miRNA families and the discovery of159novel miRNAs in maize. Among them, we identified19conserved and25novel miRNAs thatwere differentially expressed in brace roots. Fourteen conserved and16novel miRNAs wereconfirmed by qRT-PCR. With further analysis,15target genes found to be related to braceroots under miRNA regulation. Moreover, auxin represented a regulator in brace rootdevelopment in maize as well as nitrogen, phosphorus and carbohydrate nutrition.This work extends insights into miRNA-mediated gene expression regulations in braceroot and provides a useful resource for future studies on maize miRNAs. Further functionalanalysis of the differentially expressed miRNAs and their target genes will provide deeperinsight into the regulation of maize brace root development.