Genome-wide identification of microRNAs associated with taproot development in radish (Raphanus sativus L.)

• Five libraries were constructed from radish taproots at different developing stages.
• A total of 494 known miRNAs and 220 putative novel miRNAs were identified.
• 77 miRNAs were associated with radish taproot development.
• Target transcripts of the miRNAs were involved in various biological processes.

MicroRNAs (miRNAs) are small, endogenous, non-coding RNAs that play vital regulatory roles in plant growth and development. To identify the miRNAs associated with taproot development at the whole genome level, we sequenced five RNA libraries constructed from radish taproots at different developmental stages and generated a total of 148 M clean reads. Using an integrative bioinformatics analysis, 494 known miRNAs belonging to 434 families and 220 putative novel miRNAs were identified. Combining the differential expression analysis and target prediction, we found that 77 miRNAs were potentially associated with taproot development. Target transcripts generated significant GO terms relating to cell proliferation, root development and hormone-mediated signaling. The KEGG analyses revealed that plant hormone signal transduction, zeatin biosynthesis, biosynthesis of secondary metabolites, cell cycle, MAPK signaling and p53 signaling were closely associated with taproot development. These findings will provide valuable information for further functional verification of miRNAs and their targets in radish taproot development.