Genome-Wide Analysis of the lncRNAs and miRNAs Involved in Flower Development in Radish

Radish (Raphanus sativus L.) is an important root vegetable in the cruciferous family. The yield and quality of radish is seriously affected by the premature bolting and flowering. Although the microRNAs (miRNAs) in regulating flower development have been established in radish, the identification and characterization of long noncoding RNAs (lncRNAs) have yet to be explored. In this study, miRNAs and lncRNAs in vegetative and flower stage were conducted by RNA-seq and small RNA sequencing, respectively. A total of 5315 differentially expressed genes (DGEs), 263 DElncRNAs, and 38 DEmiRNAs were detected in two stages. GO analysis found that many flower DGEs associated with reproductive process, response to hormone, and pollination were enriched. In total, 202 DElncRNAs and 257 DElncRNAs were found to have potential cis- and trans-regulatory effects on 572 DEmRNAs and 3902 DGEs, respectively. A total of 93 and 82 DEGs were predicted as putative targets of 31 DEmiRNAs and 29 DEmiRNAs, respectively. Five mRNA-lncRNA-miRNA regulatory pairs involved in flowering time regulation were proposed, including miRNA156a-5p, miRNA399b, miRNA novel-23, miRNA164c-5p, and miRNA165a-5p. The qRT-PCR results showed that four mRNAs, three lncRNAs, and three miRNAs were consistent with the results of RNA-seq and small RNA sequencing. Transient overexpression of miR156a-5p significantly inhibited the expression levels of RsSPL10, RsSPL15, lncRNAs RsLinc1162, and RsLinc214. The results showed that miR156 co-expressed with RsSPL10 and RsSPL15 significantly inhibited the luciferase activity of RsSPL10 and RsSPL15 genes, indicating miR156 can directly target RsSPL10 and RsSPL15 and inhibit their expression. These findings provide a theoretical foundation for further elucidating the molecular regulation mechanism of mRNAs, lncRNAs, and miRNAs in bolting and flowering in radish.