Long non-coding RNA RsLNC2361 positively regulate anthocyanin accumulation in radish

Radish (Raphanus sativus L.) is a crucial vegetable crop in the Brassicaceae family, which has a high nutritional, medicinal, and dietary therapeutic values. Radish varieties rich in anthocyanins are favored by consumers because of their bright color and high nutritional value. However, the reports on the role of lncRNA in regulating anthocyanin accumulation in radishes are relatively rare.

Based on our previous LncRNA sequencing findings, the RsLNC2361 was differentially expressed in red and white skin radish. The results revealed that overexpression of RsLNC2361 can promote anthocyanin accumulation in radish leaves, whereas silencing of RsLNC2361 can decrease the anthocyanin content in radish flesh root using VIGS technology, indicating that RsLNC2361 has a positive regulatory effect on anthocyanin accumulation in radish. Overexpression of RsLNC2361 increased the expresssion anthocyanin structural genes, whereas silencing of RsLNC2361 had opposite effect. A total of 5,032 DEGs and 273 differental metabolites were identified in RsLNC2361-pTY and pTY (control) by transcriptome and metabolome sequencing, respectively. Combined metabolomic and transcriptomic analyses showed KEGG pathway associated with flavonoid biosynthesis and phenylpropanoid biosynthesis was commonly enriched. The results found that the miRNA858 was predicted to target RsLNC2361, with expectation values of 4.0. Therefore, we speculate that lncRNA participates in the accumulation of anthocyanins in radishes through the regulatory mechanism of the competitive endogenous RNA (ceRNA) module.

This study provides a new perspective on the regulation of anthocyanin biosynthesis by non-coding RNA and offers a theoretical basis for the breeding of high-anthocyanin radish.