A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis

PeerJ. 2023 May 19:11:e15349. doi: 10.7717/peerj.15349. eCollection 2023.

Abstract

Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.

Keywords: Anthocyanin; Purple potato; Red mutant; Small RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anthocyanins / genetics
  • MicroRNAs* / genetics
  • RNA, Messenger / genetics
  • Sequence Analysis, RNA
  • Solanum tuberosum* / genetics

Substances

  • Anthocyanins
  • MicroRNAs
  • RNA, Messenger

Grants and funding

This work was supported by the National Natural Science Foundation of China (Grant No. 31901589), the Modern Agriculture Industrial Technology System Funding of Shandong Province (Grant No. SDAIT-16-05), and the “333” Project of Shandong Academy of Agricultural Sciences-Molecular Breeding of Vegetables and Flowers (Grant No. CXGC2021B17). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.