Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling.

Area of Science:

• Plant molecular biology
• Transcriptomics
• Abiotic stress response

Background:

• Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), are increasingly recognized for their roles in plant stress responses.
• The specific functions of these ncRNAs in response to chilling stress in crops like bell pepper remain largely uncharacterized.

Purpose of the Study:

• To investigate the roles of lncRNAs, circRNAs, and miRNAs in bell pepper's response to chilling stress.
• To identify differentially expressed RNAs and their potential targets involved in chilling tolerance.

Main Methods:

• Deep sequencing was employed to profile the accumulation of lncRNAs, circRNAs, miRNAs, and messenger RNAs (mRNAs) in chilled versus non-chilled bell pepper fruit.
• Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on differentially expressed genes.

Main Results:

• The study identified 380 lncRNAs, 36 circRNAs, 18 miRNAs, and 4128 differentially expressed mRNAs under chilling conditions.
• Key target genes regulated by ncRNAs included transcription factors (MYB, bHLH, ERF), enzymes in bio-oxidation and oxidative phosphorylation, and cell wall metabolism enzymes.
• A regulatory network of interacting RNAs associated with bell pepper chilling was constructed.

Conclusions:

• ncRNAs play a significant role in the molecular response of bell pepper to chilling stress.
• The identified ncRNAs and their target genes provide a foundation for understanding and potentially improving chilling tolerance in bell pepper.