Barley long non-coding RNAs (lncRNA) responsive to excess boron.

Area of Science:

• Plant molecular biology
• Genomics
• Transcriptomics

Background:

• Long non-coding RNAs (lncRNAs) are emerging as key regulatory molecules in plants.
• Previous studies have implicated plant lncRNAs in developmental processes and environmental responses.
• Next-generation sequencing has enabled large-scale identification of lncRNAs across various species.

Purpose of the Study:

• To perform a genome-wide discovery of barley lncRNAs.
• To investigate the expression patterns of these lncRNAs under excessive boron (B) treatment.
• To explore the potential regulatory roles of lncRNAs in barley's response to B stress.

Main Methods:

• Genome-wide identification of barley lncRNAs using next-generation sequencing and bioinformatics tools.
• Analysis of lncRNA expression patterns in different tissues (leaves and roots) upon B treatment.
• Functional annotation of co-expressed coding transcripts.
• Identification of endogenous target mimics (eTMs) and their interaction with microRNAs (miRNAs).
• Quantitative real-time polymerase chain reaction (qRT-PCR) for validating RNA sequencing results.

Main Results:

• Approximately 8000 barley lncRNAs were identified.
• Leaves exhibited a higher number of B-responsive differentially expressed lncRNAs compared to roots.
• Functional enrichment analysis of co-expressed coding transcripts in leaves indicated roles in ion transport and stimulus response.
• Thirty-two barley eTMs were identified, potentially regulating 18 miRNAs.
• Specific lncRNAs (e.g., TCONS_00045190, TCONS_00056415) showed overexpression in a B-tolerant cultivar under excess B conditions.
• qRT-PCR confirmed the B-responsive expression changes observed via RNA sequencing.

Conclusions:

• Barley lncRNAs are differentially expressed in response to excessive boron.
• lncRNAs, potentially through miRNA-eTM-coding target transcript modules, may play a regulatory role in barley's response to B stress.
• Specific lncRNAs exhibit differential expression patterns in B-tolerant cultivars, suggesting a role in adaptation mechanisms.