Transcriptomic and alternative splicing reprogramming by low-dose gamma irradiation in tomato under ToBRFV infection

Area of Science:

• Plant Pathology
• Molecular Biology
• Genomics

Background:

• Tomato brown rugose fruit virus (ToBRFV) poses a significant threat to global tomato production, evading existing genetic resistance.
• Conventional antiviral strategies, including seed disinfection, are often ineffective against ToBRFV.

Purpose of the Study:

• To investigate the impact of low-dose gamma irradiation (15 Gy) on transcriptomic reprogramming and alternative splicing (AS) in ToBRFV-infected tomato seedlings.
• To elucidate the molecular mechanisms underlying radiation-induced antiviral defense in tomatoes.

Main Methods:

• RNA sequencing (RNA-Seq) was employed to analyze transcriptomic changes in irradiated versus non-irradiated tomato seedlings.
• Bioinformatic analyses included CLC Genomics Workbench, Python scripts, STRING database, and KEGG REST API for data interpretation.
• Functional enrichment analysis and miRNA-target interaction prediction were performed.

Main Results:

• Gamma irradiation induced distinct alternative splicing patterns, notably exon skipping and alternative splice site usage, in infected tomato seedlings.
• Alternative splicing events were concentrated in defense-related genomic regions.
• Six differentially expressed and alternatively spliced genes (DE-ASGs), including kinases and auxin response factors, were identified, indicating a dual regulatory response.
• Enrichment analysis highlighted gamma-induced AS genes' involvement in plant-pathogen interactions, MAPK signaling, and hormonal pathways.
• sly-miR6024 and sly-miR5303 were predicted as key regulators of alternatively spliced transcripts.

Conclusions:

• Alternative splicing is a crucial component of gamma irradiation-induced antiviral defense in tomatoes.
• A synergistic regulatory network involving transcriptional modulation, alternative splicing, and miRNA control contributes to radiation-induced resistance.
• These findings offer a basis for developing stress-resilient tomato cultivars through understanding transcriptomic plasticity and radiation effects.