Alternative splicing is associated with tissue differentiation, subgenome divergence, and agronomic trait regulation in hexaploid wheat

Alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that enhances transcript and proteome diversity. However, AS in common wheat (Triticum aestivum) remains understudied due to the large and complex genome of this crop. Full-length transcriptome sequencing, which provides long, high-quality reads, offers a powerful tool for analyzing AS in wheat. In this study, we used the PacBio Sequel platform to sequence full-length transcripts from five wheat tissues (root, stem, leaf, spike, and grain) of the cultivar Aikang58 (AK58). We identified 560,631 isoforms from 86,073 genes, with 76.7% of genes producing multiple isoforms and 45.34% undergoing AS events (ASEs). Tissue-specific analysis revealed differences in the number and function of AS genes (ASGs), underscoring the potential role of AS in tissue differentiation. A comparison across the three wheat subgenomes showed similar numbers of ASGs and ASEs but distinct functional patterns, suggesting that AS is involved in subgenomic divergence. We also examined AS in genes linked to key agronomic traits, demonstrating association with trait regulation. These findings enhance our understanding of the adaptability and post-transcriptional gene regulation in wheat, offering insights for future research and breeding efforts.