β-GlcY treatment alters transcriptome dynamics and auxin distribution during microspore embryogenesis in Brassica napus

Microspore embryogenesis (ME) is a classical model for plant cell fate reprogramming, involving extensive transcriptional and structural reorganization. Arabinogalactan proteins (AGPs), key components of the cell wall interface, have been implicated in ME, but their effects during early cell fate reprogramming remain unclear. Here, in Brassica napus, using morphological observation, embryogenic reporters, and stage-specific transcriptomics, we show that β-D-glucosyl Yariv (β-GlcY) treatment, perturbing AGP-related functions, is associated with impaired activation and spatial distribution of embryogenic markers. Transcriptome profiling reveals that the first 24 h after culture represent a major stage of AGP-associated transcriptional responses. β-GlcY treatment attenuates developmental and chromatin-associated pathways while upregulating stress-responsive and metabolic programs. Notably, 24 h marks a key transition, with altered expression of genes involved in rRNA processing, chromatin organization, and sister chromatid cohesion, suggesting AGPs help establish a permissive transcriptional and chromatin state for fate conversion. Consistently, β- GlcY treatment is associated with altered cell wall organization, auxin distribution, and PIN1 polarization, suggesting a potential connection between extracellular matrix perturbation and polarity establishment. Together, these results suggest that β-GlcY treatment is associated with changes in extracellular structure, transcriptional reprogramming, and hormone-mediated polarity during the acquisition of embryogenic competence of early ME.