Ancient Whole-Genome Duplication and Lineage-Specific Retention Shape the Diversification of bZIP Transcription...

Gene duplication is a primary evolutionary driver of gene family expansion and functional diversification in plants, yet how different duplication processes reshape the evolutionary architecture of transcription factor repertoires remains poorly resolved in lineage-specific genomic contexts. Here, we performed a comprehensive evolutionary and transcriptomic analysis of the basic leucine zipper (bZIP) family across 17 representative species, with a focus on Pooideae. We identified 1878 bZIP genes and found that, although copy numbers were relatively conserved in most diploid grasses, polyploid Triticeae showed substantial expansion. Genome-wide and Ks analyses indicated that bZIP genes were preferentially retained after whole-genome/segmental duplication, with many copies tracing back to the ancient grass-specific ρ-WGD event, the most recent shared polyploidization event in Poaceae. Phylogenetic analyses and orthology inference further resolved four evolutionary models linking ancient duplication with lineage-specific retention and expansion. Transcriptome analyses revealed structured expression divergence across developmental and stress-related contexts, and wheat homoeologous triads exhibited widespread subgenome expression bias that was dynamically reconfigured under stress and hormone treatments. Differences in transposable element landscapes among duplication models and subgenomes further suggest a role for local genomic context in regulatory divergence. Together, these findings establish a unified framework linking ancient duplication, selective retention, and transcriptional diversification of the bZIP family in Pooideae.