Comparative pan-transcriptomics for exploring genome diversification in the cereals

As climate change threatens global food security, understanding the genetic architecture of staple crops is becoming increasingly urgent. This work presents a systematic exploration of the functional consequences of polyploidization and evolutionary divergence in the Triticeae tribe, with a focus on bread wheat and barley. By treating individual wheat subgenomes (A, B, and D) as distinct entities, a novel comparative transcriptomics framework reveals subgenome-specific functional partitioning among 18,594 homeologous gene triads, offering new insights into how complex genomes regulate gene expression. Central to the methodology is a meta-network pipeline built on Weighted Gene Co-expression Network Analysis (WGCNA) and Cosine similarity measures. A key highlight is the complex network analysis of the first barley pan-transcriptome across 20 diverse genotypes, identifying six distinct co-expression communities associated with the sampled tissues and linked to corresponding biological processes, including photosynthesis, starch metabolism, and nutrient uptake. Together, these approaches illuminate the molecular underpinnings of crop adaptation and open new avenues for developing climate-resilient cultivars and advancing precision breeding strategies.