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.

• By (author) Vanda Beata Marosi