Toward a model of repeat-driven chromosomal fragility in Triticeae: an integrated structural omics perspective

Repetitive DNA dominates cereals genomes and plays a major yet poorly understood role in shaping structural genome variation. Recent advances in long-read sequencing, pangenomics, and 3D chromatin mapping have revealed that chromosomal rearrangements in Triticeae frequently arise within repeat-rich heterochromatin. However, the molecular and structural omics determinants underlying this recurrent fragility remain largely unresolved.

This review synthesizes insights from pangenome analyses, cytogenetics, long-read genome assemblies, Hi-C-based 3D chromatin architecture, and meiotic double-strand break (DSB) mapping to outline a unified Repeat-Driven Chromosomal Fragility (RDCF) model. It shows that specific repetitive DNA architectures, short sequence motifs, and chromatin environments create Repetitive Fragility Zones (RFZs) that predispose chromosomes to double strand breaks and non-allelic repair. Comparative omics evidence from Triticeae species indicates that RFZs are evolutionarily conserved, recur across lineages, and are enriched in structural variants identified by high-throughput sequencing. Integrating these multi-omics datasets highlights how repeat-driven fragility shapes genome plasticity, introgression dynamics, and polyploid evolution in cereals.

The RDCF framework connects structural omics signatures with chromosomal behavior and provides a conceptual basis for predictive fragility maps that may improve chromosome engineering, targeted introgression, and genome stabilization in crop breeding. The evidence presented here supports the view that repetitive DNA is not merely a passive component of large genomes but an active driver of structural and evolutionary innovation in Triticeae. Strengthening multi-omics integration will be essential for translating these insights into tools for crop improvement.