Role of chromosome ends in meiotic stability, recombination and wheat evolution in the context of breeding.

Wheat is one of the most important crops worldwide, and understanding its genome organisation is crucial for geneticists and breeders. In this study, we examined the dynamic roles of telomeric and subtelomeric regions in wheat, focusing on their influence on homologous chromosome pairing during meiosis, the process that produces gametes. We analysed various Triticum species and modern cultivars, uncovering a complex “barcode” at chromosome ends that rules homologous recognition. Phylogenetic analysis of the ZIP4-5B gene highlighted the evolutionary relationships among wheat species, emphasising the contribution of wild relatives to genetic diversity, especially in terminal chromosomal regions. Our findings suggest that telomeric regions, although traditionally seen as conserved, display significant variability and structural complexity influenced by genetic background and chromosomal context. We observed a strong link between telomere position and variant accumulation, with subtelomeric regions acting as hot spots for instability and chromatin remodelling. G-quadruplex (G4) structures were found to be distributed unevenly, with their density affected by telomere distance and genomic context. Subtelomeric regions were identified as key sites for genetic improvement, harbouring rapidly evolving sequences and transposable elements that may impact meiotic pairing accuracy. Our results indicate that telomeres and subtelomeres serve as dynamic genomic centres, encoding chromosomal identity and regulating homologous pairing through a balance of sequence diversity and structural motifs. This research enhances our understanding of wheat genome stability and provides insights for breeding strategies aimed at increasing genetic diversity.