Large-scale structural variations induced by transposable elements promote population-specific divergence in Triticum turgidum ssp. dicoccoides

Large-scale structural variations (SVs) are increasingly recognized as important drivers of genome evolution and crop adaptation. In wheat, a young allopolyploid with a history of extensive domestication bottlenecks, SVs remain poorly explored, particularly in its wild progenitors. Here, we analyzed 68 wild emmer wheat ( Triticum turgidum ssp. dicoccoides ) accessions representing seven geographically distinct populations across the Fertile Crescent. Comparative genomic analysis between wild emmer and bread wheat ( T. aestivum ) revealed 17 genome-specific large-scale SVs (ranging in size between 1 kb and 1 Mb), many associated with transposable elements (TEs), specifically Gypsy and Copia retrotransposons. PCR-based genotyping validated 16 loci as polymorphic, with some showing strong population specificity. Importantly, most SVs encompassed high-confidence genes, including disease resistance kinases, receptor-like kinases, and stress-response regulators. Our findings demonstrate that wild emmer harbors substantial SV diversity with functional potential for adaptation. These results expand our understanding of wheat genome evolution and highlight population-specific rearrangements as valuable resources for breeding resilient wheat varieties.