3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.

Three-dimensional (3D) chromatin architecture plays a fundamental role in eukaryotic gene regulations, its functional significance in perennial fruit trees remains poorly characterized despite extensive applications in crop genomics. Here, we developed high-resolution (∼5 kb) Hi-C maps of Pyrus and compared 3D genomic architecture of three representative pear species: the wild Asian pear 'Duli' (P. betuleafolia), the cultivated Asian pear 'Dangshansuli' (P. bretschneideri), and the cultivated European pear 'Early red Doyene du Comice' (P. communis). Approximately 78% of compartment and 73% of TAD-like domains are conserved among the three species. Interspecific structural variation correlates with TAD-like boundary repositioning, which is associated with altered expression levels of genes near these boundaries. The variations in TAD-like boundaries among three species correlated with differentially expressed whole-genome duplication (WGD) and single-copy genes. Furthermore, integration of pear population data identified 234 domestication- and 3605 divergence-associated genes near TAD-like boundaries, which are enriched in cell development pathways. One candidate gene-PyYABBY, located in a different TAD-like boundary between P. bretschneideri and P. communis, is confirmed to enhance leaf size. This study revealed 3D genomic divergence among three Pyrus species, demonstrating the functional and evolutionary roles of TAD-like structures in genome organization, thereby providing insights for crop trait evolution research.