Pedigree-resolved genome assemblies reveal the structural and functional dynamics of tropical-temperate integration...

The "tropical-temperate integration" strategy, which involves the introgression of robust stress resistance from tropical germplasm into elite temperate lines, has become increasingly important for stabilizing maize yields amid climate change. Here, we investigated the genomic architecture of this strategy using KNY8009, a representative elite hybrid from the Huang-Huai-Hai summer maize region, by generating platinum-quality, pedigree-resolved genome assemblies across its lineage. We identified massive knob180 tandem-repeat arrays as primary drivers of genome size plasticity and as hotspots for organellar DNA capture, while also demonstrating that these regions are a major source of error during reference-guided scaffolding. We identified hyperdivergent regions as discrete hotspots of extreme genetic diversity whose boundaries are enriched in known regulatory motifs. Intensive functional genomics and genome-wide association studies involving 38 traits confirmed that targeted tropical introgressions have reshaped specific genomic regions, conferring broad-spectrum resistance while preserving the elite temperate backbone. Finally, an alignment-free k-mer analysis provided an unbiased atlas of tropical-temperate divergence, which can guide future integration efforts. Our study reveals the genetic basis of tropical-temperate integration and establishes a rigorous, structure-aware framework for decoding the hidden variations that drive modern crop improvement.