Liying Feng, Zongyi Sun, Peng Zhang, Jionghao Gao, Jingxian Fu, Yang Wang, Yawen Yang, Anqiang Jia, Jiawei Zhao, Wenlong Li, Juan Li, Xiangyang Guo, Angui Wang, Pengfei Liu, Hai-Jun Liu, Haiyang Wang, Zehui Chen
The "Tropical-Temperate Integration" strategy, which involves the introgression of robust stress resistance from tropical germplasm into elite temperate lines, is a genomic imperative for stabilizing maize yields under climate change. Here, we investigated the genomic architecture of this strategy using KNY8009, a representative elite hybrid of 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 maize genome size plasticity and as hotspots for organellar DNA capture, while also demonstrating that these regions were a major source of error in reference-guided scaffolding. Furthermore, we identified hyperdivergent regions (HDRs) as punctate hotspots of extreme genetic diversity, whose boundaries were enriched for known regulatory motifs. Intensive functional genomics and novel genome-wide association studies across 38 traits confirm that targeted tropical introgressions reshaped specific genomic landscapes, 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, valuable for further integration. Our study elucidated the genetic basis of Tropical-Temperate Integration, and established a rigorous, structural-aware framework for decoding the hidden variations that drive modern crop improvement.