Divergent genetic and phenotypic trajectories in China’ s maize hybrids

Maize germplasm is fundamental for breeding progress, yet the genetic and phenotypic trajectories of China’s modern commercial hybrids are poorly characterized. Through whole-genome resequencing of the hybrids themselves—which directly represent commercially deployed varieties— and multi-trait phenotyping of 61 elite hybrids, we delineated two major germplasm groups: a broad-based V1 group and a V2 group dominated by Pioneer ancestry, with moderate genetic differentiation (Fst = 0.0555). Temporal analysis showed V1 maintained stable genetic diversity (π = 0.00488), while V2 exhibited a marked diversity increase in its later phase (from π = 0.00443 to 0.00484), indicating intensified germplasm admixture. Phenotypically, V1 achieved successful decoupling of the tassel dry weight–leaf length trade-off, reducing tassel size while increasing leaf length—a notable optimization of plant architecture. In contrast, V2 showed phenotypic stability. Our findings clarify the distinct roles of the two pools: V1 represents a valuable template for breaking trade-offs to coordinately improve architecture, whereas the V2 pool shows that its genetic base has been substantially broadened without leading to significant phenotypic optimization. This suggests that selection on this germplasm under current breeding objectives may be approaching a plateau, indicating that future substantial improvements may require the introduction of novel genetic variation or a shift in selection paradigms.