Background/Objectives: Plant architecture is a critical determinant of high-density tolerance and yield potential in maize (Zea mays L.), yet the genetic networks orchestrating these complex traits require deeper elucidation. Methods: In this study, we utilized a Multi-parent Advanced Generation Inter-cross (MAGIC) population comprising 935 recombinant inbred lines (RILs) derived from 16 diverse elite founders. A comprehensive phenotypic characterization of six pivotal architectural traits—plant height (PH), ear height (EH), ear leaf length (LL), ear leaf width (LW), tassel main axis length (TL), and tassel branch number (TBN)—was conducted across three distinct agro-ecological environments. Results: Phenotypic analysis revealed substantial natural variation and high broad-sense heritability (H2 ranging from 60% to 86%), with TBN exhibiting the most pronounced variability. Correlation architecture demonstrated a strong coupling between vertical growth traits (PH and EH, r = 0.73), while lateral leaf expansion (LW) and tassel complexity (TBN) showed significant genetic independence. Using a mixed linear model (MLM) for genome-wide association studies (GWAS), we identified 21 significant SNP–trait associations, including distinct chromosomal clusters on chromosome 8 for EH and chromosome 7 for TBN. By integrating genomic intervals with tissue-specific expression profiling, 23 core candidate genes were prioritized. Notably, Zm00001d042528 (FAS1), involved in chromatin assembly, was implicated in modulating meristematic cell division for plant stature. Other key regulators included Zm00001d020537 (O5) and Zm00001d025360 (F-box protein), which were associated with reproductive organ development and leaf elongation, respectively. Conclusions: These results indicate that maize plant architecture is regulated by a modular genetic framework, with specific loci independently regulating canopy structure and source–sink components. It should be noted that the findings of this study are based solely on statistical models identifying significant associations between genetic loci and phenotypes; the biological regulatory functions of the candidate genes have not yet been experimentally validated. Nevertheless, this study provides new insights into the molecular mechanisms underlying maize morphogenesis and lays a solid theoretical foundation for molecular design breeding aimed at developing high-yielding varieties tolerant of high planting densities.
Xu et al. (Tue,) studied this question.