Dissecting the genetic basis of heterosis for plant architecture in maize using a modified North Carolina design III

Heterosis is widely exploited in plant breeding to improve grain yield and stress tolerance. However, its genetic basis in crops such as maize ( Zea mays L.) remains poorly understood. Using a high-density genetic linkage map, we investigated the genetic architecture of heterosis for plant height (PH) and ear height (EH) using a modified North Carolina Design III. The study population consisted of 183 recombinant inbred lines (RILs) derived from KA105 and KB024 and two corresponding backcross populations (IB1 and IB2). Heterosis, including the absolute and relative values of better-parent heterosis (BPH) and mid-parent heterosis (MPH), was estimated using best linear unbiased prediction (BLUP) based on phenotypic data collected across four environments. We identified 30, 35, 58, and 75 QTLs for the MPHA (MPH absolute value), MPHR (MPH relative value), BPHA (BPH absolute value) and BPHR (BPH relative value), respectively. Among these, 14 major QTLs explained >10% of the phenotypic variation and contained known functional genes, including ZmNF-YC14 , Rough sheath 1 , and ZmPIF3.3 . In addition, 21 QTLs were co-localized across different traits or environments. By integrating functional annotation, public transcriptomic data, and previously reported plant architecture-related genes within the 34 focal QTL (fQTL) regions, we prioritized several putative candidate genes potentially associated with PH and EH heterosis. These candidates represent hypotheses for future functional validation rather than confirmed causal genes. Finally, comparative phenotypic analyses of different alleles within each QTL region were performed to evaluate their potential genetic effects and provide insights for maize breeding. Genetic mapping of PH and EH heterosis in the backcross populations identified 14 major QTLs explaining > 10% of the phenotypic variation. Integration of these QTLs with previously reported PH- and EH-related genes enabled the construction of a regulatory network and the prioritization of several novel candidate genes that may contribute to PH and EH heterosis. Therefore, these findings provide a comprehensive genetic framework for understanding maize plant and ear height heterosis and identify valuable target loci for future breeding programs.