Comprehensive Responses of Root System Architecture and Anatomy to Nitrogen Stress in Maize (Zea mays L.) Genotypes with Contrasting Nitrogen Efficiency

Root architecture and anatomy critically regulate maize nitrogen (N) acquisition, but their coordinated low-N response in N-efficient hybrids remains poorly understood. Elucidating this mechanism is essential for advancing root system regulation and breeding strategies aimed at enhancing N-use efficiency. In this study, six root architectures, twelve root anatomies, and six N-efficiency traits were evaluated in six maize hybrids and nine parental inbreds under sufficient (SN, 180 kg ha−1) and low N (LN, 30 kg ha−1), with transcriptome analysis of inbreds applied to uncover mechanisms. Hybrids were categorized as follows: EE (N-efficient under both N levels), SNE (N-efficient only under SN), and NN (inefficient under both N). Compared with other hybrids, EE developed a 6.0–15.7% narrower root opening angle (ROA), a 11.9–12.4% larger root projected area (RPA), 16.3–22.6% deeper roots (D_Wmax), and 22.6–37.1% more cortical aerenchyma (AA) under LN; SNE showed 9.49–19.51% lower RPA and higher LN-induced reductions in D_Wmax (8.84–17.09%); NN exhibited the largest ROA (60.75–64.48°) and LN-induced reductions in RPA (16.43%), D_Wmax (14.76%), and total projected structure length (11.28%). Correlation, principal component, and structural equation modeling analyses revealed significant root architecture–anatomy integration, and they collectively influence yield through traits such as D_Wmax, AA, and xylem vessel area (XVA) (r = −0.48–0.62, path coefficients: 0.19–0.27). Additionally, the EE and NN hybrids inherited and integrated the superior N-efficient root phenotypes from their parental inbred lines. Transcriptomic analysis identified eight root development genes, including GRMZM5G878558, whose expression correlated with both D_Wmax and AA (r = 0.61–0.73). These findings clarified that N-efficient maize achieved higher yield through coordinated root architecture–anatomy optimization involving associated genes, providing a theoretical foundation for N-efficiency-targeted root regulation and varietal selection.