QTL Mapping with Single-Segment Substitution Lines Reveals Genetic Links Between Nitrogen Efficiency and Root Traits in Maize

Maize requires substantial nitrogen input, and nitrogen deficiency significantly impairs root development, reducing yield. Therefore, improving maize root system architecture under low-nitrogen (LN) conditions is critical for improving nitrogen use efficiency (NUE). However, the genetic relationship between nitrogen efficiency and root traits is unclear in maize. Here, we conducted a hydroponic experiment during the seedling stage using maize single-segment substitution lines (SSSLs) derived from a cross between the N-efficient inbred line Xu178 and the N-inefficient inbred line Zong3. Quantitative trait loci (QTL) mapping was performed for root architecture traits under both high-nitrogen (HN) and LN conditions. We identified a total of 160 QTLs, with 101 and 59 detected under HN and LN conditions, respectively. These included 19 for root total length (RTL), 43 for root surface area (RSA), 24 for root average diameter (RAD), 60 for root volume (RV), and 14 for root tip number (RTN), distributed across all ten chromosomes, with the highest number on chromosome 1. Additive effects of individual QTLs ranged from −33.14% to 331.16%. Notably, we discovered a major HN-specific QTL cluster on segments end–umc1929 (Bin 7.00) and bnlg1655 (Bin 10.03), and a key LN-specific cluster on segment umc1883–bnlg249 (Bin 6.00). These findings not only highlight distinct genetic bases for nitrogen adaptation at the seedling stage but also provide valuable molecular markers and candidate genomic regions for the marker-assisted breeding of nitrogen-efficient maize varieties.