Genetic Basis of Nitrogen-Deficiency-Induced Root Cortical Aerenchyma in Maize Revealed by GWAS and Transcriptome Analysis

Nitrogen (N) is essential for maize (<i>Zea mays</i> L.) productivity, yet its acquisition is limited by the low N uptake efficiency of current varieties. Root cortical aerenchyma (RCA) formation provides a carbon-saving strategy that enhances soil exploration and N acquisition by reducing the metabolic cost of root tissue. However, the genetic basis of RCA formation remains poorly characterized. This study employed an association panel of 295 maize inbred lines to dissect the genetic architecture of RCA formation under low nitrogen (LN) stress. Phenotypic analysis demonstrated that LN stress significantly induced RCA area (RCAA) and proportion (RCAP), with responses ranging from -0.31 to 1.16 mm² for RCAA and -11.34% to 40.18% for RCAP. The non-stiff stalk (NSS) subpopulation exhibited 29.19% higher RCAA under LN than the stiff stalk subgroup. Genome-wide association analysis detected a total of 560 significant SNPs and 810 candidate genes associated with RCA-related traits. Transcriptomic profiling further identified 537 differentially expressed genes between inbred lines with contrasting RCA phenotypes. Integrated GWAS and transcriptomic analysis pinpointed 12 co-localized candidates, subsequently refined to four core genes (<i>GRMZM2G033570</i>, <i>GRMZM2G052422</i>, <i>GRMZM2G080603</i>, and <i>GRMZM2G472266</i>), which were implicated in ethylene signaling and stress-responsive root development. Favorable haplotypes of three genes were predominantly distributed in the NSS (25.64-56.00%) and tropical/subtropical (20.51-46.67%) subpopulations. These findings elucidate the genetic basis of LN-responsive RCA formation and provide fundamental resources for marker-assisted breeding of N-efficient maize.