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

## TL;DR

This study identifies genetic factors in maize that help plants adapt to low nitrogen by forming root structures that improve nitrogen uptake.

## Contribution

The study reveals the genetic basis of root cortical aerenchyma formation in maize under nitrogen deficiency using GWAS and transcriptome analysis.

## Key findings

- Low nitrogen stress significantly increases root cortical aerenchyma area and proportion in maize.
- Genome-wide association analysis identified 560 SNPs and 810 candidate genes linked to root cortical aerenchyma traits.
- Four core genes involved in ethylene signaling and stress-responsive root development were identified.

## Abstract

Nitrogen (N) is essential for maize (Zea mays 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 (GRMZM2G033570, GRMZM2G052422, GRMZM2G080603, and GRMZM2G472266), 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.