GWAS and Transcriptome Analysis Reveal Key Genes Affecting Root Growth under Low Nitrogen Supply in Maize

Abstract

Nitrogen (N) is one of the most important factors affecting crop production. Root morphology exhibits a high degree of plasticity to nitrogen deficiency. However, the mechanisms underlying the root foraging response under low-N conditions remain poorly understood. In this study, we analyzed 213 maize inbred lines using hydroponic systems and regarding their natural variations in 22 root traits and 6 shoot traits under normal (2 mM nitrate) and low-N (0 mM nitrate) conditions. Substantial phenotypic variations were detected for all traits. N deficiency increased the root length and decreased the root diameter and shoot related traits. A total of 297 significant marker-trait associations were identified by a genome-wide association study involving different N levels and the N response value. A total of 51 candidate genes with amino acid variations in coding regions or differentially expressed under low nitrogen conditions were identified. Furthermore, a candidate gene ZmNAC36 was resequenced in all tested lines. A total of 38 single nucleotide polymorphisms and 12 insertions and deletions were significantly associated with lateral root length of primary root, primary root length between 0 and 0.5 mm in diameter, primary root surface area, and total length of primary root under a low-N condition. These findings help us to improve our understanding of the genetic mechanism of root plasticity to N deficiency, and the identified loci and candidate genes will be useful for the genetic improvement of maize tolerance cultivars to N deficiency.

Genome-Wide Association Study on Seedling Phenotypic Traits of Wheat under Different Nitrogen Conditions

“…Through GWAS, 297 significant single nucleotide polymorphisms (SNPs) were detected at different N levels and 51 candidate genes with amino acid variations in coding regions or differentially expressed were identified under LN conditions. Subsequently, researchers re-sequenced the candidate gene ZmNAC36 and found that 33 variable loci in the promoter region were significantly correlated with the four root traits under LN conditions [34]. Schmidt et al identified candidate genes involved in stress signaling and hormone regulation in the MAGIC wheat population WM-800 under LN stress, such as Rht (Rht -B1 and Rht-D1) and NRT1.1 [35].…”

“…At present, the overapplication of N fertilizer in agricultural production has become a common phenomenon, but most of the current studies have been conducted under LN and normal N (NN) conditions [34,[36][37][38]. In this study, a total of 204 wheat germplasm resources were studied under three N conditions (LN, NN, and HN).…”