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Genome-wide association study for the identification and characterization of nitrogen efficiency-related genes in wheat

ZHAO Chao-Nan1,WANG Jin-Feng1,ZHANG Yu1,ZHANG Li1,LI Rui-Qi1,WANG Peng-Fei1,LI Ge-Zi1,ZHANG Hong-Jun2,YU Bo1,*,KANG Guo-Zhang1,*   

  1. 1 Henan Agricultural University / National Wheat Engineering Research Center, Zhengzhou 450046, Henan, China; 2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences / National Engineering Research Center of Crop Molecular Breeding, Beijing 100081, China
  • Received:2024-12-03 Revised:2025-04-27 Accepted:2025-04-27 Published:2025-05-13
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (32401739) and the Shennong Seed Industry Laboratory “First-class Project” (SN01-2022-01).

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Abstract:

To explore wheat germplasm and genetic resources associated with high nitrogen use efficiency, and to elucidate their molecular mechanisms and genetic effects, are key objectives of current research on nitrogen efficiency in wheat. In this study, a natural population comprising 255 wheat varieties was used as experimental material. Seedlings at the one-leaf stage were subjected to hydroponic treatments under low nitrogen (LN, 0.05 mmol L-1 NO3-) and sufficient nitrogen (SN, 1.00 mmol L-1 NO3-) conditions. After 28 days, seventeen phenotypic traits were measured under both nitrogen treatments. A total of 38,215 high-quality single nucleotide polymorphism (SNP) sites were obtained through quality control filtering of the 55K SNP chip data. Genome-wide association studies (GWAS) were conducted using the FarmCPU, MLM, and MLM+Q+K models. The distribution of LN/SN ratios for the 17 traits (denoted as LS) followed a normal distribution across the population. GWAS identified 1161 significant loci (P ≤ 0.001) associated with the 17 LS traits, of which 103 SNPs were detected in at least two models. Notably, eight SNPs were associated with at least four traits, and two novel loci—AX-110548993 (on chromosome 3B) and AX-111802919 (on chromosome 4D)—were identified. Within a 5 Mb window upstream and downstream of these novel SNPs, 267 candidate genes were predicted. Specifically, SNP AX-111802919 on chromosome 4D includes three candidate genes directly involved in or regulating nitrogen uptake and transport: TraesCS4D02G361500, TraesCS4D02G362100, and TraesCS4D02G362800, which encode a nitrate transporter (NRT1.1), a zinc finger protein CONSTANS-LIKE 1, and a GATA transcription factor, respectively.

Key words: Triticum aestivum L., nitrogen efficiency, genome-wide association study, candidate genes, mining

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