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作物学报 ›› 2025, Vol. 51 ›› Issue (7): 1801-1813.doi: 10.3724/SP.J.1006.2025.41086

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

全基因组关联分析定位与挖掘小麦氮高效基因

赵超男1,王金凤1,张玉1,张丽1,李瑞琦1,王鹏飞1,李鸽子1,张宏军2,虞波1,*,康国章1,*   

  1. 1 河南农业大学 / 国家小麦工程技术研究中心, 河南郑州 450046; 2 中国农业科学院作物科学研究所 / 作物分子育种国家工程实验室, 北京 100081
  • 收稿日期:2024-12-03 修回日期:2025-04-27 接受日期:2025-04-27 出版日期:2025-07-12 网络出版日期:2025-05-13
  • 基金资助:
    本研究由国家自然科学基金项目(32401739)和神农种业实验室“一流课题”项目(SN01-2022-01)资助。

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:2025-07-12 Published online: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).

摘要:

挖掘小麦氮高效的种质和基因资源,揭示其分子机制和遗传效应,是当前小麦氮效率研究的重要内容和目标。本研究以255份不同小麦品种组成的自然群体为试验材料,对每个品种1叶1心幼苗分别进行低氮(low nitrogen, LN, 0.05 mmol L-1 NO3-)和充足供氮(sufficient nitrogen, SN, 1.00 mmol L-1 NO3-2个水培条件处理,培养28 d后,在低氮和充足供氮处理下测定17个表型指标,通过对55K SNP芯片进行质控过滤筛选出38,215个高质量单核苷酸多态性(single nucleotide polymorphism, SNPs)位点,结合FarmCPUMLM以及MLM+Q+K模型进行全基因组关联分析(genome-wide association study, GWAS)。该群体在LNSN水平下17个表型指标比值(LS, LN/SN)的频率分布均呈正态分布,对17LS指标进行全基因组关联分析,共检测到1161个显著位点(P0.001),发现有103个标记至少在2个模型中同时被检测到,有8SNP至少关联了4个性状,其中AX-110548993(3B)AX-111802919(4D)为新位点。2个新位点上下游5 Mb范围区间内含有267个候选基因,其中位于4D染色体上的SNP AX-111802919包括3个直接参与或调控氮吸收转运的候选基因:TraesCS4D02G361500编码硝酸盐转运蛋白(NRT1.1)TraesCS4D02G362100编码锌指蛋白CONSTANS-LIKE 1TraesCS4D02G362800编码1GATA转录因子蛋白。

关键词: 小麦, 氮效率, 全基因组关联分析, 候选基因, 挖掘

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, TraesCS4D02G362100and 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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