全基因组关联分析方法挖掘控制玉米根系发育的数量性状位点

doi:10.1016/j.jia.2023.10.040

Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (5): 1656-1670.DOI: 10.1016/j.jia.2023.10.040

全基因组关联分析方法挖掘控制玉米根系发育的数量性状位点

收稿日期:2023-07-28 修回日期:2023-11-02 接受日期:2023-10-07 出版日期:2025-05-20 发布日期:2025-04-14

Genome wide association analysis reveals multiple QTLs controlling root development in maize

Huairen Zhang¹, Tauseef Taj Kiani^{1, 3}, Huabang Chen¹, Juan Liu¹, Xunji Chen^2#

¹Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
²Institute of Nuclear Technology and Biotechnology, Xinjiang Academy of Agriculture/Xinjiang Key Laboratory of Crop Biotechnology, Urumqi 830091, China
³University of Chinese Academy of Sciences, Beijing 101408, China

Received:2023-07-28 Revised:2023-11-02 Accepted:2023-10-07 Online:2025-05-20 Published:2025-04-14
About author:#Correspondence Xunji Chen, E-mail: chenxj713@163.com
Supported by:
This work was supported by the National Natural Science Foundation of China (32160440), the Manas County National Hybrid Corn Seed Production Base Construction Project, China (MNSZZDX-2021-01), and the National Key Research and Development Programs of China (2022YFF1003304).

摘要/Abstract

摘要：

玉米根系在地上植物的发育中起着至关重要的作用，并通过吸收田间的水分和养分来决定产量。然而，由于玉米根系构造复杂，而且其根系构型受环境影响较大，所以目前人们对玉米根系的遗传结构知之甚少。本研究利用研究组自主开发的高通量半自动水培系统对518个玉米核心材料进行了玉米根系的表型鉴定和遗传研究。研究发现，不同自交系材料之间主根和苗期根系发育进程都存在较大的差异；群体结构分析表明该群体具有分层性，其连锁不平衡衰减距离平均小于50Kb。利用600 K 高密度SNP芯片，我们对这518个核心材料进行了基因分型，并对24个根系性状进行了全基因组关联分析（GWAS），通过显著位点区间分析，最终确定了9个显著相关的SNP和7个候选基因。其中候选基因GRMZM2G400533位于主效SNP位点（AX-91771718）上游5Kb范围内，与主根长度变异显著相关，并优先在主根和冠根中表达。表达分析发现该候选基因表达随着主根的发育而升高，但与主根伸长呈负相关。基于GRMZM2G400533的候选基因分析，我们还鉴定了三种功能变异和八种等位基因单倍型。本研究将深化我们对玉米根系发育的理解，为玉米根系优化改良提供理论依据。

Abstract:

Maize root system plays a crucial role in the development of the aboveground plant and determines the yield through the uptake of water and nutrients in the field. However, the genetic architecture of the maize root system is largely unknown mainly due to its complexity and the interactions between genotype and environment. Using a high-throughput semi-automatic hydroponic platform with stable conditions, we comprehensively characterized the root system in a core population of 518 diverse inbred lines of maize. Population structure analysis revealed that the panel has stratification and a linkage disequilibrium decay distance of less than 50 kb. Based on genotyping with the high-density 600 K SNPs, we conducted a genome wide association analysis (GWAS) and identified nine SNPs and seven candidate genes significantly associated with 24 traits. One candidate gene, GRMZM2G400533, is located at the upstream 5 kb region from the leading SNP (AX-91771718) and was significantly associated with primary root length and preferentially expressed in the primary root and crown root. Expression of GRMZM2G400533 increased as the primary root developed but was negatively correlated with primary root elongation. An analysis of candidate gene GRMZM2G400533 identified three functional variants and eight allelic haplotypes. This study will broaden our understanding of maize root development and provide a theoretical basis for maize improvement through optimization of the root system.

Key words: maize , primary root , seedling root system , candidate gene , GWAS

Huairen Zhang, Tauseef Taj Kiani, Huabang Chen, Juan Liu, Xunji Chen. 全基因组关联分析方法挖掘控制玉米根系发育的数量性状位点[J]. Journal of Integrative Agriculture, 2025, 24(5): 1656-1670.

Huairen Zhang, Tauseef Taj Kiani, Huabang Chen, Juan Liu, Xunji Chen. Genome wide association analysis reveals multiple QTLs controlling root development in maize [J]. Journal of Integrative Agriculture, 2025, 24(5): 1656-1670.

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全基因组关联分析方法挖掘控制玉米根系发育的数量性状位点

Genome wide association analysis reveals multiple QTLs controlling root development in maize

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