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Journal of Integrative Agriculture
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Dissecting the genetic architecture of microelement accumulation in wheat grains through genome-wide association study

Yi Du1*, Qun Wu1*, Xing Lu1, Xuemei Jin2, Junsheng Sun1, Junyuan Chen1, Zhiren Guan1, Qi Zhao1, Haimeng Wu1, Hui Wang1, Mingxia Zhang1, Yan Zhao1, Yanrong An1, Sishen Li1, Baojin Guo3#, Min Li1#, Ying Guo1#

1 State Key Laboratory of Wheat Improvement/College of AgronomyShandong Agricultural University, Tai’an 271018, China

2 Rizhao Academy of Agricultural Science, Rizhao 276800, China

3 Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China

 Highlights 

•Using 176,357 RNA-Seq-based molecular markers, 196 significant loci associated with eight grain microelement contents were identified by GWAS in 272 wheat varieties.

•The 14 significant markers were consistently identified across multi-environments, forming 13 stable QTLs that were linked to 45 candidate genes.

•Haplotype analysis indicated TraesCS6A02G204300Hap2 notably enhanced grain iron content.

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摘要  

小麦(Triticum aestivum L.)是全球重要的主要粮食作物,其籽粒微量元素含量对人类营养和健康起着至关重要的作用。本研究以来自黄淮麦区和北部冬麦区选育的272份小麦品种(系)作为试验材料,通过电感耦合等离子体质谱法(ICP-MS)测定了三环境下小麦籽粒铁、锰、铜、锌、硒、镉、铬和砷含量。基于RNA测序获得的176357个分子标记(包括163223SNP13134InDel)进行全基因组关联分析(GWAS。研究结果显示,环境下检测到196个与籽粒微量元素含量性状关联显著标记,分布在21条染色体。其中,14个显著标记同时多个环境中稳定检测到形成13QTL45个候选基因相关联同源比对显示29拟南芥/水稻中已知功能基因的直系同源基因16个是新发现的候选基因。单倍型分析表明,TraesCS6A02G204300Hap2显著提高了籽粒铁含量。因此,本研究为小麦籽粒微量元素积累的遗传结构提供了一定的参考价值,同时将为培育提高微量元素含量小麦品种和保障食品安全提供了新的遗传资源。



Abstract  

Wheat (Triticum aestivum L.) is a vital staple crop globally, with its grain microelement content playing a crucial role in human nutrition and health. In this study, the concentrations of eight essential microelements (micronutrients and toxic elements): iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), selenium (Se), chromium (Cr), cadmium (Cd), and arsenic (As), were quantified in 272 wheat varieties using inductively coupled plasma mass spectrometry (ICP-MS) under three different environments. A genome-wide association study (GWAS) was conducted using 176,357 molecular markers, comprising 163,223 single-nucleotide polymorphisms (SNPs) and 13,134 insertion-deletion (InDels) variants, identified through RNA sequencing. A total of 196 significant markers associated with microelement content traits were identified across 21 chromosomes in various environments. Of these, 14 significant markers consistently appeared across environments, forming 13 QTLs and linking to 45 candidate genes. Among these, 29 genes were homologs of known genes in Arabidopsis and rice, while 16 were novel candidates. Haplotype analysis indicated significant phenotypic variation in microelement accumulation, with TraesCS6A02G204300Hap2 notably enhancing iron content. This study provides valuable insights into the genetic architecture of microelement accumulation in wheat grains and introduces novel genetic resources for breeding wheat varieties aimed at improving micronutrient content and ensuring food safety.

Keywords:  wheat       grain microelement content       genome-wide association study       candidate genes       haplotype  
Online: 25 April 2025  
Fund: 

This research was funded by the Agricultural Variety Program of Shandong Province, China (2021LZGC013-6), the Modern Agricultural Industry Technology System of Shandong Province, China (SDAIT-01-04), the Taishan Scholars Program (tsqn202408131), and the 'First Class Discipline' Construction Project of Shandong Agricultural University (SKL81108).

About author:  #Correspondence Ying Guo, E-mail: guoying@sdau.edu.cn; Min Li, E-mail: mli015@sdau.edu.cn; Baojian Guo, E-mail: guobaojin@caas.cn *These authors contributed equally to this work.

Cite this article: 

Yi Du, Qun Wu, Xing Lu, Xuemei Jin, Junsheng Sun, Junyuan Chen, Zhiren Guan, Qi Zhao, Haimeng Wu, Hui Wang, Mingxia Zhang, Yan Zhao, Yanrong An, Sishen Li, Baojin Guo, Min Li, Ying Guo. 2025. Dissecting the genetic architecture of microelement accumulation in wheat grains through genome-wide association study. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.04.031

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