Genome-wide association study of novel genetic loci for cadmium accumulation and germplasm screening for low-cadmium accumulation in common wheat (Triticum aestivum L.)

doi:10.1016/j.jia.2024.11.029

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Genome-wide association study of novel genetic loci for cadmium accumulation and germplasm screening for low-cadmium accumulation in common wheat (Triticum aestivum L.)

Li Zhe¹, Hui Wang², Jiping Chen², Xiaoge Fu¹, Liang Wang³, Yang Yang⁴, Tauqeer Ahmad Yasir⁵, Huili Yan⁶, Hongyan Chu⁷, Chi Zhang⁸, Yingang Hu¹, Xiaoyong Liao³, Hanzhong Jia⁸, Liang Chen¹

¹ State Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling 712100, China

² Shaanxi Hygrogeology Engineering Geology and Environment Geology Survey Center, Xi’an 710068, China

³ Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China

⁴ College of Agriculture, Shanxi Agricultural University (Institute of Crop Sciences), Taiyuan 030031, China

⁵ Department of Agronomy, Bahauddin Zakariya University, Multan 60800, Pakistan

⁶ Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China

⁷Xinjiang Agricultural Vocational Technical University, Changji 831100, China

⁸College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China

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摘要

小麦耕地中镉（Cd）污染正以令人担忧的速度增长，对粮食安全和公共健康构成威胁。育种并利用镉积累水平较低的小麦品种是对抗小麦Cd污染的有效策略。采用分子标记辅助方法可以大大加快选择和改良镉积累水平较低的小麦品种。然而，有关小麦镉积累的基因研究仍然很少。本研究采用高密度660K SNP阵列对175个小麦种质进行了籽粒Cd浓度（GCdC）、生物富集因子（BCF）和转运因子（TF）的全基因组关联研究（GWAS）。结果显示，在三种不同环境下发现了401个显著的SNP。连锁不平衡分析揭示了30个核心的定量性状位点（QTLs），能够可靠地调节小麦Cd积累表型。通过基因注释、转录组学和基因分子特征，确定了四个候选基因（TraesCS7B02G000200、TraesCS4A02G035900、TraesCS4A02G040900、TraesCS5D02G564000）可能成为小麦Cd积累生物过程的组成部分。此外，本研究筛选出6个表现出低籽粒Cd积累的小麦种质，并开发了两种有助于育种选择的Kompetitive Allele Specific PCR（KASP）标记。这些发现为培育低Cd积累小麦提供了宝贵的遗传资源，并为了解小麦低Cd积累的分子机制奠定了基础。本研究阐明的候选基因和KASP标记在小麦低Cd积累育种中具有潜在的应用价值。

Abstract

Cadmium (Cd) contamination in wheat farmland is increasing at an alarming rate, posing threats to food security and public health. Breeding and utilizing wheat varieties characterized by low Cd accumulation levels constitute an effective strategy in the battle against wheat Cd contamination. The adoption of molecular marker-assisted approaches can greatly expedite the selection and enhancement of wheat varieties with low Cd accumulation. Nonetheless, research concerning genes associated with wheat cadmium accumulation remains scarce. In this study, a high-density 660K SNP array was employed for conducting genome-wide association studies (GWASs) on the grain Cd concentration (GCdC), bioconcentration factor (BCF) and translocation factor (TF) in 175 wheat germplasms. The findings revealed 401 significant SNPs identified across three diverse environments. Linkage disequilibrium analysis revealed 30 core quantitative trait locus (QTLs)capable of reliably modulating wheat Cd accumulation phenotypes. Through gene annotation, transcriptomics, and gene molecular features, four candidate genes (TraesCS7B02G000200, TraesCS4A02G035900, TraesCS4A02G040900, TraesCS5D02G564000) were identified as potential constituents of the biological process of wheat Cd accumulation. Furthermore, in this study 6 wheat germplasms exhibiting low grain Cd accumulation were isolated, and two Kompetitive Allele Specific PCR (KASP) markers conducive to breeding selection were developed. These findings provide valuable genetic resources for cultivating wheat with low Cd accumulation and establish a foundation for understanding the molecular mechanisms underlying low Cd accumulation in wheat. The candidate genes and KASP markers elucidated in this research have potential for effective employmentuse in genetic enhancement and marker-assisted selection in the breeding of wheat with low Cd accumulation.

Keywords: Triticum aestivum cadmium accumulation genome-wide association analysis functional prediction molecular marker

Received: 26 June 2024 Online: 14 November 2024

Fund:

This work was supported by the National Key Research and Development Program of China (2023YFD1700100 and 2023YFD1700102) and the Shaanxi Public Welfare Special Project of geological prospecting, China (201908).

About author: #Correspondence Yingang Hu, E-mail: huyingang@nwsuaf.edu.cn; Liang Chen, E-mail: chenliang9117@nwafu.edu.cn

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Li Zhe, Hui Wang, Jiping Chen, Xiaoge Fu, Liang Wang, Yang Yang, Tauqeer Ahmad Yasir, Huili Yan, Hongyan Chu, Chi Zhang, Yingang Hu, Xiaoyong Liao, Hanzhong Jia, Liang Chen. 2024. Genome-wide association study of novel genetic loci for cadmium accumulation and germplasm screening for low-cadmium accumulation in common wheat (Triticum aestivum L.). Journal of Integrative Agriculture, Doi:10.1016/j.jia.2024.11.029

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