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Mapping Novel Loci and Candidate Genes Associated with Cadmium Content in Maize Using Genome-Wide Association Analysis

Author

Listed:
  • Ruiqiang Lai

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
    These authors contributed equally to this work.)

  • Xiaoming Xue

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
    These authors contributed equally to this work.)

  • Zaid Chachar

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
    These authors contributed equally to this work.)

  • Hang Zhu

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China)

  • Weiwei Chen

    (Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou 510316, China)

  • Xuhui Li

    (Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou 510316, China)

  • Yuanqiang Hu

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China)

  • Ming Chen

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China)

  • Xiangbo Zhang

    (Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510641, China)

  • Jiajia Li

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China)

  • Lina Fan

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China)

  • Yongwen Qi

    (College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China)

Abstract

Cadmium is a toxic, carcinogenic element that threatens food safety due to its tendency to be absorbed by plants along with essential nutrients. This study conducted a genome-wide association study (GWAS) using SNP genotyping data from 170 natural maize populations to analyze cadmium content in maize grains across three environments. The MLM_Q+Kinship and MLM_PCA+Kinship models identified 6424 (HN), 991 (JMO), and 1358 (JMT) SNPs linked to cadmium accumulation in the MLM_Q+Kinship model, with 121 SNPs common across all environments. Additionally, the MLM_PCA+Kinship model detected 824 (HN), 950 (JMO), and 910 (JMT) SNPs, with 14 shared loci. In total, 126 reliable SNP loci, representing 14 QTLs, were identified, highlighting 12 superior haplotypes and 2 favorable alleles. A negative correlation between these loci and cadmium content was observed. Within 100 kbp of the QTLs, 45 candidate genes were identified, associated with 11 GO terms and 5 KEGG pathways. Analysis revealed 12 maize lines with at least one stable locus, all of which showed reduced Cd levels. Key hybrids, such as CAU95×CAU65 and CAU95×CAU266, demonstrated the potential for low Cd accumulation. This study provides valuable insights for breeding maize with reduced Cd uptake using stable gene loci discovered through GWAS.

Suggested Citation

  • Ruiqiang Lai & Xiaoming Xue & Zaid Chachar & Hang Zhu & Weiwei Chen & Xuhui Li & Yuanqiang Hu & Ming Chen & Xiangbo Zhang & Jiajia Li & Lina Fan & Yongwen Qi, 2025. "Mapping Novel Loci and Candidate Genes Associated with Cadmium Content in Maize Using Genome-Wide Association Analysis," Agriculture, MDPI, vol. 15(4), pages 1-20, February.
    • Handle: RePEc:gam:jagris:v:15:y:2025:i:4:p:389-:d:1589713
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    References listed on IDEAS

    as
    1. Bin Yang & Jiali Zeng & Shaona Chen & Shengyu Li & Longmei Wu & Xiaorong Wan, 2022. "Genome-Wide Association Study Reveals the Genetic Basis of Seed Germination in Japonica Rice," Agriculture, MDPI, vol. 13(1), pages 1-14, December.
    2. Muhammad Suleman & Muhammad Ashraf & Qurat-Ul-Ain Raza & Muhammad Amjad Bashir & Shafeeq Ur Rahman & Muhammad Aon & Saba Ali & Sher Muhammad Shahzad & Muhammad Usman Khalid & Hafiz Muhammad Ali Raza &, 2022. "Determining the Cadmium Accumulation in Maize ( Zea mays L.) and Soil Influenced by Phosphoric Fertilizers in Two Different Textured Soils," Land, MDPI, vol. 11(8), pages 1-15, August.
    Full references (including those not matched with items on IDEAS)

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    More about this item

    Keywords

    maize; cadmium; candidate gene;
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