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

Ruiqiang Lai, Xiaoming Xue, Zaid Chachar, Hang Zhu, Weiwei Chen, Xuhui Li, Yuanqiang Hu, Ming Chen, Xiangbo Zhang, Jiajia Li, Lina Fan () and Yongwen Qi ()
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Ruiqiang Lai: College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
Xiaoming Xue: College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
Zaid Chachar: College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
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

Agriculture, 2025, vol. 15, issue 4, 1-20

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.

Keywords: maize; cadmium; candidate gene (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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