Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels
Clarifying the genetic basis of trace element accumulation is of great significance to breed new maize varieties with high quality. In this study, an integrated variant map with 1.25 million (M) SNPs and 489 inbred lines was used for a genome-wide association study on the accumulation of iron (Fe),...
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MDPI AG
2022-02-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/12/2/262 |
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| author | Fucheng Zhao Nan Wang Fei Bao Guangwu Zhao Liquan Jing Guiyue Wang Qinghui Han Zhuanfang Hao Bin Chen |
| author_facet | Fucheng Zhao Nan Wang Fei Bao Guangwu Zhao Liquan Jing Guiyue Wang Qinghui Han Zhuanfang Hao Bin Chen |
| author_sort | Fucheng Zhao |
| collection | DOAJ |
| description | Clarifying the genetic basis of trace element accumulation is of great significance to breed new maize varieties with high quality. In this study, an integrated variant map with 1.25 million (M) SNPs and 489 inbred lines was used for a genome-wide association study on the accumulation of iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), cadmium (Cd) and Arsenic (As) in maize kernels. Seventeen SNPs linked with six genes were overlapped by different trace elements. After further analysis, 65 SNPs located in 28 genes with a <i>p</i>-value lower than 10<sup>−10</sup> were associated with Cd content by genome-wide association studies (GWAS). There was a 3.1-fold difference in Cd content between different groups, which was divided by SNP haplotype in <i>chr2.S_160782359</i>, <i>chr2.S_161045498</i> and <i>chr2.S_161273716</i>. The amino acid sequences of <i>GRMZM2G150608</i> and <i>GRMZM2G051367</i> only shared 68.85% and 88.16% similarity between B73 and Mo17, and the Cd content of Mo17 was 2.2-fold that of B73. In addition, 19 lines with higher contents of Fe, Zn, Cu, Mn and fewer contents of As and Cd were screened from GWAS associated populations. This study will lay a foundation for revealing the molecular mechanism of trace element accumulation in maize kernels and provide candidate genes for breeding new maize varieties with high nutritional quality. |
| first_indexed | 2024-03-09T22:52:20Z |
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| last_indexed | 2024-03-09T22:52:20Z |
| publishDate | 2022-02-01 |
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| series | Agriculture |
| spelling | doaj.art-6ef9d30eba1b409998dfac1ae46f6f3b2023-11-23T18:17:19ZengMDPI AGAgriculture2077-04722022-02-0112226210.3390/agriculture12020262Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize KernelsFucheng Zhao0Nan Wang1Fei Bao2Guangwu Zhao3Liquan Jing4Guiyue Wang5Qinghui Han6Zhuanfang Hao7Bin Chen8Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang 322100, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang 322100, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou 311300, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaInstitute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang 322100, ChinaThe Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou 311300, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang 322100, ChinaClarifying the genetic basis of trace element accumulation is of great significance to breed new maize varieties with high quality. In this study, an integrated variant map with 1.25 million (M) SNPs and 489 inbred lines was used for a genome-wide association study on the accumulation of iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), cadmium (Cd) and Arsenic (As) in maize kernels. Seventeen SNPs linked with six genes were overlapped by different trace elements. After further analysis, 65 SNPs located in 28 genes with a <i>p</i>-value lower than 10<sup>−10</sup> were associated with Cd content by genome-wide association studies (GWAS). There was a 3.1-fold difference in Cd content between different groups, which was divided by SNP haplotype in <i>chr2.S_160782359</i>, <i>chr2.S_161045498</i> and <i>chr2.S_161273716</i>. The amino acid sequences of <i>GRMZM2G150608</i> and <i>GRMZM2G051367</i> only shared 68.85% and 88.16% similarity between B73 and Mo17, and the Cd content of Mo17 was 2.2-fold that of B73. In addition, 19 lines with higher contents of Fe, Zn, Cu, Mn and fewer contents of As and Cd were screened from GWAS associated populations. This study will lay a foundation for revealing the molecular mechanism of trace element accumulation in maize kernels and provide candidate genes for breeding new maize varieties with high nutritional quality.https://www.mdpi.com/2077-0472/12/2/262maize (<i>Zea mays</i> L.)trace elementsgenome-wide association studies (GWAS)kernel |
| spellingShingle | Fucheng Zhao Nan Wang Fei Bao Guangwu Zhao Liquan Jing Guiyue Wang Qinghui Han Zhuanfang Hao Bin Chen Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels Agriculture maize (<i>Zea mays</i> L.) trace elements genome-wide association studies (GWAS) kernel |
| title | Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels |
| title_full | Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels |
| title_fullStr | Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels |
| title_full_unstemmed | Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels |
| title_short | Genome-Wide Association Study Reveals Genetic Basis of Trace Elements Accumulation in Maize Kernels |
| title_sort | genome wide association study reveals genetic basis of trace elements accumulation in maize kernels |
| topic | maize (<i>Zea mays</i> L.) trace elements genome-wide association studies (GWAS) kernel |
| url | https://www.mdpi.com/2077-0472/12/2/262 |
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