Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain
Tocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The toco...
| Autores principales: | , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2022
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| Acceso en línea: | https://hdl.handle.net/10568/175615 |
| _version_ | 1855513561161269248 |
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| author | Wu, Di Li, Xiaowei Tanaka, Ryokei Wood, Joshua C. Tibbs-Cortes, Laura E. Magallanes-Lundback, Maria Bornowski, Nolan Hamilton, John P. Vaillancourt, Brieanne Diepenbrock, Christine H. Li, Xianran Deason, Nicholas T. Schoenbaum, Gregory R. Yu, Jianming Buell, C. Robin DellaPenna, Dean Gore, Michael A. |
| author_browse | Bornowski, Nolan Buell, C. Robin Deason, Nicholas T. DellaPenna, Dean Diepenbrock, Christine H. Gore, Michael A. Hamilton, John P. Li, Xianran Li, Xiaowei Magallanes-Lundback, Maria Schoenbaum, Gregory R. Tanaka, Ryokei Tibbs-Cortes, Laura E. Vaillancourt, Brieanne Wood, Joshua C. Wu, Di Yu, Jianming |
| author_facet | Wu, Di Li, Xiaowei Tanaka, Ryokei Wood, Joshua C. Tibbs-Cortes, Laura E. Magallanes-Lundback, Maria Bornowski, Nolan Hamilton, John P. Vaillancourt, Brieanne Diepenbrock, Christine H. Li, Xianran Deason, Nicholas T. Schoenbaum, Gregory R. Yu, Jianming Buell, C. Robin DellaPenna, Dean Gore, Michael A. |
| author_sort | Wu, Di |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Tocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The tocochromanol biosynthetic pathway is conserved across plant species but an integrated view of the genes and mechanisms underlying natural variation of tocochromanol levels in seed of most cereal crops remains limited. To address this issue, we utilized the high mapping resolution of the maize Ames panel of ∼1,500 inbred lines scored with 12.2 million single-nucleotide polymorphisms to generate metabolomic (mature grain tocochromanols) and transcriptomic (developing grain) data sets for genetic mapping. By combining results from genome- and transcriptome-wide association studies, we identified a total of 13 candidate causal gene loci, including 5 that had not been previously associated with maize grain tocochromanols: 4 biosynthetic genes (arodeH2 paralog, dxs1, vte5, and vte7) and a plastid S-adenosyl methionine transporter (samt1). Expression quantitative trait locus (eQTL) mapping of these 13 gene loci revealed that they are predominantly regulated by cis-eQTL. Through a joint statistical analysis, we implicated cis-acting variants as responsible for colocalized eQTL and GWAS association signals. Our multiomics approach provided increased statistical power and mapping resolution to enable a detailed characterization of the genetic and regulatory architecture underlying tocochromanol accumulation in maize grain and provided insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in maize and other cereals. |
| format | Journal Article |
| id | CGSpace175615 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1756152025-10-26T12:55:15Z Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain Wu, Di Li, Xiaowei Tanaka, Ryokei Wood, Joshua C. Tibbs-Cortes, Laura E. Magallanes-Lundback, Maria Bornowski, Nolan Hamilton, John P. Vaillancourt, Brieanne Diepenbrock, Christine H. Li, Xianran Deason, Nicholas T. Schoenbaum, Gregory R. Yu, Jianming Buell, C. Robin DellaPenna, Dean Gore, Michael A. maize health genes biofortification vitamin E Tocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The tocochromanol biosynthetic pathway is conserved across plant species but an integrated view of the genes and mechanisms underlying natural variation of tocochromanol levels in seed of most cereal crops remains limited. To address this issue, we utilized the high mapping resolution of the maize Ames panel of ∼1,500 inbred lines scored with 12.2 million single-nucleotide polymorphisms to generate metabolomic (mature grain tocochromanols) and transcriptomic (developing grain) data sets for genetic mapping. By combining results from genome- and transcriptome-wide association studies, we identified a total of 13 candidate causal gene loci, including 5 that had not been previously associated with maize grain tocochromanols: 4 biosynthetic genes (arodeH2 paralog, dxs1, vte5, and vte7) and a plastid S-adenosyl methionine transporter (samt1). Expression quantitative trait locus (eQTL) mapping of these 13 gene loci revealed that they are predominantly regulated by cis-eQTL. Through a joint statistical analysis, we implicated cis-acting variants as responsible for colocalized eQTL and GWAS association signals. Our multiomics approach provided increased statistical power and mapping resolution to enable a detailed characterization of the genetic and regulatory architecture underlying tocochromanol accumulation in maize grain and provided insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in maize and other cereals. 2022-07-30 2025-07-11T17:09:41Z 2025-07-11T17:09:41Z Journal Article https://hdl.handle.net/10568/175615 en Open Access Oxford University Press Wu, Di; Li, Xiaowei; Tanaka, Ryokei; Wood, Joshua C.; Tibbs-Cortes, Laura E.; Magallanes-Lundback, Maria; et al. 2022. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics 221(4): iyac091. https://doi.org/10.1093/genetics/iyac091 |
| spellingShingle | maize health genes biofortification vitamin E Wu, Di Li, Xiaowei Tanaka, Ryokei Wood, Joshua C. Tibbs-Cortes, Laura E. Magallanes-Lundback, Maria Bornowski, Nolan Hamilton, John P. Vaillancourt, Brieanne Diepenbrock, Christine H. Li, Xianran Deason, Nicholas T. Schoenbaum, Gregory R. Yu, Jianming Buell, C. Robin DellaPenna, Dean Gore, Michael A. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain |
| title | Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain |
| title_full | Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain |
| title_fullStr | Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain |
| title_full_unstemmed | Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain |
| title_short | Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain |
| title_sort | combining gwas and twas to identify candidate causal genes for tocochromanol levels in maize grain |
| topic | maize health genes biofortification vitamin E |
| url | https://hdl.handle.net/10568/175615 |
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