Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain
Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain
Abstract 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 five that had not been previously associated with maize grain tocochromanols: four 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 co-localized eQTL and GWAS association signals. Our multi-omics 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.
Schoenbaum Gregory R.、Robin Buell C.、Tibbs-Cortes Laura E.、Li Xiaowei、Deason Nicholas T.、Magallanes-Lundback Maria、DellaPenna Dean、Diepenbrock Christine H.、Wood Joshua C.、Yu Jianming、Wu Di、Gore Michael A.、Li Xianran、Vaillancourt Brieanne、Bornowski Nolan、Hamilton John P.、Tanaka Ryokei
Department of Agronomy, Iowa State UniversityDepartment of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, AthensDepartment of Agronomy, Iowa State UniversityPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityDepartment of Biochemistry and Molecular Biology, Michigan State UniversityDepartment of Biochemistry and Molecular Biology, Michigan State UniversityDepartment of Biochemistry and Molecular Biology, Michigan State UniversityDepartment of Plant Sciences, University of CaliforniaDepartment of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, AthensDepartment of Agronomy, Iowa State UniversityPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell UniversityUnited States Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research UnitDepartment of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, AthensDepartment of Plant Biology, Michigan State UniversityDepartment of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, AthensPlant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University
农业科学研究植物学生物科学研究方法、生物科学研究技术
Schoenbaum Gregory R.,Robin Buell C.,Tibbs-Cortes Laura E.,Li Xiaowei,Deason Nicholas T.,Magallanes-Lundback Maria,DellaPenna Dean,Diepenbrock Christine H.,Wood Joshua C.,Yu Jianming,Wu Di,Gore Michael A.,Li Xianran,Vaillancourt Brieanne,Bornowski Nolan,Hamilton John P.,Tanaka Ryokei.Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain[EB/OL].(2025-03-28)[2025-05-04].https://www.biorxiv.org/content/10.1101/2022.04.01.486706.点此复制
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