Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice

Yang, Meng; Lu, Kai; Zhao, Fang-Jie; Xie, Weibo Xie; Ramakrishna, Priya; Wang, Guangyuan; Du, Qingqing; Liang, Limin; Sun, Cuiju; Zhao, Hu; Zhang, Zhanyi; Liu, Zonghao; Salt, David E.; Tian, Jingjing; Huang, Xin-Yuan; Wang, Wensheng; Dong, Huaxia; Hu, Jintao; Ming, Luchang; Xing, Yongzhong; Wang, Gongwei; Xiao, Jinhua; Lian, Xingming

Abstract

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at ∼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.

Citation

Yang, M., Lu, K., Zhao, F.-J., Xie, W. X., Ramakrishna, P., Wang, G., …Lian, X. (2018). Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. Plant Cell, 30(11), 2720–2740. https://doi.org/10.1105/tpc.18.00375

• Journal Article Type: Article
• Acceptance Date: Oct 24, 2018
• Online Publication Date: Oct 29, 2018
• Publication Date: Nov 1, 2018
• Deposit Date: Jan 23, 2019
• Publicly Available Date: Jan 23, 2019
• Journal: The Plant Cell
• Print ISSN: 1040-4651
• Electronic ISSN: 1532-298X
• Publisher: American Society of Plant Biologists
• Peer Reviewed: Peer Reviewed
• Volume: 30
• Issue: 11
• Pages: 2720–2740
• DOI: https://doi.org/10.1105/tpc.18.00375
• Public URL: https://nottingham-repository.worktribe.com/output/1490855
• Publisher URL: http://www.plantcell.org/content/30/11/2720
• Additional Information: Title on accepted manuscript: Genetic basis of rice ionomic variation revelaed by genome-wide association studies
• Contract Date: Jan 23, 2019