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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

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


Meng Yang

Kai Lu

Fang-Jie Zhao

Weibo Xie Xie

Priya Ramakrishna

Guangyuan Wang

Qingqing Du

Limin Liang

Cuiju Sun

Hu Zhao

Zhanyi Zhang

Zonghao Liu

David E. Salt

Jingjing Tian

Xin-Yuan Huang

Wensheng Wang

Huaxia Dong

Jintao Hu

Luchang Ming

Yongzhong Xing

Gongwei Wang

Jinhua Xiao

Xingming Lian


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.

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
Public URL
Publisher URL
Additional Information Title on accepted manuscript: Genetic basis of rice ionomic variation revelaed by genome-wide association studies


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