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The Plant cell
11, 2018;30 (11): 2720-2740.

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

Meng Yang, Kai Lu, Fang-Jie Zhao, Weibo Xie, Priya Ramakrishna, Guangyuan Wang, Qingqing Du, Limin Liang, Cuiju Sun, Hu Zhao, Zhanyi Zhang, Zonghao Liu, Jingjing Tian, Xin-Yuan Huang, Wensheng Wang, Huaxia Dong, Jintao Hu, Luchang Ming, Yongzhong Xing, Gongwei Wang, Jinhua Xiao, David E Salt, Xingming Lian
Author Information
  1. Meng Yang: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  2. Kai Lu: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  3. Fang-Jie Zhao: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
  4. Weibo Xie: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  5. Priya Ramakrishna: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom.
  6. Guangyuan Wang: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  7. Qingqing Du: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  8. Limin Liang: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  9. Cuiju Sun: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  10. Hu Zhao: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  11. Zhanyi Zhang: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  12. Zonghao Liu: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  13. Jingjing Tian: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  14. Xin-Yuan Huang: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
  15. Wensheng Wang: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  16. Huaxia Dong: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  17. Jintao Hu: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  18. Luchang Ming: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  19. Yongzhong Xing: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  20. Gongwei Wang: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  21. Jinhua Xiao: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
  22. David E Salt: Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom.
  23. Xingming Lian: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China xmlian@mail.hzau.edu.cn.
PMID: 30373760 DOI: 10.1105/tpc.18.00375

Abstract

Rice () 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 for sodium, for molybdenum, and , , for nitrogen. Comparison of GWAS data from rice versus Arabidopsis () 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.

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MeSH Term

Genetic Variation
Genome-Wide Association Study
Genotype
Linkage Disequilibrium
Oryza
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 20

Word Cloud

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