Plant and Soil

, Volume 329, Issue 1–2, pp 139–153 | Cite as

Genetic mapping of the rice ionome in leaves and grain: identification of QTLs for 17 elements including arsenic, cadmium, iron and selenium

  • Gareth J. Norton
  • Claire M. Deacon
  • Lizhong Xiong
  • Shaoying Huang
  • Andrew A. Meharg
  • Adam H. Price
Regular Article


Research into the composition of cereal grains is motivated by increased interest in food quality. Here multi-element analysis is conducted on leaves and grain of the Bala x Azucena rice mapping population grown in the field. Quantitative trait loci (QTLs) for the concentration of 17 elements were detected, revealing 36 QTLs for leaves and 41 for grains. Epistasis was detected for most elements. There was very little correlation between leaf and grain element concentrations. For selenium, lead, phosphorus and magnesium QTLs were detected in the same location for both tissues. In general, there were no major QTL clusters, suggesting separate regulation of each element. QTLs for grain iron, zinc, molybdenum and selenium are potential targets for marker assisted selection to improve seed nutritional quality. An epistatic interaction for grain arsenic also looks promising to decrease the concentration of this carcinogenic element.


Arsenic Ionomics Iron QTL mapping Rice Selenium 



GJN was funded by BBSRC-DFID grant BBF0041841. The implementation of the field work was conducted under a joint EU project (FP6 no. 015468 “CEDROME”) to AHP and LX. The authors would like to thank The International Rice Research Institute for providing the seeds of the mapping population.


  1. Abedin MJ, Feldmann J, Meharg AA (2002) Uptake kinetics of arsenic species in rice plants. Plant Physiol. 128:1120–1128CrossRefPubMedGoogle Scholar
  2. Broadley MR, White PJ, Bryson RJ, Meacham MC, Bowen HC, Johnson SE, Hawkesford MJ, McGrath SP, Zhao FJ, Breward N, Harriman M, Tucker M (2006) Biofortification of UK food crops with selenium. Proc. Nutr. Soc. 65:169–181CrossRefPubMedGoogle Scholar
  3. Carneiro JMT, Rossete ALRM, Oliveira GS, Bendassolli JA (2007) Versatile flow injection system for spectrophotometric determination of silicon in agronomic samples. Commun. Soil Sci. Plant Anal. 38:1411–1423CrossRefGoogle Scholar
  4. Colangelo EP, Guerinot ML (2006) Put the metal to the petal: metal uptake and transport throughout plants. Curr. Opin. Plant Biol. 9:322–330CrossRefPubMedGoogle Scholar
  5. Dasgupta T, Hossain SA, Meharg AA, Price AH (2004) An arsenate tolerance gene on chromosome 6 of rice. New Phytol. 163:45–49CrossRefGoogle Scholar
  6. Ghandilyan A, Ilk N, Hanhart C, Mbengue M, Barboza L, Schat H, Koornneef M, El-Lithy M, Vreugdenhil D, Reymond M, Aarts MGM (2009) A strong effect of growth medium and organ type on the identification of QTLs for phytate and mineral concentrations in three Arabidopsis thaliana RIL populations. J Exp Bot 60:1409–1425CrossRefPubMedGoogle Scholar
  7. Goffinet B, Gerber S (2000) Quantitative Trait Loci: a meta-analysis. Genetics 155:463–473PubMedGoogle Scholar
  8. Graham R, Sendhira D, Beebe S, Iglesias C, Monasterio I (1999) Breeding for micronutrient density in edible portions of staple food crops: conventional approaches. Field Crop Res 60:57–80CrossRefGoogle Scholar
  9. Ishikawa S, Ae N, Yano M (2005) Chromosomal regions with quantitative trait loci controlling cadmium concentration in brown rice (Oryza sativa). New Phytol. 168:345–350CrossRefPubMedGoogle Scholar
  10. Izawa T, Shimamoto K (1996) Becoming a model plant: the importance of rice to plant science. Trends Plant Sci. 1:95–99CrossRefGoogle Scholar
  11. López-Millán A-F, Ellis DR, Grusak MA (2004) Identification and characterization of several new members of the ZIP family of metal ion transporters in Medicago truncatula. Plant Mol. Biol. 54:583–596CrossRefPubMedGoogle Scholar
  12. Ma JF, Yamaji N, Mitani N, Xu XY, Su YH, McGrath SP, Zhao FJ (2008) Transporters of arsenite in rice and their role in arsenic accumulation in rice grain. PNAS 105:9931–9935CrossRefPubMedGoogle Scholar
  13. Meharg AA, Hartley-Whitaker J (2002) Arsenic uptake and metabolism in arsenic resistant and nonresistant plant species. New Phytol. 154:29–43CrossRefGoogle Scholar
  14. Monsen ER (2000) Dietary reference intakes for the antioxidant nutrients: vitamin C, vitamin E, selenium, and carotenoids. J. Am. Diet. Assoc. 100:637–640CrossRefPubMedGoogle Scholar
  15. Navarro-Alarcón M, López-Martínez MC (2000) Essentiality of selenium in the human body: relationship with different diseases. Sci. Total Environ. 249:347–371CrossRefPubMedGoogle Scholar
  16. Nestel P, Bouis HE, Meenakshi JV, Pfeiffer W (2006) Biofortification of staple food crops. J. Nutr. 136:1064–1067PubMedGoogle Scholar
  17. Norton GJ, Nigar M, Williams PN, Dasgupta T, Meharg AA, Price AH (2008) Rice-arsenate interactions in hydroponics: a three-gene model for tolerance. J Exp Bot 59:2277–2284CrossRefPubMedGoogle Scholar
  18. Norton GJ, Price AH (2009) Mapping of quantitative trait loci for seminal root morphology and gravitropic response in rice. Euphytica 66:229–237CrossRefGoogle Scholar
  19. Patra M, Bhowmik N, Bandopadhyay B, Sharma A (2004) Comparison of mercury, lead and arsenic with respect to genotoxic effects on plant systems and the development of genetic tolerance. Environ. Exp. Bot. 52:199–223CrossRefGoogle Scholar
  20. Price AH, Steele KA, Moore BJ, Jones RGW (2002) Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes. II. Mapping quantitative trait loci for root morphology and distribution. Field Crops Res. 76:25–43CrossRefGoogle Scholar
  21. Salt DE, Baxter I, Lahner B (2008) Ionomics and the study of the plant ionome. Annu. Rev. Plant Biol. 59:709–733CrossRefPubMedGoogle Scholar
  22. Sandstead HH (1991) Zinc deficiency: a public health problem? Am J Di Child 145:853–859Google Scholar
  23. Shimizu A, Guerta CQ, Gregorio GB, Kawasaki S, Ikehashi H (2005) QTLs for nutritional contents of rice seedlings (Oryza sativa L.) in solution cultures and its implication to tolerance to iron-toxicity. Plant Soil 275:57–66CrossRefGoogle Scholar
  24. U.S. Department of Agriculture, Agricultural Research Service (2008) USDA National Nutrient Database for Standard Reference, Release 21. Nutrient Data Laboratory Home Page, Accessed 28 Jan 2009
  25. Verret F, Gravot A, Auroy P, Preveral S, Forestier C, Vavasseur A, Richaud P (2005) Heavy metal transport by AtHMA4 involves the N-terminal degenerated metal binding domain and the C-terminal His11 stretch. FEBS Lett. 579:1515–1522CrossRefPubMedGoogle Scholar
  26. Vreugdenhil D, Aarts MGM, Koornneef M, Nelissen H, Ernst WHO (2004) Natural variation and QTL analysis for cationic mineral content in seeds of Arabidopsis thaliana. Plant Cell Environ. 27:828–839CrossRefGoogle Scholar
  27. Wang DL, Zhu J, Li ZK, Paterson AH (1999a) Mapping QTLs with epistatic effects and QTL x environment interactions by mixed linear model approaches. Theor Appl Genet. 99:1255–1264CrossRefGoogle Scholar
  28. Wang DL, Zhu J, Li ZK, Paterson AH (1999b) User manual for QTLMapper version 1.0. Texas A&M Univ., College Station, TX.Google Scholar
  29. Williams PN, Islam MR, Adomako EE, Raab A, Hossain SA, Zhu YG, Feldmann J, Meharg AA (2006) Increase in rice grain arsenic for regions of Bangladesh irrigating paddies with elevated arsenic in groundwaters. Environ Sci Technology. 40:4903–4908CrossRefGoogle Scholar
  30. Williams PN, Raab A, Feldmann J, Meharg AA (2007) Market basket survey shows elevated levels of arsenic in South Central U.S. processed rice compared to California: Consequences for human dietary exposure. Environ Sci Technology. 41:2178–2183CrossRefGoogle Scholar
  31. Williams PN, Lombi E, Sun G-X, Schekel K, Zhu Y-G, Feng X, Zhu J, Carey A-M, Adomako E, Lawgali Y, Deacon C, Meharg AA (2009) Selenium characterization in the global rice supply chain. Environ Sci Technology. 43:6024–6030CrossRefGoogle Scholar
  32. World Heath Organization (WHO) (2002). World health report reducing Risks, Promoting Healthy Life. WHO: Geneva, SwitzerlandGoogle Scholar
  33. World Heath Organization (WHO) (2009) Micronutrient deficiencies. Iron deficiency anaemia. http://www.who/nutrition of subordinate document. Accessed 24 July 2009
  34. Wissuwa M, Wegner J, Ae N, Yano M (2002) Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil. Theor Appl Genet. 105:890–897CrossRefPubMedGoogle Scholar
  35. Wu P, Ni J (2000) Detection of the quantitative trait loci with AFLP and RFLP markers for phosphorus uptake and use efficiency in rice. Acta Botanica Sinica 42:229–233Google Scholar
  36. Xue D, Chen M, Zhang G (2009) Mapping of QTLs associated with cadmium tolerance and accumulation during seedling stage in rice (Oryza sativa L.). Euphytica 165:587–596CrossRefGoogle Scholar
  37. Zhang J, Zhu Y, Zeng D, Cheng W, Qian Q, Duan G (2008) Mapping quantitative trait loci associated with arsenic accumulation in rice (Oryza sativa). New Phytol. 177:350–355PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Gareth J. Norton
    • 1
  • Claire M. Deacon
    • 1
  • Lizhong Xiong
    • 2
  • Shaoying Huang
    • 2
  • Andrew A. Meharg
    • 1
  • Adam H. Price
    • 1
  1. 1.Department of Plant and Soil Science, Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenUK
  2. 2.National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina

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