Theoretical and Applied Genetics

, Volume 112, Issue 1, pp 85–96 | Cite as

QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred line population derived from an elite rice hybrid

  • Xingming Lian
  • Yongzhong Xing
  • Hua Yan
  • Caiguo Xu
  • Xianghua Li
  • Qifa Zhang
Original Paper


Tolerance to low nitrogen conditions is a highly desired characteristic for sustainable crop production. In this study, we analyzed the genetic components associated with low N tolerance in rice at seedling stage, including main effects, epistatic effects of the quantitative trait locus (QTLs), and QTL by environment interactions (QEs), using a population of 239 recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Minghui 63, the parents of an elite hybrid. A genetic linkage map with 253 DNA maker loci was constructed. Seedlings of RILs were cultivated in low N and normal N solutions. Root, shoot and plant weight in the two N treatments were measured and the relative weight of the two treatments for each trait was considered as measurements for low N tolerance. Four to eight QTLs with main effects were detected for each of the nine traits. Very few QTLs were detected in both low and normal N conditions, and most QTLs for the relative measurements were different from those for traits under the two N treatments, indicating very little commonality in the genetic basis of the traits and their relative performance under low and normal N conditions. A total of 103 digenic interactions were detected for the nine traits. While the epistatic effects collectively accounted for large proportions of the variation for several traits, the effects of QEs appeared to be trivial. It was concluded that low N tolerance of rice seedling had complex genetic basis that requires extensive studies for full characterization.


  1. Agrama HAS, Zakaria AG, Said FB, Tuinstra MR (1999) Identification of quantitative trait loci for nitrogen use efficiency in maize. Mol Breed 5:187–195CrossRefGoogle Scholar
  2. Bertin P, Gallais A (2000) Physiological and genetic basis of nitrogen use efficiency in maize: II. QTL detection and coincidences. Maydica 45:67–80Google Scholar
  3. Bertin P, Gallais A (2001) Physiological and genetic basis of nitrogen use efficiency in maize. II. QTL detection and coincidences. Maydica 46:53–68Google Scholar
  4. Campbell WH (1988) Nitrate reductase and its role in nitrate assimilation in plants. Physiol Plant 74:214–219CrossRefGoogle Scholar
  5. Crawford NM, Glass ADM (1998) Molecular and physiological aspects of nitrate uptake in plants. Trends Plant Sci 3:389–395CrossRefGoogle Scholar
  6. Fang P, Wu P (2001) QTL × N-level interaction for plant height in rice (Oryza sativa L.). Plant and Soil 236:237–242CrossRefGoogle Scholar
  7. Forde BG (2000) Nitrate transporters in plants: structure, function and regulation. Biochem Biophys Acta 1465:219–235CrossRefPubMedGoogle Scholar
  8. Frink CR, Waggoner PE, Ausubel JH (1999) Nitrogen fertilizer: retrospect and prospect. Proc Natl Acad Sci USA 96:1175–1180CrossRefPubMedPubMedCentralGoogle Scholar
  9. Gallais A, Hirel B (2004) An approach to the genetics of nitrogen use efficiency in maize. J Exp Bot 55:295–306CrossRefPubMedGoogle Scholar
  10. Glass ADM, Brito DT, Kaiser BN, Kronzucker HJ, Kumar A, Okamoto M, Rawat SR, Siddiqi MY, Silim SM, Vidmar JJ, Zhuo D (2001) Nitrogen transport in plants, with an emphasis on the regulation of fluxes to match plant demand. J Plant Nutr Soil Sci 164:199–207CrossRefGoogle Scholar
  11. Hirel B, Lea PJ (2001) Ammonia assimilation. In: Lea PJ, Morot-Gaudry J-F (eds) Plant Nitrogen. Springer, Berlin Heidelberg New York, pp 79–99CrossRefGoogle Scholar
  12. Hirel B, Bertin P, Quillere´ I, Bourdoncle W, Attagnant C, Dellay C, Gouy A, Cadiou S, Retailliau C, Falque M, et al (2001) Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize. Plant Physiol 125:1258–1270CrossRefPubMedPubMedCentralGoogle Scholar
  13. Howitt SM, Udvardi MK (2000) Structure, function and regulation of ammonium transporters in plants. Biochem Biophys Acta 1465:152–170CrossRefPubMedGoogle Scholar
  14. Ishimaru K, Kobayashi N, Ono K, Yano M, Ohsugi R (2001) Are contents of Rubisco, soluble protein and nitrogen in flag leaves of rice controlled by the same genetics? J Exp Bot 52:1827–1833CrossRefPubMedGoogle Scholar
  15. Lam HM, Coschigano KT, Oliveira IC, Melooliveira R, Coruzzi GM (1996) The molecular-genetics of nitrogen assimilation into amino acids in higher plants. Annu Rev Plant Physiol Plant Mol Biol 47:569–593CrossRefPubMedGoogle Scholar
  16. Lincoln S, Daly M, Lander E (1992) Constructing genetics maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, Whitehead Institute, Cambridge, Massachusctts, USAGoogle Scholar
  17. Liu KD, Wang J, Li HB, Xu CG, Liu AM, Li XH, Zhang Q (1997) A genome-wide analysis of wide compatibility in rice and the precise location of the S5 locus on the molecular map. Theor Appl Genet 95:809–814CrossRefGoogle Scholar
  18. Loudet O, Chaillou S, Merigout P, Talbotec J, Daniel-Vedele F (2003a) Quantitative trait loci analysis of nitrogen use efficiency in arabidopsis. Plant Physiol 131:345–358CrossRefPubMedPubMedCentralGoogle Scholar
  19. Loudet O, Chaillou S, Krapp A, Daniel-Vedele F (2003b) Quantitative trait loci analysis of water and anion contents in interaction with nitrogen availability in Arabidopsis thaliana. Genetics 163:711–722PubMedPubMedCentralGoogle Scholar
  20. Obara M, Kajiura M, Fukuta Y, Yano M, Hayashi M, Yamaya T, Sato T (2001) Mapping of QTLs associated with cytosolic glutamine synthetase and NADH-glutamate synthase in rice (Oryza sativa L.). J Exp Bot 52:1209–1217CrossRefPubMedGoogle Scholar
  21. Obara M, Sato T, Sasaki S, Kashiba K, Nagano A, Nakamura I, Ebitani T, Yano M, Yamaya T (2004) Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice. Theor Appl Genet 110:1–11CrossRefPubMedGoogle Scholar
  22. Rauh BL, Basten C, Buckler ES IV (2002) Quantitative trait loci analysis of growth response to varying nitrogen sources in Arabidopsis thaliana. Theor Appl Genet 104:743–750CrossRefPubMedGoogle Scholar
  23. Socolow RH (1999) Nitrogen management and the future of food: lessons from the management of energy and carbon. Proc Natl Acad Sci USA 96:6001–6008CrossRefPubMedPubMedCentralGoogle Scholar
  24. Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang Q (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642–648CrossRefPubMedGoogle Scholar
  25. Tan YF, Sun M, Xing YZ, Hua JP, Sun XL, Zhang QF, Corke H (2001) Mapping quantitative trait loci for milling quality, protein content and color characteristics of rice using a recombinant inbred line population derived from an elite rice hybrid. Theor Appl Genet 103:1037–1045CrossRefGoogle Scholar
  26. UNEP (1999) Global environment outlook 2000. United Nations Environment Programme and London Earthscan, Nairobi, KenyaGoogle Scholar
  27. Vlek PLG, Byrnes BH (1986) The efficacy and loss of fertilizer N in lowland rice. Fertilizer Res 9:131–147CrossRefGoogle Scholar
  28. Wang DL, Zhu J, Li ZK, Paterson AH (1999) A computer software for mapping quantitative trait loci QTLs with main effects, epistatic effects and QTL × environment interactions. Copyright by Zhejiang University, Hangzhou, ChinaGoogle Scholar
  29. Williams LE, Miller AJ (2001) Transporters responsible for the uptake and partitioning of nitrogenous solutes. Annu Rev Plant Physiol Plant Mol Biol 52:659–688CrossRefPubMedGoogle Scholar
  30. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235CrossRefPubMedGoogle Scholar
  31. Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257CrossRefPubMedGoogle Scholar
  32. Yamaya T, Obara M, Nakajima H, Sasaki S, Hayakawa T, Sato T (2002) Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice. J Exp Bot 53:917–925CrossRefPubMedGoogle Scholar
  33. Yoshida S, Forno DA, Cook JH, Gomez KA (1976) Laboratory manual for physiological studies of rice, 3rd edn. International Rice Research Institute, ManilaGoogle Scholar
  34. Zhu J, Weir BS (1998) Mixed model approaches for genetic analysis of quantitative traits. In: Chen LS, Ruan SG, Zhu J (eds) Advanced topics in biomathematics. Proceedings of international conference on mathematical biology. World Scientific Publishing Co., Singapore, pp 321–330Google Scholar
  35. Zhu Z (2000) Loss of fertilizer N from plant-soil system and the strategies and techniques for its reduction (in Chinese with English abstract). Soil Environ Sci 9:1–6Google Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Xingming Lian
    • 1
  • Yongzhong Xing
    • 1
  • Hua Yan
    • 1
  • Caiguo Xu
    • 1
  • Xianghua Li
    • 1
  • Qifa Zhang
    • 1
  1. 1.National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina

Personalised recommendations