, Volume 172, Issue 2, pp 159–168 | Cite as

QTLs associated with tolerance of flooding during germination in rice (Oryza sativa L.)

  • S. Abdolhamid Angaji
  • Endang M. Septiningsih
  • D. J. Mackill
  • Abdelbagi M. Ismail


Direct seeding of rice is increasingly being practiced in both rainfed and irrigated areas because of labor shortage for transplanting and opportunities for crop intensification. However, poor crop establishment remains a major obstacle facing its large-scale adoption in areas prone to flooding. Screening of over 8,000 gene bank accessions and breeding lines identified a few tolerant genotypes. One of these, Khao Hlan On, was selected for mapping QTLs associated with tolerance using a backcross population with IR64 as a recurrent parent. Survival of BC2F2 lines varied from 0 to 68%, and averaged about 28%. A linkage map of 1475.7 cM with an average interval of 11.9 cM was constructed using 135 polymorphic SSRs and 1 indel marker. Five putative QTLs were detected, on chromosomes 1 (qAG-1-2), 3 (qAG-3-1), 7 (qAG-7-2), and 9 (qAG-9-1 and qAG-9-2), explaining 17.9 to 33.5% of the phenotypic variation, and with LOD scores of 5.69–20.34. Khao Hlan On alleles increased tolerance of flooding during germination for all the QTLs. Graphical genotyping of the lines with highest and lowest survival verified the detected QTLs that control tolerance and some QTLs co-localize with previously identified QTLs for traits relevant to tolerance, which warrant further studies.


Direct seeding Flooding tolerance Germination Oryza sativa L. QTL mapping 



Technical assistance from E. Ella, G. Vergara, R. Maghirang-Rodriguez, A. M. Pamplona, D. Sanchez, and J. Mendoza is gratefully acknowledged. The authors thank Dr. Michael Thomson for helpful comments. The work reported here was supported in part by a grant from the German Federal Ministry for Economic Cooperation and Development (BMZ).

Supplementary material

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  1. Atwell BJ, Waters I, Greenway H (1982) The effect of oxygen and turbulence on elongation of coleoptiles of submergence-tolerant and -intolerant rice cultivars. J Exp Bot 33:1030–1044. doi: 10.1093/jxb/33.5.1030 CrossRefGoogle Scholar
  2. Basten CJ, Weir BS, Zeng Z-B (1997) QTL Cartographer: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, Raleigh, NCGoogle Scholar
  3. Biswas JK, Yamauchi M (1997) Mechanism of seedling establishment of direct-seeded rice (Oryza sativa L.) under lowland conditions. Bot Bull Acad Sin 38:29–32Google Scholar
  4. Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 100:840–846. doi: 10.1007/s001220051360 CrossRefGoogle Scholar
  5. Dilday RH, Mgonja MA, Amonsilpa SA, Collins FC, Wells BR (1990) Plant height vs. mesocotyl and coleoptile elongation in rice: linkage or pleiotropism? Crop Sci 30:815–818Google Scholar
  6. Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 154:823–835PubMedGoogle Scholar
  7. Harushima Y, Jano M, Shomura A (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494PubMedGoogle Scholar
  8. Ikehashi H (1973) Studies on the environmental and varietal differences of germination habits in rice seeds with special reference to plant breeding (in Japanese with English summary). J Cent Agric Exp Stan 19:1–60Google Scholar
  9. International Rice Genome Sequencing Project (IRGSP) (2005) The map-based sequence of the rice genome. Nature 436:793–800. doi: 10.1038/nature03895 CrossRefGoogle Scholar
  10. Ismail AM, Ella ES, Vergara GV, Mackill DJ (2009) Mechanisms associated with tolerance of flooding during germination and early seedling growth in rice (Oryza sativa L.). Ann Bot (Lond) 103:197–209. doi: 10.1093/aob/mcn211 CrossRefGoogle Scholar
  11. Jiang L, Ming-yu HW, Ming C, Jian-min W (2004) Quantitative trait loci and epistatic analysis of seed anoxia germinability in rice (Oryza sativa L.). Ric Sci 11(5–6):238–244Google Scholar
  12. Jiang L, Liu S, Hou M, Tang J, Chen L, Zhai H, Wan J (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crops Res 98:68–75. doi: 10.1016/j.fcr.2005.12.015 CrossRefGoogle Scholar
  13. Kordan HA (1976) Oxygen as an environmental factor in influencing normal morphogenetic development in germinating rice seedlings. J Exp Bot 27:947–952. doi: 10.1093/jxb/27.5.947 CrossRefGoogle Scholar
  14. Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465PubMedGoogle Scholar
  15. Miura K, Lin SY, Yano M, Nagamine T (2002) Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.). Theor Appl Genet 104:981–986. doi: 10.1007/s00122-002-0872-x CrossRefPubMedGoogle Scholar
  16. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776. doi: 10.1007/s00122-007-0607-0 CrossRefPubMedGoogle Scholar
  17. Nievergelt CM, Douglas W, Smith J, Kohlenberg B, Schork NJ (2004) Large-scale integration of human genetic and physical maps. Genome Res 14:1199–1205. doi: 10.1101/gr.1475304 CrossRefPubMedGoogle Scholar
  18. Opik H (1973) Effect of anaerobiosis on respiratory rate, cytochrome oxidase activity and mitochondrial structure in coleoptiles of rice (Oryza sativa L.). J Cell Sci 12:725–739PubMedGoogle Scholar
  19. Ota Y, Takemura Y (1970) Rice grain storage and seed dormancy (in Japanese). J Agric Sci Tokyo 25:218–222Google Scholar
  20. Pandey S, Mortimer M, Wade L, Tuong TP, Lopez K, Hardy B (eds) (2002) Direct seeding: research strategies and opportunities. Proceedings of the international workshop on direct seeding in Asia rice systems: strategic research issues and opportunities, 25–28 January 2000, Bangkok, Thailand. International Rice Research Institute, Los Baños, Philippines, p 383Google Scholar
  21. Paterson A, Tanksley S, Sorrels ME (1991) DNA markers in plant improvement. Adv Agron 44:39–90. doi: 10.1016/S0065-2113(08)60578-7 CrossRefGoogle Scholar
  22. Pflieger S, Lefebvre V, Causse M (2001) The candidate gene approach in plant genetics: a review. Mol Breed 7:275–291. doi: 10.1023/A:1011605013259 CrossRefGoogle Scholar
  23. Redoña ED, Mackill DJ (1996) Genetic variation for seedling-vigor traits in rice. Crop Sci 36:285–290Google Scholar
  24. Report of Ministry of Agriculture and Irrigation Union of Myanmar (2004) Rice varieties in Myanmar. Ministry of Agriculture and Irrigation Union of Myanmar, p 333Google Scholar
  25. Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432. doi: 10.1007/s00122-003-1373-2 CrossRefPubMedGoogle Scholar
  26. Septiningsih EM, Pamplona AM, Sanchez DL, Maghirang-Rodriguez R, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence-tolerant rice cultivars: the Sub1 gene and beyond. Ann Bot (Lond) 103:151–160. doi: 10.1093/aob/mcn206 CrossRefGoogle Scholar
  27. Seshu DV, Krishnasamy V, Siddique SB (1988) Seed vigor in rice. In: Rice seed health. Manila (Philippines): International Rice Research Institute, pp 315–329Google Scholar
  28. Siddique SB, Seshu DV, Pardee WD (1988) Rice cultivar variability for accelerated aging of seed. In: IRRI research paper series number 131. Manila (Philippines): International Rice Research Institute, pp 1–7Google Scholar
  29. Takahashi N (1978) Adaptive importance of mesocotyl and coleoptile growth in rice under different moisture regimes. Aust J Plant Physiol 5:511–517CrossRefGoogle Scholar
  30. Tripathy JN, Zhang J, Robin S, Nguyen THT (2000) QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theor Appl Genet 100:1197–1202. doi: 10.1007/s001220051424 CrossRefGoogle Scholar
  31. van Berloo R (1999) GGT: software for the display of graphical genotypes. J Hered 90:328–329. doi: 10.1093/jhered/90.2.328 CrossRefGoogle Scholar
  32. van Berloo R (2007) GGT: user manual Version 2.0. Wageningen (The Netherlands), Wegeningen University. Available from
  33. Xu K, Xia X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene response factor-like gene that confers submergence tolerance to rice. Nature 442:705–708. doi: 10.1038/nature04920 CrossRefPubMedGoogle Scholar
  34. Yamauchi M, Winn T (1996) Rice seed vigor and seedling establishment in anaerobic soil. Crop Sci 36:680–686CrossRefGoogle Scholar
  35. Yamauchi M, Aguilar AM, Vaughan DA, Seshu DV (1993) Rice (Oryza sativa L.) germplasm suitable for direct sowing under soil surface. Euphytica 67:177–184. doi: 10.1007/BF00040619 CrossRefGoogle Scholar
  36. Yamauchi M, Herradura PS, Aguilar AM (1994) Genotype difference in rice postgermination growth under hypoxia. Plant Sci 100:105–113. doi: 10.1016/0168-9452(94)90138-4 CrossRefGoogle Scholar
  37. Young ND (1996) QTL mapping and quantitative disease resistance in plants. Annu Rev Phytopathol 34:479–501. doi: 10.1146/annurev.phyto.34.1.479 CrossRefPubMedGoogle Scholar
  38. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar
  39. Zheng K, Subudhi PK, Domingo J, Magpantay G, Huang N (1995) Rapid DNA isolation for marker assisted selection in rice breeding. Rice Genet Newsl 12:255–258Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • S. Abdolhamid Angaji
    • 1
    • 2
  • Endang M. Septiningsih
    • 1
  • D. J. Mackill
    • 1
  • Abdelbagi M. Ismail
    • 1
  1. 1.International Rice Research InstituteMetro ManilaPhilippines
  2. 2.Department of BiologyTarbiat Moallem UniversityTehranIran

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