Journal of Crop Science and Biotechnology

, Volume 14, Issue 1, pp 45–56 | Cite as

Molecular mapping of QTLs for yield and its components under two water supply conditions in rice (Oryza sativa L.)

  • Akkareddy Srividhya
  • Lakshminarayana R. Vemireddy
  • Sakile Sridhar
  • Mudduluru Jayaprada
  • Puram V. Ramanarao
  • Arremsetty S. Hariprasad
  • Hariprasad K. Reddy
  • Ghanta Anuradha
  • Ebrahimali Siddiq
Research Article


Moisture stress is the major constraint to rice production and its stability in rainfed, mainly irrigated, and aerobic environments. Identification of genomic regions conferring tolerance to stress would improve our understanding of the genetics of stress response and result in the development of drought tolerant cultivars. In the present study, quantitative trait loci for drought response related traits and as well as grain yield were identified using a set of 140 recombinant inbred lines derived from a cross between the popular high-yielding variety, IR64 and the landrace, INRC10192. A total of 36 QTL were identified for grain yield and its components under control and stress conditions. Strikingly, a QTL cluster flanked by the markers RM38 and RM331 on chromosome 8 was found to be associated with grain yield, plant height, no. of productive tillers, chaffy grains, and spikelet fertility on secondary rachis and biomass under stress treatment. The genomic regions associated with these QTL under drought stress will be useful for the development of marker-based breeding for drought tolerant, high-yielding varieties suited to drought-prone areas.

Key words

drought Oryza sativa QTL and SSR markers rice 



Recombinant inbred lines


Simple sequence repeat


Quantitative trait locus


Rice microsatellites


Logarithm of odds


Marker-assisted selection


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abebe T, Guenzi AC, Martin B, Cushman JC. 2003. Tolerance of mannitol-accumulating transgenic wheat to water stress and salinity. Plant Physiol. 131: 1748–1755PubMedCrossRefGoogle Scholar
  2. Ali AJ, Xu JL, Ismail AM, Fu BY, Vijaykumar CHM, Gao YM, Domingo J, Maghirang R, Yu SB, Gregorio G, Yanaghihara S. et al. 2006. Hidden diversity for abiotic and biotic stress tolerances inthe primary gene pool of rice revealed by a large backcrossbreeding program. Field Crops Res. 97: 66–76CrossRefGoogle Scholar
  3. Arisz SA, Valianpour F, van Gennip AH, Munnik T. 2003. Substrate preference of stress-activated phospholipase D in Chlamydomonas and its contribution to PA formation. Plant J. 34: 595–604PubMedCrossRefGoogle Scholar
  4. Babu RC, Nguyen BD, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, Ganesh SK, Palchamy A, Sadasivam S, Sarkarung S, Wade LJ, et al.. 2003. Genetic analysis of drought resistance in rice by molecular markers. Association between secondary traits and field performance. Crop Sci. 43: 1457–1469CrossRefGoogle Scholar
  5. Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin G. 2007. A Large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Sci. 47: 505–516CrossRefGoogle Scholar
  6. Blum A, Mayer J, Golan G, Sinmena B. 1999. Drought toler ance of a doubled-haploid line population of rice in the field. In O Ito et al., ed, Genetic improvement of rice for water-lim ited environments, International Rice Research Institute, Los Baños, PhilippinesGoogle Scholar
  7. Bray EA. 1997. Plant responses to water deficit. Trends Plant Sci. 2: 48–54CrossRefGoogle Scholar
  8. Brondani C, Rangel PHN, Brondani RPV, Ferreira ME. 2002. QTL mapping and introgression of yield-related traits from Oryza glumaepetula to cultivated rice (Oryza sativa L.) using microsatellite makers. Theor. Appl. Genet. 104:1192–1203PubMedCrossRefGoogle Scholar
  9. Cui K, Huang J, Xing Y, Yu S, Xu C, Peng S. 2008. Mapping QTLs for seedling characteristics under different water sup ply conditions in rice (Oryza sativa L.). Physiol. Plant. 132: 53–68PubMedGoogle Scholar
  10. Diedhiou CJ, Popova OV, Dietz KJ, Golldack D. 2008. The SNF1-type serine-threonine protein kinase SAPK4 regulates stress-responsive gene expression in rice. BMC Plant Biol. 8: 49PubMedCrossRefGoogle Scholar
  11. Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding fac tors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12: 393–404PubMedCrossRefGoogle Scholar
  12. Gaxiola RA, Li J, Undurraga S, Dang LM, Allen GJ, Alper SL, Fink GR. 2001. Drought- and salt-tolerant plants result from overexpression of the AVP1 H+-pump. Proc. Natl. Acad. Sci. USA, 98: 11444–11449PubMedCrossRefGoogle Scholar
  13. Hariprasad AS. 2003. Identification of new yield genes from land races in rice (Oryza sativa L) through molecular marker approach. PhD thesis submitted to Osmania University, HyderabadGoogle Scholar
  14. Hemamalini GS, Shashidhar HE, Hittalmani S. 2000. Molecular marker assisted tagging of morphological and physiological traits under two contrasting moisture regimes at peak vegeta tive stage in rice (Oryza sativa L.). Euphytica V112: 69–78CrossRefGoogle Scholar
  15. Hua TH, Wei MH, Qiao YX, Yan XX, Shou LM, Qing ZS, Jun LL. 2006. Identification of related QTLs at late develop mental stage in rice (Oryza sativa L.) under two nitrogen levels. Acta Genet. Sin. 33: 458–467CrossRefGoogle Scholar
  16. Jongdee B, Fukai S, Cooper M. 2002. Leaf water potential and osmotic adjustment as physiological traits to improve drought tolerance in rice. Field Crops Res. 76: 153–163CrossRefGoogle Scholar
  17. Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zhang J, Sakarung S, Nguyen HT. 2002a. Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions. Theor. Appl. Genet. 104: 880–893PubMedCrossRefGoogle Scholar
  18. Kamoshita A, Zhang JX, Siopongco J, Sakarung S, Nguyen HT, Wade LJ. 2002b. Effects of phenotyping environment on identification of quantitative trait loci for rice root morpholo gy under anaerobic conditions. Crop Sci. 42: 255–265PubMedCrossRefGoogle Scholar
  19. Kanbar A, Toorchi M, Chandrashekar M, Hittalmani S, Shashidhar HE. 2004. Identification of QTL for maximum root length in rice (Oryza sativa L.) using molecular markers In Abstract on 9th National rice biotechnology network meeting, April 15–17, NASC complex, New Delhi, pp 68Google Scholar
  20. Kathiresan A, Lafitte HR, Chen J, Mansueto L, Bruskiewich R, Bennett J. 2006. Gene expression microarrays and their application in drought stress research. Field Crops Res. 97: 101–110CrossRefGoogle Scholar
  21. Kubo T, Yoshiniura A. 1999. Complementary genes causing F2 sterility in Japonica/Indica cross of rice. Rice Genet. Newsl. 16: 68–70.Google Scholar
  22. Lafitte HR, Li ZK, Vijayakumar CHM, Gao YM, Shi Y, Xu JL, Fu BY, Yu SB, Ali AJ, Domingo J, Maghirang R, et al.. 2006. Improvements of rice drought tolerance through back cross breeding. Evaluation of donors and selection in drought nurseries. Field Crops Res. 97: 77–86CrossRefGoogle Scholar
  23. Lafitte HR, Price AH, Courtois B. 2004. Yield response to water deficit in an upland rice mapping population. Associations among traits and genetic markers. Theor. Appl. Genet. 109: 1237–1246PubMedCrossRefGoogle Scholar
  24. Lanceras JC, Pantuwan G, Jongdee B, Toojinda T. 2004. Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol. 135: 384–399PubMedCrossRefGoogle Scholar
  25. Li C, Zhou A, Sang T. 2006. Genetic analysis of rice domestica tion syndrome with the wild annual species, Oryza nivara. New Phytol. 170: 185–193PubMedCrossRefGoogle Scholar
  26. Li Z, Mu P, Li C, Zhang H, Li Z, Gao Y, Wang X. 2005a. QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments. Theor. Appl. Genet. 110: 1244–1252PubMedCrossRefGoogle Scholar
  27. Li ZK, Fu BY, Gao YM, Xu JL, Ali J, Laffitte JR, Jiang YZ, Rey RD, Vijayakumar CHM, Maghirang R, Zheng TQ et al. 2005b. Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant Mol. Biol. 59: 33–52PubMedCrossRefGoogle Scholar
  28. Li ZK, Luo LJ, Mei HW, Shu QY, Wang DL, Tabien R, Zhong DB, Ying CS, Stancel JW, Khush GS, Paterson AH. 2001. Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in Rice. I Biomass and grain yield. Genetics 158: 1737–1753PubMedGoogle Scholar
  29. Li ZK, Pinson SRM, Paterson AH, Park WD, Stancel JW. 1997. Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145: 453–465.PubMedGoogle Scholar
  30. Lilley JM, Ludlow MM. 1996. Expression of osmotic adjust ment and dehydration tolerance in diverse rice lines. Field Crops Res. 48: 185–197CrossRefGoogle Scholar
  31. Lin HX, Qian HR, Zhuang JY, Lu J, Min SK, Xiong ZM, Huang N, Zheng KL. 1996. RFLP mapping of QTLs for yield and related characters in rice (Oryza sativa L.) Theor. Appl. Genet. 92: 920–927CrossRefGoogle Scholar
  32. Liu GL, Mei HW, Yu XQ, Zou GH, Liu HY, Hu SP, Li MS, Wu JH, Chen L, Luo LJ. 2008. QTL analysis of panicle neck diameter a trait highly correlated with panicle size under well-watered and drought conditions in rice(Oryza sativa L.). Plant Sci. 174(1): 71–77CrossRefGoogle Scholar
  33. Liu JK, Liao DQ, Oane R, Estenor L, Yang XE, Li ZC, Bennett J. 2006. Genetic variation in the sensitivity of anther dehis cence to drought stress in rice. Field Crops Res. 97: 87–100CrossRefGoogle Scholar
  34. Liu HY, Zou GH, Liu GL, Hu SP, Li MS, Yu XQ, Mei HW, Luo LJ. 2005. Correlation analysis and QTL identification for canopy temperature, leaf water potential and spikelet fertility in rice under contrasting moisture regimes. Chinese Sci. Bull. 50: 317–326Google Scholar
  35. Marri PR, Sarla N, Reddy LV, Siddiq EA. 2005. Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genetics, UK 6.33 DOI. 101186/1471-2156-1186-1133Google Scholar
  36. McCouch SR, Sweeney M, Li J, Jiang H, Thomson M, Septiningsih E, Edwards J, Moncada P, Xiao J, Garris A, Tai T et al. 2007. Through the genetic bottleneck. O. rufipogon as a source of trait-enhancing alleles for O. sativa L. Euphytica 154: 317–339.Google Scholar
  37. Murray MG, Thompson WF. 1980. Rapid isolation of high mol ecular weight plant DNA. Nucleic Acids Research. 8: 4321–4325PubMedCrossRefGoogle Scholar
  38. Onishi K, Horiuchi Y, Ishigoh-Oka N, Takagi K, Ichikawa N, Maruoka M, Sano Y. 2007. A QTL cluster for plant architectture and its ecological significance in Asian wild rice. Breed. Sci. 57: 7–16.CrossRefGoogle Scholar
  39. O’Toole JC, Namuco OS. 1983. Role of panicle exertion in water stress induced sterility. Crop Sci. 23: 1093–1097CrossRefGoogle Scholar
  40. Pantuwan G, Fukai S, Cooper M, Rajatasereejul S, O’Toole JC. 2002. Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands. 3. Plant factors contributing to drought resistance. Field Crops Res. 73: 181–200CrossRefGoogle Scholar
  41. Park S, Li J, Pittman JK, Berkowitz GA, Yang H, Undurraga S, Morris J, Hirschi KD, Gaxiola RA. 2005. Up-regulation of a H+-pyrophosphatase (H+-Ppase) as a strategy to engineer drought-resistant crop plants. Proc. Natl. Acad. Sci. USA 102: 18830–18835PubMedCrossRefGoogle Scholar
  42. Paterson AH, Tanskley SD, Sorrels ME. 1991. DNA markers in plant Improvement. Adv. Agron. 46: 39–90CrossRefGoogle Scholar
  43. 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
  44. Rabbani MA, Maruyama K, Abe H, Khan A, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2003. Monitoring expression profiles of rice genes under cold, drought and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analy ses. Plant Physiol. 133: 1755–1767PubMedCrossRefGoogle Scholar
  45. Robin S, Pathan MS, Courtois B, Lafitte R, Carandang C, Lanceras S, Amante M, Nguyen HT, Li Z. 2003. Mapping osmotic adjustment in an advanced back-cross inbred population of rice. Theor. Appl. Genet. 107: 1288–1296PubMedCrossRefGoogle Scholar
  46. Saini HS, Lalonde S. 1998. Injuries to reproductive development under water stress, and their consequences for crop productivity. J. Crop Prod. 1: 223–248Google Scholar
  47. Salekdeh GhH, Siopongco J, Wade LJ, Ghareyazie B, Bennett J. 2002. A proteomic approach to analyzing drought and salt responsiveness in rice. Field Crops Res. 76: 199–219CrossRefGoogle Scholar
  48. Sanguineti MC, Tuberosa R, Landi P, Salvi S, Maccaferri M, Casarini E, Conti S. 1999. QTL analysis of drought-related traits and grain yield in relation to genetic variation for leaf abscisic acid concentration in field-grown maize. J. Exp. Bot. 50(337): 1289–1297CrossRefGoogle Scholar
  49. Sheoran IS, Saini HS. 1996. Drought-induced male sterility in rice. changes in carbohydrate levels and enzyme activity associated with the inhibition of starch accumulation in pollen. Sex. Plant Reprod. 9: 161–169CrossRefGoogle Scholar
  50. Spielmeyer W, Ellis MH, Chandler PM. 2002. Semidwarf (sd-1) “green revolution” rice contains a defective gibberellin 20-oxidase gene. Proc. Natl. Acad. Sci. USA 99: 9043–9048PubMedCrossRefGoogle Scholar
  51. Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang QF. 1999. The three important traits for cooking and eating qualities of rice grain are controlled by a single locus. Theor. Appl. Genet. 99: 642–648CrossRefGoogle Scholar
  52. Tian F, Zhu Z, Zhang B, Tan L, Fu Y, Wang X, Sun CQ. 2006. Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.). Theor. Appl. Genet. DOI 101007/s00122-00-0326-yGoogle Scholar
  53. Tripathy JN, Zhang J, Robin S, Nguyen ThT, Nguyen HY. 2000. QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theor. Appl. Genet. 100: 1197–1202CrossRefGoogle Scholar
  54. Vijayakumar CHM, Lafitte R, Fu BY, Yan S, Yu SB, Gao YM, Mighirang G, Zhai MF, Hu FY, Ali J, Domingo J, et al. 2002. Selective introgression and discovery of genes/QTLs for drought tolerance in elite genetic backgrounds In Abstract on workshop on international rice breeding program, International Rice Congress, 16–20 September, Beijing, China, pp 123Google Scholar
  55. Wan XY, Wan JM, Weng JF, Jiang L, Bi JC, Wang CM, Zhai HQ. 2005. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environ ments. Theor. Appl. Genet. 110: 1334–1346PubMedCrossRefGoogle Scholar
  56. Wang C, Zhu C, Zhai H, Wan J. 2005. Mapping segregation distortion loci and quantitative trait loci for spikelet sterility in rice (Oryza sativa L.). Genet. Res. 86: 97–106PubMedCrossRefGoogle Scholar
  57. Wang S, Basten CJ, Zeng ZB. 2007. Windows QTL Cartographer 2.5, Department of Statistics, North Carolina State University, Raleigh, NC, User manual pp 1–87Google Scholar
  58. Xiao J, Li J, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR. 1998. Identification of trait-improving quantitative trait loci alleles from a wild rice relative Oryza rufipogon. Genetics 150: 899–909PubMedGoogle Scholar
  59. Xiong L, Zhu JK, 2001. Abiotic stress signal transduction in plants: Molecular and genetic perspectives. Physiol. Plant, 112:152–166PubMedCrossRefGoogle Scholar
  60. Xiong L, Schumaker KS, Zhu JK. 2002. Cell signaling during cold, drought, and salt stress. Plant Cell, 14: S165–183PubMedCrossRefGoogle Scholar
  61. Yue B, Xue W, Luo L, Xing Y. 2008. Identification of quantitative trait loci for four morphologic traits under water stress in rice (Oryza sativa L.). J. Genet. Genomics 35: 569–575PubMedCrossRefGoogle Scholar
  62. Yue B, Xue WY, Xiong LZ, Yu XQ, Luo LJ, Cui KH, Jin DM, Xing YZ, Zhang QF. 2006. Genetic basis of drought resistance at reproductive stage in rice. Separation of drought tolerance from drought avoidance. Genetics 172: 1213–1228PubMedCrossRefGoogle Scholar
  63. Zhang WP, Shen XY, Wu P, Hu B, Liao CY. 2001. QTLs and epistasis for seminal root length under a different water supply in rice (Oryza sativa L.). Theor. Appl. Genet. 103: 118–123CrossRefGoogle Scholar
  64. Zhao XQ, Xu JL, Zhao M, Lafitte R, Zhu LH, Fu BY, Gao YM, Li ZK. 2008. QTLs affecting morph-physiological traits related to drought tolerance detected in overlapping introgres sion lines of rice (Oryza sativa L.). Plant Sci. 174: 618–625CrossRefGoogle Scholar
  65. Zheng BS, Yang L, Zhang WP, Mao CZ, Wu YR, Yi KK, Liu Y, Wu P. 2003. Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations. Theor. Appl. Genet. 107: 1505–1515PubMedCrossRefGoogle Scholar
  66. Zou GH, Mei HW, Liu HY, Liu GL, Hu SP, Yu XQ, Li MS, Wu JH, Luo LJ. 2005. Grain yield responses to moisture regimes in a rice population. Association among traits and genetic markers. Theor. Appl. Genet. 112: 106–113PubMedCrossRefGoogle Scholar

Copyright information

© Korean Society of Crop Science and Springer Netherlands 2011

Authors and Affiliations

  • Akkareddy Srividhya
    • 1
  • Lakshminarayana R. Vemireddy
    • 1
  • Sakile Sridhar
    • 1
  • Mudduluru Jayaprada
    • 1
  • Puram V. Ramanarao
    • 1
  • Arremsetty S. Hariprasad
    • 2
  • Hariprasad K. Reddy
    • 3
  • Ghanta Anuradha
    • 1
  • Ebrahimali Siddiq
    • 1
  1. 1.Institute of BiotechnologyAcharya N G Ranga Agricultural UniversityRajendranagar, HyderabadIndia
  2. 2.Directorate of Rice ResearchRajendranagar, HyderabadIndia
  3. 3.Department of Genetics and Plant breedingS.V. Agricultural CollegeTirupatiIndia

Personalised recommendations