Acta Physiologiae Plantarum

, Volume 32, Issue 2, pp 355–364 | Cite as

Molecular mapping and location of QTLs for drought-resistance traits in indica rice (Oryza sativa L.) lines adapted to target environments

  • Selvaraj Michael Gomez
  • N. Manikanda Boopathi
  • S. Satheesh Kumar
  • T. Ramasubramanian
  • Zhu Chengsong
  • P. Jeyaprakash
  • A. Senthil
  • R. Chandra Babu
Original Paper


Drought is a major limitation for rice production in rainfed ecosystems. Identifying quantitative trait loci (QTLs) linked to drought resistance provides opportunity to breed high yielding rice varieties suitable for drought-prone areas. Although considerable efforts were made in mapping QTLs associated with drought-resistance traits in rice, most of the studies involved indica × japonica crosses and hence, the drought-resistance alleles were contributed mostly by japonica ecotypes. It is desirable to look for genetic variation within indica ecotypes adapted to target environment (TE) as the alleles from japonica ecotype may not be expressed under lowland conditions. A subset of 250 recombinant inbred lines (RILs) of F8 generation derived from two indica rice lines (IR20 and Nootripathu) with contrasting drought-resistance traits were used to map the QTLs for morpho-physiological and plant production traits under drought stress in the field in TE. A genetic linkage map was constructed using 101 polymorphic PCR-based markers distributed over the 12 chromosomes covering a total length of 1,529 cM in 17 linkage groups with an average distance of 15.1 cM. Composite interval mapping analysis identified 22 QTLs, which individually explained 4.8–32.2% of the phenotypic variation. Consistent QTLs for drought-resistance traits were detected using locally adapted indica ecotypes, which may be useful for rainfed rice improvement.


Recombinant inbred lines Drought resistance indica rice Genetic linkage map Quantitative trait loci 



The research was supported by Rockefeller Foundation, New York, USA, through a research grant to RCB. The authors thank Dr. J.C. O’Toole for his guidance and encouragement though out the research.


  1. Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S, Nguyen HT (2000) Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice. Theor Appl Genet 101:756–766CrossRefGoogle Scholar
  2. Amaravathi Y, Singh R, Singh AK, Singh VP, Mohapatra T, Sharma TR, Singh NK (2008) Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol Breed 21:49–65CrossRefGoogle Scholar
  3. Babu RC, Shashidhar HE, Lilley JM, Thanh ND, Ray JD, Sadasivam S, Sarkarang S, O’Toole JC, Nguyen HT (2001) Variation in root penetration ability, osmotic adjustment and dehydration tolerance among accessions of rice adapted to rainfed lowland and upland ecosystems. Plant Breed 120(3):233–238CrossRefGoogle Scholar
  4. Babu RC, Nguyen BD, Chamarerk V, Shanmugasundaram P, Chezhian P, Jeyaprakash P, Ganesh SK, Palchamy A, Sadasivam S, Sarkarung S, Wade LJ, Nguyen HT (2003) Genetic analysis of drought resistance in rice by molecular markers: association between secondary traits and field performance. Crop Sci 43:1457–1469Google Scholar
  5. Barrs HD, Weatherley PE (1962) A re-examination of the relative turgidity technique for estimating water deficits in leaves. Aust Biol Sci 15:413–428Google Scholar
  6. Basten CJ, Weir BS, Zeng ZB (2005) QTL Cartographer version 2.5. Department of Statistics, North Carolina State University, USAGoogle Scholar
  7. 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 47:507–518CrossRefGoogle Scholar
  8. Bernier J, Atlin GN, Serraj R, Kumar A, Spaner D (2008) Review: breeding upland rice for drought resistance. J Sci Food Agric 88(6):927–939CrossRefGoogle Scholar
  9. Biji KR, Jeyaprakash P, Ganesh SK, Senthil A, Babu RC (2008) Quantitative trait loci linked to plant production traits in rice under drought stress in a target environment. Sci Asia 34:265–272CrossRefGoogle Scholar
  10. Blum A, Mayer J, Golan G, Sinmena B (1999) Drought tolerance of a doubled-haploid line population of rice in the field. In: Ito O (ed) Genetic improvement of rice for water limited environments. International Rice Research Institute, Los BanosGoogle Scholar
  11. Courtois B, Huang N, Guiderdoni E (1995) RFLP mapping of genes controlling yield components and plant height in an indica × japonica doubled haploid population. In: Proceedings of the International Rice Research Conference, Los Banos, 13–15 February 1995, pp 963–976Google Scholar
  12. Courtois B, McLaren G, Sinha PK, Prasad K, Yadav R, Shen L (2000) Mapping QTL associated with drought avoidance in upland rice. Mol Breed 6:55–66CrossRefGoogle Scholar
  13. Evenson RE, Gollin G (2003) Assessing the impact of the green revolution, 1960–2000. Science 300:758–762CrossRefPubMedGoogle Scholar
  14. Garrity DP, O’Toole JC (1995) Selection for reproductive stage drought avoidance in rice using infrared thermometry. Agron J 87:773–779Google Scholar
  15. Huang N, Courtois B, Khush GS, Lin H, Wang G, Wu P, Zheng K (1996) Association of quantitative trait loci for plant height with major dwarfing genes in rice. Heredity 77:130–137CrossRefGoogle Scholar
  16. Ingram K, Bueno TFD, Namuca OS, Yambao EB, Beyrouty CA (1994) Rice root traits for drought resistance and their genetic variation. In: Kirk GD (ed) Rice roots: nutrient and water use. IRRI, Los Banos, pp 67–77Google Scholar
  17. IRRI (1995) Challenges and opportunities in a less favourable ecosystem: rainfed low land rice. IRRI information series No. 1. IRRI, Los BanosGoogle Scholar
  18. IRRI (International Rice Research Institute) (1996) International network for genetic evaluation of rice: Standard evaluation system for rice. IRRI, Los BanosGoogle Scholar
  19. IRRI (International Rice Research Institute) (2002) Rice almanac. IRRI-WARDA-CIAT-FAO, Los BanosGoogle Scholar
  20. Kamoshita A, Zhang J, Siopongo J, Sarkarung S, Nguyen HT, Wade LJ (2002a) Effects of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions. Crop Sci 42(1):255–265PubMedCrossRefGoogle Scholar
  21. Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zhang J, Sarkarung S, Nguyen HT (2002b) Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions. Theor Appl Genet 104:880–893CrossRefPubMedGoogle Scholar
  22. Kamoshita A, Babu RC, Manikanda Boopathi N, Fukai S (2008) Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments. Field Crops Res 109:1–23CrossRefGoogle Scholar
  23. Kanbar A, Shashidhar HE, Hittalmani S (2003) Mapping QTL associated with root and related traits in DH population of rice. Indian J Genet 62:287–290Google Scholar
  24. Khush GS (2001) Green revolution: the way forward. Nature Rev 2:815–822Google Scholar
  25. Lander ES, Green P, Abrahamson J, Barlow A, Daly M, Lincoln SE, Newburg L (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  26. Lang NT, Buu BC, Ismail A (2008) Molecular mapping and marker assisted selection for salt tolerance in rice. Omorice 16:50–56Google Scholar
  27. Li ZK, Xu JL (2007) Breeding for drought and salt tolerant rice (oryza sativa L.): progress and perspectives. In: Jenks MA et al (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, USA, pp 531–564Google Scholar
  28. Lincoln S, Daly M, Lander E (1992) Mapping genes controlling quantitative traits with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, 3rd edn. Whitehead Institute, CambridgeGoogle Scholar
  29. Lou Q, Chen L, Sun Z, Xing Y, Li J, Xu J, Mei J, Luo L (2007) A major QTL associated with cold tolerance at seedling stage in rice. Euphytica 158:87–94CrossRefGoogle Scholar
  30. Manickavelu A, Nadarajan N, Ganesh SK, Gnanamalar RP, Chandra Babu R (2006) Drought tolerance in rice: morphological and molecular genetic consideration. Plant Growth Regul 50:121–138CrossRefGoogle Scholar
  31. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829CrossRefGoogle Scholar
  32. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, Declerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new D SSR markers for rice. DNA Res 9(6):199–207Google Scholar
  33. Michael Gomez S, Satheesh Kumar S, Jeyaprakash P, Suresh R, Biji KR, Manikanda Boopathi N, Price AH, Chandra Babu R (2006) Mapping QTLs linked to physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.) in the target environment. Am J Biochem Biotechnol 2(4):161–169CrossRefGoogle Scholar
  34. Nguyen HT, Babu RC, Blum A (1997) Breeding for drought resistance in rice: physiology and molecular genetics considerations. Crop Sci 37:1426–1434CrossRefGoogle Scholar
  35. Nguyen TTT, Klueva N, Chamareck V, Aarti A, Magpantay G, Millena ACM, Pathan MS, Nguyen HT (2004) Saturation mapping of QTL regions and identification of putative candidate genes for drought tolerance in rice. Mol Genet Genomics 272:35–46CrossRefPubMedGoogle Scholar
  36. Price AH, Tomos AD (1997) Genetic dissection of root growth in rice (Oryza sativa L.). II: mapping quantitative trait loci using molecular markers. Theor Appl Genet 95:143–152CrossRefGoogle Scholar
  37. 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(1):25–43CrossRefGoogle Scholar
  38. Reddy AR, Ramakrishna W, Sekhar AS, Ithal N, Babu PR, Bonaldo MF, Soares MB, Bennetzen JL (2002) Novel genes are enriched in normalized cDNA libraries from drought stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22). Genome 45:204–211CrossRefPubMedGoogle Scholar
  39. Redona ED, Mackil DJ (1996) Mapping quantitative trait loci for seedling vigor in rice using RFLPs. Theor Appl Genet 92:395–492CrossRefGoogle Scholar
  40. Robin S, Pathan MS, Courtois B, Lafitte R, Carandang S, Lanceras S, Amante M, Nguyen HT, Li Z (2003) Mapping osmotic adjustment in an advanced backcross inbred population of rice. Theor Appl Genet 107:1288–1296CrossRefPubMedGoogle Scholar
  41. SAS Institute Inc (1990) SAS/STAT user’s guide, Version 6, vols 1 and 2, 4th edn. SAS Institute Inc., CaryGoogle Scholar
  42. Srinivasan S, Michael Gomez S, Satheesh Kumar S, Ganesh SK, Biji KR, Senthil A, Chandra Babu R (2008) QTLs linked to leaf epicuticular wax, physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.). Plant Growth Regul 56:245–256CrossRefGoogle Scholar
  43. Temnykh S, DeClerk G, Lukashova A, Lipovich L, Cartinhour S, McCouch SR (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa): frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452CrossRefPubMedGoogle Scholar
  44. Wang GL, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434PubMedGoogle Scholar
  45. Xia BS, Hanada K, Kizhuchi F (1991) Character expression of the semi-dwarfism gene sd-1 in rice. Effect of nitrogen levels on the expression of some agronomic characteristics. Japan J Crop Sci 60:36–41Google Scholar
  46. Yadav R, Courtois B, Huang N, Mclaren G (1997) Mapping genes controlling root morphology and root distribution in a doubled-haploid population of rice. Theor Appl Genet 94:619–632CrossRefGoogle Scholar
  47. Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153CrossRefPubMedGoogle Scholar
  48. Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S, Blum A, Nguyen HT (2001) Locating genomic regions associated with components of drought resistance in rice: Comparative mapping within and across species. Theor Appl Genet 103:19–29CrossRefGoogle Scholar
  49. Zhao XQ, Xu JL, Zhao M, Lafitte R, Zhu LH, Fu BY, Gao YM, Li ZK (2008) QTLs affecting morpho-physiological traits related to drought tolerance detected in overlapping introgression lines of rice (Oryza sativa L.). Plant Sci (in press)Google Scholar
  50. 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 112:106–113CrossRefPubMedGoogle Scholar

Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2009

Authors and Affiliations

  • Selvaraj Michael Gomez
    • 1
  • N. Manikanda Boopathi
    • 2
  • S. Satheesh Kumar
    • 3
  • T. Ramasubramanian
    • 4
  • Zhu Chengsong
    • 3
  • P. Jeyaprakash
    • 5
  • A. Senthil
    • 2
  • R. Chandra Babu
    • 2
  1. 1.Texas Agri Life ResearchTexas A&M University SystemLubbockUSA
  2. 2.Centre for Plant Molecular BiologyTamil Nadu Agricultural UniversityCoimbatoreIndia
  3. 3.Department of Agronomy, Throckmorton Plant Sciences CentreKansas State UniversityManhattanUSA
  4. 4.Central Research Institute for Jute and Allied Fibres (ICAR)KolkataIndia
  5. 5.Agricultural Research StationTamil Nadu Agricultural UniversityParamakudiIndia

Personalised recommendations