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Fine Mapping QTL for Drought Resistance Traits in Rice (Oryza sativa L.) Using Bulk Segregant Analysis

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Abstract

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212–RM302–RM8085–RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.

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References

  1. Nguyen, H. T., Babu, R. C., & Blum, A. (1997). Breeding for drought resistance in rice: Physiology and molecular genetics considerations. Crop Science, 37, 1426–1434.

    Article  Google Scholar 

  2. FAO (Food and Agricultural Organization). (2007). http//www.fao.org.

  3. Huke, R. E., & Huke, E. H. (1997). Rice area by type of culture: South, Southeast and East Asia. Los Banos: IRRI.

    Google Scholar 

  4. Bernier, J., Kumar, A., Serraj, R., Spaner, D., & Atlin, G. N. (2008). Breeding upland rice for drought resistance. Journal of the Science of Food and Agriculture, 88, 927–939.

    Article  CAS  Google Scholar 

  5. Venuprasad, R., Lafitte, H. R., & Atlin, G. N. (2007). Response to direct selection for grain yield under drought stress in rice. Crop Science, 47, 285–293.

    Article  Google Scholar 

  6. Kamoshita, A., Babu, R. C., Boopathi, N. M., & Fukai, S. (2008). Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments. Field Crops Research, 109, 1–23.

    Article  Google Scholar 

  7. Fukai, S., & Cooper, M. (1995). Development of drought-resistant cultivars using physio-morphological traits in rice. Field Crops Research, 40, 67–86.

    Article  Google Scholar 

  8. Lafitte, R., Blum, A., & Atlin, G. (2003). Using secondary traits to help identify drought-tolerant genotypes. In Breeding rice for drought-prone environments. Los Banos: IRRI.

  9. Richards, R. A., Rebetzke, G. J., Watt, M., Condon, A. G., Spielmeyer, W., & Dolferus, R. (2010). Breeding for improved water productivity in temperate cereals: Phenotyping, quantitative trait loci, markers and the selection environment. Functional Plant Biology, 37, 85–97.

    Article  Google Scholar 

  10. Blum, A. (1988). Plant breeding for Stress environments. Boca Raton, FL: CRC Inc.

    Google Scholar 

  11. Fischer, K. S., & Fukai, S. (2003). How rice responds to drought. In K. S. Fischer, R. Lafitte, S. Fukai, G. Atlin, & B. Hardy (Eds.), Breeding rice for drought prone environments (pp. 32–36). Los Banos: IRRI.

    Google Scholar 

  12. De Datta, S. K., Malabuyot, J. A., & Aragon, E. L. (1988). A field screening technique for evaluating rice germplasm for drought tolerance during the vegetative stage. Field Crops Research, 19, 123–134.

    Article  Google Scholar 

  13. Courtois, B., McLaren, G., Sinha, P. K., Prasad, K., Yadav, R., & Shen, L. (2000). Mapping QTL associated with drought avoidance in upland rice. Molecular Breeding, 6, 55–66.

    Article  CAS  Google Scholar 

  14. Chang, T. T., Loresto, G., & Tagum, P. O. (1974). Screening rice germplasm for drought resistance. SABRAO Journal, 6(1), 9–16.

    Google Scholar 

  15. O’Toole, J. C., & Moya, T. B. (1978). Genotypic variation in maintenance of leaf water potential. Crop Science, 18, 873–876.

    Article  Google Scholar 

  16. Price, A. H., Cairns, J. E., Horton, P., Jones, H. G., & Griffiths, H. (2002). Linking drought-resistance mechanisms to drought avoidance in upland rice using a QTL approach: Progress and new opportunities to integrate stomatal and mesophyll responses. Journal of Experimental Botany, 53, 989–1004.

    Article  CAS  Google Scholar 

  17. Singh, B. N., & Mackill, D. J. (1991). Genetics of leaf rolling under drought stress. In Rice genetics II (pp. 159–166). Manila: IRRI.

  18. Lafitte, R. (2003). Managing water for controlled drought in breeding plots. In K. S. Fischer, R. Lafitte, S. Fukai, G. Atlin, & B. Hardy (Eds.) Breeding rice for drought-prone environments (pp. 23–26). Los Banos: IRRI.

  19. Khowaja, F. S., & Price, A. H. (2008). QTL mapping rolling, stomatal conductance and dimension traits of excised leaves in the Bala × Azucena recombinant inbred population of rice. Field Crops Research, 106, 248–257.

    Article  Google Scholar 

  20. Mohan, M., Nair, S., Bhagwat, A., Krishna, T. G., Masahiro, Y., Bhatia, C. R., et al. (1997). Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular Breeding, 3, 87–103.

    Article  CAS  Google Scholar 

  21. Sun, Y., Wang, J., Crouch, J. H., & Xu, Y. (2010). Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement. Molecular Breeding, 26, 493–511.

    Article  Google Scholar 

  22. Navabi, A., Mather, D. E., Bernier, J., Spaner, D. M., & Atlin, G. N. (2009). QTL detection with bidirectional and unidirectional selective genotyping: Marker-based and trait-based analyses. Theoretical and Applied Genetics, 118, 347–358.

    Article  Google Scholar 

  23. Michelmore, R. W., Paranand, I., & Kessele, R. V. (1991). Identification of markers linked to disease resistance genes by bulk segregant analysis: A rapid method to detect markers in specific genome using segregant population. Proceedings of the National Academy of Science, 88, 9828–9832.

    Article  CAS  Google Scholar 

  24. Venuprasad, R., Dalid, C. O., Del Valle, M., Zhao, D., Espiritu, M., Sta Cruz, M. T., et al. (2009). Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis. Theoretical and Applied Genetics, 120, 177–190.

    Article  Google Scholar 

  25. Wang, G. L., & Paterson, A. H. (1994). Assessment of DNA pooling strategies for mapping of QTLs. Theoretical and Applied Genetics, 88, 355–361.

    Google Scholar 

  26. Altinkut, A., Kazan, K., & Gozukirmizi, N. (2003). AFLP markers linked to water-stress-tolerant bulks in barley. Genetics and Molecular Biology, 26, 77–82.

    Article  CAS  Google Scholar 

  27. Altinkut, A., & Gozukirmizi, N. (2003). Search for microsatellites associated with water stress tolerance in wheat through bulked segregant analysis. Molecular Biotechnology, 23, 97–106.

    Article  CAS  Google Scholar 

  28. Quarrie, S. A., Lazic-Jancic, V., Kovacevic, D., Steed, A., & Pekic, S. (1999). Bulked segregant analysis with molecular markers and its use for improving drought resistance in maize. Journal of Experimental Botany, 50, 1299–1306.

    Article  CAS  Google Scholar 

  29. Shashidar, H. E., Vinod, M. S., Naveen, S., Sharma, G. V., & Krishnamurthy, K. (2005). Markers linked to grain yield using bulk segregant analysis approach in rice (Oryza sativa L.). Rice Genetics Newsletter, 22, 69–71.

    Google Scholar 

  30. Gomez, S. M., Boopathi, N. M., Kumar, S. S., Ramasubramanian, T., Chengsong, Z., Jeyaprakash, P., et al. (2010). Molecular mapping and location of QTLs for drought-resistance traits in indica rice lines adapted to target environments. Acta Physiologiae Plantarum, 32, 355–364.

    Article  Google Scholar 

  31. Kanagaraj, P., Prince, K. S. J., Sheeba, J. A., Biji, K. R., Paul, S. B., Senthil, A., et al. (2010). Microsatellite markers linked to drought resistance in rice (Oryza sativa L.). Current Science, 98(6), 836–839.

    CAS  Google Scholar 

  32. 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 Science, 47, 505–516.

    Article  Google Scholar 

  33. Babu, R. C., Shashidhar, H. E., Lilley, J. M., Thanh, N. D., Ray, J. D., Sadasivam, S., et al. (2001). Variation in root penetration ability, osmotic adjustment and dehydration tolerance among accessions of rice adapted to rainfed lowland and upland ecosystems. Plant Breeding, 120, 233–238.

    Article  Google Scholar 

  34. Gawel, N. J., & Jarret, R. L. (1991). A modified CTAB DNA extraction procedure for musa and ipomoea plant. Molecular Biology Reports, 9, 262–266.

    Article  CAS  Google Scholar 

  35. McCouch, S. R., Teytelman, L., Xu, Y., Lobos, K. B., Clare, K., Walton, M., et al. (2002). Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research, 9, 199–207.

    Article  CAS  Google Scholar 

  36. Sambrook, J., & Russell, D. W. (2006). Detection of DNA in agarose gels. Cold Spring Harbor Protocols. doi:10.1101/pdb.prot4022.

  37. Kumari, S., Sheba, J. M., Marappan, M., Ponnusamy, S., Seetharaman, S., Pothi, N., et al. (2010). Screening of IR50 × Rathu Heenati F7 RILs and identification of SSR Markers linked to brown planthopper (Nilaparvata lugens Stal) resistance in rice (Oryza sativa L.). Molecular Biotechnology, 46, 63–71.

    Article  CAS  Google Scholar 

  38. Steele, K. A., Edwards, G., Zhu, J., & Witcombe, J. R. (2004). Maker-evaluated selection in rice: Shifts in allele frequency among bulks selected in contrasting agricultural environments identify genomic regions of importance to rice adaptation and breeding. Theoretical and Applied Genetics, 109, 1247–1260.

    Article  CAS  Google Scholar 

  39. Khowaja, F. S., Norton, G. J., Courtois, B., & Price, A. H. (2009). Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genomics, 10, 276–290.

    Article  Google Scholar 

  40. Venuprasad, R., Bool, M. E., Dalid, C. O., Bernier, J., Kumar, A., & Atlin, G. N. (2009). Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population. Euphytica, 167, 261–269.

    Article  CAS  Google Scholar 

  41. Zhao, X. Q., Xu, J. L., Zhao, M., Lafitte, R., Zhu, L. H., Fu, B. Y., et al. (2008). QTLs affecting morph-physiological traits related to drought tolerance detected in overlapping introgression lines of rice (Oryza sativa L.). Plant Science, 174, 618–625.

    Article  CAS  Google Scholar 

  42. Subashri, M., Robin, S., Vinod, K. K., Rajeswari, S., Mohanasundaram, K., & Raveendran, T. S. (2009). Trait identification and QTL validation for reproductive stage drought resistance in rice using selective genotyping of near flowering RILs. Euphytica, 166, 291–305.

    Article  Google Scholar 

  43. Qu, Y., Ping, M., Hongliang, Z., Chen, Y., Gao, Y., Tian, Y., et al. (2008). Mapping QTLs of root morphological traits at different growth stages in rice. Genetica, 133, 187–200.

    Article  Google Scholar 

  44. Liu, G., Mei, H., Liu, H., Yu, X., Zou, G., & Luo, L. (2010). Sensitivities of rice grain yield and other panicle characters to late-stage drought stress revealed by phenotypic correlation and QTL analysis. Molecular Breeding, 25, 603–613.

    Article  CAS  Google Scholar 

  45. Courtois, R., Ahmadi, N., Khowaja, F., Price, A. H., Rami, J. H., Frouin, J., et al. (2009). Rice root architecture: Meta analysis from a drought QTL database. Rice, 2, 115–128.

    Article  Google Scholar 

  46. Hubner, N., Wallace, C. A., & Zimdahl, H. (2005). Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics, 37, 243–253.

    Article  CAS  Google Scholar 

  47. Zhu, M., & Zhao, S. (2007). Candidate Gene Identification Approach: Progress and Challenges. International Journal of Biological Sciences, 3(7), 420–427.

    CAS  Google Scholar 

  48. Zheng, B. S., Yang, L., Zhang, W. P., Mao, C. Z., & Wu, Y. R. (2003). Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations. Theoretical and Applied Genetics, 107, 1505–1515.

    Article  CAS  Google Scholar 

  49. Zheng, B. S., Mao, C. Z., Zhang, W. P., & Wu, Y. R. (2006). QTLs and candidate genes for rice root growth under flooding and upland conditions. Acta Genetica Sinica, 33(2), 33141–33151.

    Article  Google Scholar 

  50. Xiong, L. (2009). Drought frontiers in rice—Crop improvement for increased rainfed production. Singapore: World Scientific Publishing Co. Pte. Ltd.

    Google Scholar 

  51. Yano, M., Kojima, S., Takahashi, Y., Lin, H., & Sasaki, T. (2001). Genetic control of flowering time in rice, a short day plant. Plant Physiology, 127, 1425–1429.

    Article  CAS  Google Scholar 

  52. Jian, X., Zhang, L., Li, G., Zhang, L., Wang, X., Cao, X., et al. (2010). Identification of novel stress-regulated microRNAs from Oryza sativa. Genomics, 95, 47–55.

    Article  CAS  Google Scholar 

  53. Malamy, J. E. (2005). Intrinsic and environmental response pathways that regulate root system architecture. Plant Cell and Environment, 28, 67–77.

    Article  CAS  Google Scholar 

  54. Nibau, C., Gibbs, D. J., & Coates, J. C. (2008). Branching out in new directions: The control of root architecture by lateral root formation. New Phytologist, 179(3), 595–614.

    Article  CAS  Google Scholar 

  55. Rebouillat, J., Dievart, A., Verdeil, J. L., Escoute, J., Giese, E., & Breitler, J. C. (2008). Molecular genetics of rice root development. Rice, 2(1), 15–34.

    Article  Google Scholar 

  56. Norton, G. J., Aitkenhead, M. J., Khowaja, F. S., Whalley, W. R., & Price, A. H. (2008). A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping; an example using rice root-growth QTLs. Genomics, 92, 344–352.

    Article  CAS  Google Scholar 

  57. Larmande, P., Gay, C., Lorieux, M., Perin, C., Bouniol, M., & Droc, G. (2008). Oryza Tag Line, a database for the phenotypic characterization of the genoplante rice insertion line library. Nucleic Acids Research, 36, 1022–1027.

    Article  Google Scholar 

  58. Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., et al. (2007). The TIGR Genome Annotation Resource: Improvements and new features. Nucleic Acids Research, 35, 883–887.

    Article  Google Scholar 

  59. Thongjuea, S., Ruanjaichon, V., Bruskiewich, R., & Vanavichit, A. (2009). Rice Gene Thresher: A web-based application for mining genes underlying QTL in rice genome. Nucleic Acids Research, 638, 1–5.

    Google Scholar 

  60. Shen, L., Courtois, B., McNally, K. L., Robin, S., & Li, Z. (2001). Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theoretical and Applied Genetics, 103, 75–83.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore, 641003, India

    Arvindkumar Shivaji Salunkhe, R. Poornima, K. Silvas Jebakumar Prince, P. Kanagaraj, J. Annie Sheeba, K. Amudha, K. K. Suji, A. Senthil & R. Chandra Babu

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  1. Arvindkumar Shivaji Salunkhe
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  2. R. Poornima
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  3. K. Silvas Jebakumar Prince
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  4. P. Kanagaraj
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  5. J. Annie Sheeba
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  6. K. Amudha
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  8. A. Senthil
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  9. R. Chandra Babu
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Correspondence to R. Chandra Babu.

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Salunkhe, A.S., Poornima, R., Prince, K.S.J. et al. Fine Mapping QTL for Drought Resistance Traits in Rice (Oryza sativa L.) Using Bulk Segregant Analysis. Mol Biotechnol 49, 90–95 (2011). https://doi.org/10.1007/s12033-011-9382-x

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