Combining In Silico Mapping and Arraying: an Approach to Identifying Common Candidate Genes for Submergence Tolerance and Resistance to Bacterial Leaf Blight in Rice

  • Kottapalli, Kameswara Rao (Plant Genome Research Unit, National Institute of Agrobiological Sciences) ;
  • Satoh, Kouji (Plant Genome Research Unit, National Institute of Agrobiological Sciences) ;
  • Rakwal, Randeep (Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST) West) ;
  • Shibato, Junko (Plant Genome Research Unit, National Institute of Agrobiological Sciences) ;
  • Doi, Koji (Plant Genome Research Unit, National Institute of Agrobiological Sciences) ;
  • Nagata, Toshifumi (Plant Genome Research Unit, National Institute of Agrobiological Sciences) ;
  • Kikuchi, Shoshi (Plant Genome Research Unit, National Institute of Agrobiological Sciences)
  • 투고 : 2007.06.07
  • 심사 : 2007.07.03
  • 발행 : 2007.12.31

초록

Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 93-11 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region [Kottapalli et al. (2006)]. Transcriptional profiling of FR13A and IET8585 using a rice 22K oligo array validated the above findings. Based on in silico analysis and arraying we observed that both cultivars respond to the above stresses through a common signaling system involving protein kinases, adenosine mono phosphate kinase, leucine rich repeat, PDZ/DHR/GLGF, and response regulator receiver protein. The combined approaches suggest that transcription factor EREBP on long arm of chromosome 5 regulates both submergence tolerance and blb resistance. Pyruvate decarboxylase and alcohol dehydrogenase, co-located in the same region, are candidate downstream genes for submergence tolerance at the seedling stage, and t-snare for bs-blb resistance. We also detected up-regulation of novel defense/stress-related genes including those encoding fumaryl aceto acetate (FAA) hydrolase, scramblase, and galactose oxidase, in response to the imposed stresses.

키워드

참고문헌

  1. Altman, N. (2005) Replication, variation and normalization in microarray experiments. Applied Bioinformatics 4, 33-44 https://doi.org/10.2165/00822942-200504010-00004
  2. Coego, A., Ramirez, V., Gil, M. J., Flors, V., Mauch-Mani, B., et al. (2005) An Arabidopsis homeodomain transcription factor, overexpressor of cationic peroxidase 3, mediates resistance to infection by necrotrophic pathogens. Plant Cell 17, 2123- 2137 https://doi.org/10.1105/tpc.105.032375
  3. Collins, N. C., Thordal-Christensen, H., Lipka, V., Bau, S., Kombrink, E., et al. (2003) SNARE-protein-mediated disease resistance at the plant cell wall. Nature 425, 973-977 https://doi.org/10.1038/nature02076
  4. Fukao, T. and Bailey-Serres, J. (2004) Plant responses to hypoxia-- is survival a balancing act? Trends in Plant Sci. 9, 449-456 https://doi.org/10.1016/j.tplants.2004.07.005
  5. Gutterson, N. and Reuber, T. (2004) Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7, 465-471 https://doi.org/10.1016/j.pbi.2004.04.007
  6. Hammond-Kosack, K. E. and Jones, J. D. G. (1996) Resistance gene-dependent plant defense responses. Plant Cell 8, 1773- 1791 https://doi.org/10.1105/tpc.8.10.1773
  7. Jakoby, M., Weisshaar, B., Droge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., et al. (2002) bZIP transcription factors in Arabidopsis. Trends Plant Sci. 7, 106-111 https://doi.org/10.1016/S1360-1385(01)02223-3
  8. Kameswara Rao, K., Lakshminarasu, M., and Jena, K. K. (2002) DNA markers and marker-assisted breeding for durable resistance to bacterial blight disease in rice. Biotechnol. Adv. 20, 33-47 https://doi.org/10.1016/S0734-9750(02)00002-2
  9. Kameswara Rao, K., Jena, K. K., and Lakshminarasu, M. (2003) Molecular tagging of a new bacterial blight resistance gene in rice using RAPD and SSR markers. International Rice Research Notes 20, 16-17
  10. Kauffman, H. E., Reddy, A. P. K., Hsieh, S. P. Y., and Merca, S. D. (1973) An improved technique for evaluation of rice varieties to Xanthomonas oryzae. Plant Disease Report 57, 537-541
  11. Kikuchi, S., Satoh, K., Nagata, T., Kawagashira, N., Doi, K., et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301, 376- 379 https://doi.org/10.1126/science.1081288
  12. Kottapalli, K. R. (2004) Molecular mapping and pyramiding bacterial blight resistance genes into the rice cultivar 'Samba Mashuri' using DNA markers. Ph.D. Thesis, Jawaharlal Nehru Technology University, Hyderabad, India
  13. Kottapalli, K. R., Sarla, N., and Kikuchi, S. (2006) In silico insight into two rice chromosomal regions associated with submergence tolerance and resistance to bacterial leaf blight and gall midge. Biotechnol. Adv. 24, 561-589 https://doi.org/10.1016/j.biotechadv.2006.05.003
  14. Kroymann, J. and Mitchell-Olds, T. (2005) Epistasis and balanced polymorphism influencing complex trait variation. Nature 435, 95-98 https://doi.org/10.1038/nature03480
  15. Lee, S. W., Han, S. W., Bartley, L. E., and Ronald, P. C. (2006) Unique characteristics Xanthomonas oryzae pv. oryzae AvrXa21 and implications for plant innate immunity. Proc. Natl. Acad. Sci. USA 103, 18395-18400
  16. Martin-Magniette, M. L., Aubert, J., Cabannes, E., and Daudin, J. J. (2005) Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 21, 1995-2000 https://doi.org/10.1093/bioinformatics/bti302
  17. Ponting, C. P. (1997) Evidence for PDZ domains in bacteria, yeast, and plants. Protein Sci. 6, 464-468 https://doi.org/10.1002/pro.5560060225
  18. Ponting, C. P., Phillips, C., Davies, K. E., and Blake, D. J. (1997) PDZ domains: targeting signalling molecules to sub-membranous sites. Bioassays 19, 469-479 https://doi.org/10.1002/bies.950190606
  19. Rosenzweig, B. A., Pine, P. S., Domon, O. E., Morris, M., Chen, J. J., et al. (2004) Dye bias correction in dual-labeled cDNA microarray gene expression measurements. Environ. Health Perspect. 112, 480-487 https://doi.org/10.1289/ehp.6694
  20. Shanti, M. L., George, M. L. C., Vera Cruz, C. M., Bernardo, M. A., Nelson, R. J., et al. (2001) Identification of resistance genes effective against rice bacterial blight pathogen in Eastern India. Plant Disease 85, 506-512 https://doi.org/10.1094/PDIS.2001.85.5.506
  21. Shimizu, T., Satoh, K., Kikuchi, S., and Omura, T. (2006) The repression of cell wall- and plastid-related genes and the induction of defense-related genes in rice plants infected with Rice dwarf virus. Mol. Plant-Microbe Interact. 20, 247-254 https://doi.org/10.1094/MPMI-20-3-0247
  22. Sinagliw, M., Toojinda, T., Trangoonrung, S., and Vanavichit, A. (2003) Thai jasmine rice carrying QTLch9 (Sub QTL) is submergence tolerant. Ann. Bot. 91, 255-261 https://doi.org/10.1093/aob/mcf123
  23. Toojinda, T., Siangliw, M., Tragoonrung, S., and Vanavichit, A. (2003) Molecular genetics of submergence tolerance in rice: QTL analysis of key traits. Ann. Bot. 91, 243-253 https://doi.org/10.1093/aob/mcf072
  24. Tron, A. E., Bertoncini, C. W., Chan, R. L., and Gonzalez, D. H. (2002) Redox regulation of plant homeodomain transcription factors. J. Biol. Chem. 277, 34800-34807 https://doi.org/10.1074/jbc.M203297200
  25. Van Zhong, G. and Burns, J. (2003) Profiling ethylene-regulated gene expression in Arabidopsis thaliana by microarray analysis. Plant Mol. Biol. 53, 117-131 https://doi.org/10.1023/B:PLAN.0000009270.81977.ef
  26. Wang, K., Li, H., and Ecker, J. (2002) Ethylene biosynthesis and signaling networks. Plant Cell 14, 153-164 https://doi.org/10.1105/tpc.000679
  27. Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., et al. (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442, 705- 708 https://doi.org/10.1038/nature04920
  28. Xu, K. N. and Mackill, D. J. (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Mol. Breeding 2, 219-224 https://doi.org/10.1007/BF00564199
  29. Yazaki, J., Shimatani, Z., Hashimoto, A., Nagata, Y., Fujii, F., et al. (2004) Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol. Genomics 17, 87-100 https://doi.org/10.1152/physiolgenomics.00201.2003
  30. Yoshitala, J., Krishnaveni, D., Reddy, A. P. K., and Sonti, R. V. (1997) Genetic diversity within the population of Xanthomonas oryzae pv oryzae in India. Phytopathology 87, 760-765 https://doi.org/10.1094/PHYTO.1997.87.7.760
  31. Zhu, J., Shi, H., Lee, B. H., Damsz, B., Cheng, S., et al. (2004) An Arabidopsis homeodomain transcription factor gene, HOS9, mediates cold tolerance through a CBF-independent pathway. Proc. Natl. Acad. Sci. USA 101, 9873-9878