Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems

Frontiers in Plant Science

Volumn 6, Issue MAY, 2015, Pages

  Dossa, Gerbert S ^a,b   Sparks, Adam ^a   Cruz, Casiana Vera ^a   Oliva, Ricardo ^a  

^a INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

^b LEIBNIZ UNIVERSITY HANNOVER   (Germany)

Author keywords

Customized deployment; Forward breeding; Genome editing; R genes; TAL effectors

Indexed keywords

BACTERIA (MICROORGANISMS); XANTHOMONAS ORYZAE PV. ORYZAE;

EID: 84934872909     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00305     Document Type: Article

References (41)

1. Antony, G., Zhou, J., Huang, S., Li, T., Liu, B., White, F. F., et al. (2010). Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell 22, 3864-3876. doi: 10. 1105/tpc. 110. 078964.
2. Boch, J., Bonas, U., and Lahaye, T. (2014). TAL effectors-pathogen strategies and plant resistance engineering. New Phytol. 204, 823-832. doi: 10. 1111/nph. 13015.
3. Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., et al. (2009). Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509-1512. doi: 10. 1126/science. 1178811.
4. Chen, L. Q., Hou, B. H., Lalonde, S., Takanaga, H., Hartung, M. L., Qu, X. Q., et al. (2010). Sugar transporters for intercellular exchange and nutrition of pathogens. Nature 468, 527-532. doi: 10. 1038/nature09606.
5. Chen, X. L., Yu, L., Gao, L. L., Jiang, T., Li, Q. Y., and Huang, Q. (2012). Elevational variation in diversity of Xanthomonas oryzae pv. oryzae in South-West China. J. Phytopathol. 160, 261-268. doi: 10. 1111/j. 1439-0434. 2012. 01892. x.
6. Choi, S. H., Vera Cruz, C. M., and Leach, J. E. (1998). Distribution of Xanthomonas oryzae pv. oryzae DNA modification systems in Asia. Appl. Environ. Microbiol. 64, 1663-1668.
7. Doyle, E. L., Booher, N. J., Standage, D. S., Voytas, D. F., Brendel, V. P., Van Dyk, J. K., et al. (2012). TAL Effector-Nucleotide Targeter (TALE-NT) 2. 0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40, 117-122. doi: 10. 1093/nar/gks608.
8. Fichtner, F., Castellanos, R. U., and Ülker, B. (2014). Precision genetic modifications: a new era in molecular biology and crop improvement. Planta 239, 921-939. doi: 10. 1007/s00425-014-2029-y.
9. Gawehns, F., Cornelissen, B. J. C., and Takken, F. L. W. (2013). The potential of effector-target genes in breeding for plant innate immunity. Microb. Biotechnol. 6, 223-229. doi: 10. 1111/1751-7915. 12023.
10. Gijzen, M., Ishmael, C., and Shrestha, S. D. (2014). Epigenetic control of effectors in plant pathogens. Front. Plant Sci. 5: 638. doi: 10. 3389/fpls. 2014. 00638.
11. Grau, J., Wolf, A., Reschke, M., Bonas, U., Posch, S., and Boch, J. (2013). Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput. Biol. 9: e1002962. doi: 10. 1371/journal. pcbi. 1002962.
12. Gu, K. Y., Yang, B., Tian, D. S., Wu, L. F., Wang, D. J., Sreekala, C., et al. (2005). R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435, 1122-1125. doi: 10. 1038/nature03630.
13. Gu, K., Tian, D., Qiu, C., and Yin, Z. (2009). Transcription activator-like type III effector AvrXa27 depends on OsTFIIAgamma5 for the activation of Xa27 transcription in rice that triggers disease resistance to Xanthomonas oryzae pv. oryzae. Mol. Plant Pathol. 10, 829-835. doi: 10. 1111/j. 1364-3703. 2009. 00567. x.
14. Hogenhout, S. A., van der Hoorn, R. A. L., Terauchi, R., and Kamoun, S. (2009). Emerging concepts in effector biology of plant-associated organisms. Mol. Plant Microbe Interact. 22, 115-122. doi: 10. 1094/MPMI-22-2-0115.
15. Ismail, A. M., Singh, U. S., Singh, S., Dar, M. H., and Mackill, D. J. (2013). The contribution of submergence tolerant (Sub1) rice variety to food security in flood-prone rainfed areas in Asia. Field Crops Res. 152, 83-93. doi: 10. 1016/j. fcr. 2013. 01. 007.
16. Kay, S., and Bonas, U. (2009). How Xanthomonas type III effectors manipulate the host plant. Curr. Opin. Microbiol. 12, 37-43. doi: 10. 1016/j. mib. 2008. 12. 006.
17. Khan, M. A., Naeem, M., and Iqbal, M. (2014). Breeding approaches for bacterial leaf blight resistance in rice (Oryza sativa L.), current status and future directions. Eur. J. Plant Pathol. 139, 27-37. doi: 10. 1007/s10658-014-0377-x.
18. Li, J. Y., Wang, J., and Zeigler, R. S. (2014). The 3, 000 rice genomes project: new opportunities and challenges for future rice research. GigaScience 3: 8. doi: 10. 1186/2047-217X-3-8.
19. Li, T., Liu, B., Spalding, M. H., Weeks, D. P., and Yang, B. (2012). High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat. Biotechnol. 30, 390-392. doi: 10. 1038/nbt. 2199.
20. Miao, J., Guo, D., Zhang, J., Huang, Q., Qin, G., Zhang, X., et al. (2013). Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res. 23, 1233-1236. doi: 10. 1038/cr. 2013. 123.
21. Mishra, D., Vishnupriya, M. R., Anil, M. G., Konda, K., Raj, Y., and Sonti, R. V. (2013). Pathotype and genetic diversity amongst Indian isolates of Xanthomonas oryzae pv. oryzae. PLoS ONE8: e81996. doi: 10. 1371/journal. pone. 0081996.
22. Moscou, M. J., and Bogdanove, A. J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501. doi: 10. 1126/science. 1178817.
23. Noël, L. D., Denancé, N., and Szurek, B. (2013). Predicting promoters targeted by TAL effectors in plant genomes: from dream to reality. Front. Plant Sci. 4: 333. doi: 10. 3389/fpls. 2013. 00333.
24. Ogawa, T., Yamamoto, T., Khush, G. S., Mew, T. W., and Kaku, H. (1988). Near-isogenic lines as international differentials for resistance to bacterial blight of rice. RGN 5, 106-107.
25. Oliver, R. P., Friesen, T. L., Faris, J. D., and Solomon, P. S. (2012). Stagonospora nodorum: from pathology to genomics and host resistance. Annu. Rev. Phytopathol. 50, 23-43. doi: 10. 1146/annurev-phyto-081211-173019.
26. Pérez-Quintero, A., Rodriguez, R. L., Dereeper, A., Lopez, C., Koebnik, R., Szurek, B., et al. (2013). An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS ONE 8: e68464. doi: 10. 1371/journal. pone. 0068464.
27. Rietman, H., Bijsterbosch, G., Cano, L. M., Lee, H. R., Vossen, J. H., Jacobsen, E., et al. (2012). Qualitative and quantitative late blight resistance in the potato cultivar Sarpo Mira is determined by the perception of five distinct RXLR effectors. Mol. Plant Microbe Interact. 25, 910-919. doi: 10. 1094/MPMI-01-12-0010-R.
28. Römer, P., Recht, S., and Lahaye, T. (2009). A single plant resistance gene promoter engineered to recognize multiple TAL effectors from disparate pathogens. Proc. Natl. Acad. Sci. U. S. A. 106, 20526-20531. doi: 10. 1073/pnas. 0908812106.
29. Savary, S., and Castilla, N. P. (2009). A survey portfolio for the characterization of rice pest constraints. IRRI Discuss. Paper 18, 32.
30. Thomson, J. M. (2014). High-throughput SNP genotyping to accelerate crop improvement. Plant Breed. Biotechnol. 2, 195-212. doi: 10. 9787/PBB. 2014. 2. 3. 195.
31. Tian, D., Wang, J., Zeng, X., Gu, K., Qiu, C., Yang, X., et al. (2014). The rice TAL effector-dependent resistance protein Xa10 triggers cell death and calcium depletion in the endoplasmic reticulum. Plant Cell 26, 497-515. doi: 10. 1105/tpc. 113. 119255.
32. Vleeshouwers, V. G., and Oliver, R. P. (2014). Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens. Mol. Plant Microbe Interact. 27, 196-206. doi: 10. 1094/MPMI-10-13-0313-IA.
33. Vleeshouwers, V. G., Raffaele, S., Vossen, J., Champouret, N., Oliva, R., Segretin, M. E., et al. (2011). Understanding and exploiting late blight resistance in the age of effectors. Annu. Rev. Phytopathol. 49, 507-531. doi: 10. 1146/annurev-phyto-072910-095326.
34. Waltz, E. (2012). Tiptoeing around transgenics. Nat. Biotechnol. 30, 215-217. doi: 10. 1038/nbt. 2143.
35. Wang, C., Zhang, X., Fan, Y., Gao, Y., Zhu, Q., Zheng, C., et al. (2014). Xa23 is an executor R protein and confers broad-spectrum disease resistance in rice. Mol. Plant 8, 290-302. doi: 10. 1016/j. molp. 2014. 10. 010.
36. Yang, B., Sugio, A., and White, F. F. (2006). Os8N3 is a host disease susceptibility gene for bacterial blight of rice. Proc. Natl. Acad. Sci. U. S. A. 103, 10503-10508. doi: 10. 1073/pnas. 0604088103.
37. Yang, B., and White, F. F. (2004). Diverse members of the AvrBs3/PthA family of type III effectors are major virulence determinants in bacterial blight disease of rice. Mol. Plant Microbe Interact. 17, 1192-1200. doi: 10. 1094/MPMI. 2004. 17. 11. 1192.
38. Yuan, M., Chu, Z., Li, X., Xu, C., and Wang, S. (2010). The bacterial pathogen Xanthomonas oryzae overcomes rice defenses by regulating host copper redistribution. Plant Cell 22, 3164-3176. doi: 10. 1105/tpc. 110. 078022.
39. Zhang, F., Zhuo, D. L., Zhang, F., Huang, L. Y., Wang, W. S., Xu, J. L., et al. (2014a). Xa39, a novel dominant gene conferring broad-spectrum resistance to Xanthomonas oryzae pv. oryzae in rice. Plant Pathol. doi: 10. 1111/ppa. 12283 [Epub ahead of print].
40. Zhang, H., Zhang, J., Wei, P., Zhang, B., Gou, F., Feng, Z., et al. (2014b). The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12, 797-807. doi: 10. 1111/pbi. 12200.
41. Zhou, H., Liu, B., Weeks, D. P., Spalding, M. H., and Yang, B. (2014). Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res. 42, 10903-10914. doi: 10. 1093/nar/gku806.