Molecular Screening of Blast Resistance Genes in Rice using SSR Markers |
Singh, A.K.
(Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University)
Singh, P.K. (Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University) Arya, Madhuri (Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University) Singh, N.K. (National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute) Singh, U.S. (STRASA-IRRI-India Office, Rajendra Place, 9th Floor, Aggrawal Corporate Tower) |
1 | Lin, F., Chen, S., Que, Z., Wang, L., Liu, X. and Pan, Q. 2007. The blast resistance gene Pi37 encodes a nucleotide binding siteleucine-rich repeat proteinand is a member of a resistance gene cluster on rice chromosome 1. Genetics 177:1871-1880. DOI ScienceOn |
2 | Liu, B., Zhang, S. H., Zhu, X. Y., Yang, Q. Y., Wu, S. Z., Mei, M. T., Mauleon, R., Leach, J., Mew, T. and Leung, H. 2004. Cadidate defense genes as predictors of quantitative blast resistance in rice. Mol. Plant-Microbe Interact. 17:1146-1152. DOI ScienceOn |
3 | Liu, J., Wang, X., Mitchell, T., Hu, Y., Liu, X., Dai, L. and Wang, G. L. 2010. Recent progress and understanding of the molecular mechanisms of the rice Magnaporthe oryzae interaction. Mol. Plant Pathol. 11:419-427. DOI ScienceOn |
4 | Liu, X. Q., Wang, L., Chen, S., Lin, F. and Pan, Q. H. 2005. Genetic and physical mapping of Pi36(t), a novel rice blast resistance gene located on rice chromosome 8. Mol. Genet. Genomics 274:394-401. DOI |
5 | Liu, X., Lin, F., Wang, L. and Pan, Q. 2007. The in silico map-based cloning of Pi36, a rice coiled-coil nucleotide-binding site leucine-rich repeat gene that confers race-specific resistance to the blast fungus. Genetics 176:2541-2549. DOI ScienceOn |
6 | Mackill, D. J. and Bonman, J. M. 1992. Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology 82:746-749. DOI |
7 | Okuyama, Y., Kanzaki, H., Abe, A., Yoshida, K., Tamiru, M., Saitoh, H., Fujibe, T., Matsumura, H., Shenton, M., Galam, D. C., Undan, J., Ito, A., Sone, T. and Terauchi, R. 2011. A multi-faceted genomics approach allows the isolation of rice Pia blast resistance gene consisting of two adjacent NBS-LRR protein genes. Plant J. 66:467-479. DOI ScienceOn |
8 | Qu, S., Liu, G., Zhou, B., Bellizzi, M., Zeng, L., Dai, L., Han, B. and Wang, G. L. 2006. The broad spectrum blast resistance gene Pi9 encodes a nucleotide-binding site leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901-1914. DOI |
9 | Roy-Chowdhury, M., Jia, Y., Jackson, A., Jia, M. H., Fjellstrom, R. and Cartwright, R. 2012a. Analysis of rice blast resistance gene Pi-z using pathogenicity assays and DNA markers. Euphytica 184:35-47. DOI |
10 | Roy-Chowdhury, M., Jia, Y., Jia, M. H., Fjellstrom, B. and Cartwright, R. 2012b. Identification of the rice blast resistance gene Pib in the national small grains collection. Phytopathology 102:700-706. DOI ScienceOn |
11 | Shang, J., Tao, Y., Chen, X., Zou, Y., Lei, C., Wang, J., Li, X., Zhao, X., Zhang, M., Lu, Z., Xu, J., Cheng, Z., Wan, J. and Zhu, L. 2009. Identification of a new rice blast resistance gene Pid3 by genome-wide comparison of paired nucleotidebinding site-leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 182:1303-1311. DOI ScienceOn |
12 | Sharma, T. R., Madhav, M. S., Singh, B. K., Shanker, P., Jana, T. K., Dalal, V., Pandit, A., Singh, A., Gaikwad, K., Upreti H. C. and Singh, N. K. 2005. High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea. Mol. Genet. Genomics 274:569-578. DOI |
13 | Sharma, T. R., Rai, A. K., Gupta, S. K., Vijayan, J., Devanna, B. N. and Ray, S. 2012. Rice blast management through host-plant resistance: retrospect and prospects. Agric. Res. 1:37-52. DOI |
14 | Shikari, A. B., Khanna, A., Krishnan, S. G., Singh, U. D., Rathour, R., Tonapi, V., Sharma, T. R., Nagarajan, M., Prabhu, K. V. and Singh, A. K. 2013. Molecular analysis and phenotypic validation of blast resistance genes Pita and Pita2 in landraces of rice (Oryza sativa L.). Indian J. Genet. 73:131-141. |
15 | Valent, B. 1990. Rice blast as a model system for plant pathology. Phytopathology 80:33-36. DOI |
16 | Takahashi, A., Hayashi, N., Miyao, A. and Hirochika, H. 2010. Unique features of the rice blast resistance Pish locus revealed by large scale retrotransposon-tagging. BMC Plant Biol. 10:175. DOI ScienceOn |
17 | Tang, J., Zhu, X., Wang, Y., Liu, L., Xu, B., Li, F., Fang, J. and Chu, C. 2011. Semi-dominant mutations in the CC-NB-LRR-type R gene, NLS1, lead to constitutive activation of defense responses in rice. Plant J. 66:996-1007. DOI ScienceOn |
18 | Tanksley, S. D. and Mc-Couch, S. R. 1997. Seeds banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063-1066. DOI ScienceOn |
19 | Variar, M., Vera, C. C. M., Carrillo, M. G., Bhatt, J. C. and Sangar, R. B. S. 2009. Rice blast in India and strategies to develop durably resistant cultivars. In: Xiaofan, W. and Valent, B. (eds). Advances in genetics, genomics and control of rice blast disease. Springer, New York, 359-374 pp. |
20 | Wang, C., Hirano, K. and Kawasaki, S. 2002. Cloning of Pita-2 in the centromeric region of chr-12 with HEGS: high efficiency genome scanning. Third International Rice Blast Conference. 25 p. |
21 | Wang, X., Fjellstrom, R. G., Jia, Y., Yan, W., Jia, M. H., Scheffer, B. E., Wu, D., Shu, Q. and Mc-Clung, A. M. 2010. Characterization of Pita blast resistance gene in an international rice core collection. Plant Breed. 129:491-501. |
22 | Wang, Z. X., Yano, M., Yamanouchi, U., Iwamoto, M., Monna, L., Hayasaka, H., Katayose, Y. and Sasaki, T. 1999. The Pib gene for rice blast resistance belongs to the nucleotide-binding and leucine-rich repeat class of plant disease resistance genes. Plant J. 19:55-64. DOI ScienceOn |
23 | Yuan, B., Zhai, C., Wang, W., Zeng, X., Xu, X., Hu, H., Lin, F., Wang, L. and Pan, Q. 2011. The Pik-p resistance to Magnaporthe oryzae in rice is mediated by a pair of closely linked CC-NBSLRR genes. Theor. Appl. Genet. 122:1017-1028. DOI |
24 | Xiao, W. M., Yang, Q. Y., Wang, H., Guo, T., Liu, Y. Z., Zhu, X. Y. and Chen, Z. Q. 2010. Identification and fine mapping of a resistance gene to Magnaporthe oryzae in a space-induced rice mutant. Mol. Breed. 28:303-312. |
25 | Yan, W., Rutger, J. N., Bockelman, H. E., Fjellstrom, R. G., Chen, M. H., Tai, T. and Mc-Clung, A. M. 2007. Development and evaluation of a core subset of the USDA rice (Oryza sativa L.) germplasm collection. Crop Sci. 47:869-878. DOI ScienceOn |
26 | Yang, J. Y., Chen, S., Zeng, L. X., Li, Y. L., Chen, Z., Li, C. Y. and Zhu, X. Y. 2008. Race specificity of major rice blast resistance genes to Magnaporthe grisea isolates collected from indica rice in Guangdong. Rice Sci. 15:311-318. DOI ScienceOn |
27 | Zhai, C., Lin, F., Dong, Z., He, X., Yuan, B., Zeng, X., Wang, L. and Pan, Q. 2011. The isolation and characterization of Pik, a rice blast resistance gene which emerged after rice domestication. New Phytol. 189:321-334. DOI ScienceOn |
28 | Zhou, B., Qu, S., Liu, G., Dolan, M., Sakai, H., Lu, G., Bellizzi, M. and Wang, G. L. 2006. The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea. Mol. Plant-Microbe Interact. 19:1216-1228. DOI ScienceOn |
29 | Zhu, M., Wang, L. and Pan, Q. H. 2004. Identification and characterization of a new blast resistance gene located on rice chromosome 1 through linkage and differential analyses. Phytopathology 94:515-519. DOI ScienceOn |
30 | Ashikawa, I., Hayashi, N., Yamane, H., Kanamori, H., Wu, J., Matsumoto, T., Ono, K. and Yano, M. 2008. Two adjacent nucleotide- binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance. Genetics 180:2267-2276. DOI ScienceOn |
31 | Ballini, E., Morel, J. B., Droc, G., Price, A., Courtois, B., Notteghem, J. L. and Tharreau, D. 2008. A genome-wide metaanalysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol. Plant-Microbe Interact. 21:859-868. DOI ScienceOn |
32 | Barman, S. R., Gowda, M., Venu, R. C. and Chattoo, B. B. 2004. Identification of a major blast resistance gene in the rice cultivar Tetep. Plant Bleed. 123:300-302. |
33 | Berruyer, R., Adreit, H., Milazzo, J., Gaillard, S., Berger, A., Dioh, W., Lebrun, M. H. and Tharreau, D. 2003. Identification and fine mapping of Pi33, the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1. Theor. Appl. Genet. 107:1139-1147. DOI |
34 | Bryan, G. T., Wu, K. S., Farrall, L., Jia, Y. L., Hershey, H. P., Mc-Adams, S. A., Faulk, K. N., Donaldson, G. K., Tarchini, R. and Valent, B. 2000. A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant Cell 12:2033-2045. DOI |
35 | Chauhan, S., Farman, M. L., Zhang H. B. and Leong, N. 2002. Genetic and physical mapping of a rice blast resistance locus, PiCO39(t), that corresponds to the avirulence gene AVR1- CO39 of Magnaporthe grisea. Mol. Genet. Genomics 267:603-612. DOI |
36 | Chen, J., Shi, Y., Liu, W., Chai, R., Fu, Y., Zhuang, J. and Wu, J. 2011. A Pid3 allele from rice cultivar Gumei-2 confers resistance to Magnaporthe oryzae. J. Genet. Genomics 38:209-216. DOI ScienceOn |
37 | Cuong, N. M., Lang, T. and Buu, B. C. 2006. Applications of microsatellite and sequence tagged site marker to detect blast resistance in local rice (Oryza sativa L.). Hanoi: Nong Nghiep. 52-68 pp. |
38 | Chen, M., Presting, G. and Barbazuk, W. B. 2002. An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545. DOI |
39 | Chen, X., Shang, J., Chen, D., Lei, C., Zou, Y., Zhai, W., Liu, G., Xu, J., Ling, Z., Cao, G., Ma, B., Wang, Y., Zhao, X., Li, S. and Zhu, L. 2006. A B-lectin receptor kinase gene conferring rice blast resistance. Plant J. 46:794-804. DOI ScienceOn |
40 | Cho, Y. C., Jeung, J. U., Park, H. J., Yang, C. I., Choi, Y. H., Choi, I. B., Won, Y. J., Yang, S. J. and Kim, Y. G. 2008. Haplotype diversity and durability of resistance genes to blast in Korean Japonica rice varieties. J. Crop Sci. Biotech. 11:205-214. |
41 | Das, A., Soubam, D., Singh, P. K., Thakur, S., Singh, N. K. and Sharma, T. R. 2012. A novel blast resistance gene, Pi54rh cloned from wild species of rice, Oryza rhizomatis confers broad spectrum resistance to Magnaporthe oryzae. Funct. Integr. Genomics 12:215-228. DOI ScienceOn |
42 | Doyle, J. J. and Doyle, J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:11-15. |
43 | Eizenga, G. C., Agrama, H. A., Lee, F. N., Yan, W. G. and Jia, Y. 2006. Identification of novel resistance genes in newly introduced blast resistance rice germplasm. Crop Sci. 46:1870-1878. DOI ScienceOn |
44 | Fjellstrom, R., Mc-Clung, A. M. and Shank, A. R. 2006. SSR markers closely linked to the Pi-z locus are useful for selection of blast resistance in a broad array of rice germplasm. Mol. Breed. 17:149-157. DOI |
45 | Han, S. S., Ryu, J. D., Shim, H. S., Lee, S. W., Hong, Y. K. and Cha, K. H. 2001. Breakdown of resistant cultivars by new race KI-1117a and race distribution of rice blast fungus during 1999-2000 in Korea. Res. Plant Dis. 7:86-92. |
46 | Fuentes, J. L., Correa-Victiria, F. J., Escobar, F., Prado, G., Aricapa, G., Duque, M. C. and Tohme, J. 2007. Identification of microsatellite markers linked to the blast resistance gene Pi-1(t) in rice. Euphytica 160:295-304. |
47 | Fukuoka, S., Saka, N., Koga, H., Ono, K., Shimizu, T., Ebana, K., Hayashi, N., Takahashi, A., Hirochika, H., Okuno, K. and Yano, M. 2009. Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325:998-1001. DOI ScienceOn |
48 | Gu, K., Yang, B., Tian, D., Wu, L., Wang, D., Sreekala, C., Yang, F., Chu, Z., Wang, G. L., White, F. F. and Yin, Z. 2005. R gene expression induced by type-III effecter triggers disease resistance in rice. Nature 435:1122-1125. DOI ScienceOn |
49 | Hayashi, K. and Yoshida, H. 2009. Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter. Plant J. 57:413-425. DOI ScienceOn |
50 | Hayashi, K., Yoshida, H. and Ashikawa, I. 2006. Development of PCR-based allele specific and InDel marker sets for nine rice blast resistance genes. Theor. Appl. Genet. 113:251-260. DOI |
51 | Hayashi, N., Inoue, H., Kato, T., Funao, T., Shirota, M., Shimizu, T., Kanamori, H., Yamane, H., Hayano-Saito, Y., Matsumoto, T., Yano, M. and Takatsuji, H. 2010. Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication. Plant J. 64:498-510. DOI ScienceOn |
52 | Jia, Y., Bryan, G. T., Farrall, L. and Valent, B. 2003. Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93:1452-1459. DOI ScienceOn |
53 | Hittalmani, S., Parco, T. A., Mew, T. V. and Zeigler, R. S. 2000. Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor. Appl. Genet. 100:1121-1128. DOI |
54 | Huang, H., Huang, L., Feng, G., Wang, S., Wang, Y., Liu, J., Jiang, N., Yan, W., Xu, L., Sun, P., Liu, Z., Pan, S., Liu, X., Xiao, Y., Liu, E., Dai, L. and Wang, G. 2010. Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi 3150. Phytopathology 101:620-626. |
55 | Imam, J., Alam, S., Mandal, N. P., Variar, M. and Shukla, P. 2014. Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers. Euphytica 196:199-211. DOI ScienceOn |
56 | Kim, J. S., Ahn, S. N., Kim, C. K. and Shim, C. K. 2010. Screening of rice blast resistance genes from aromatic rice germplasms with SNP markers. Plant Pathol. J. 26:70-79. DOI ScienceOn |
57 | Lee, S. K., Song, M. Y., Seo, Y. S., Kim, H. K., Ko, S., Cao, P. J., Suh, J. P., Yi, G., Roh, J. H., Lee, S., An, G., Hahn, T. R., Wang, G. L., Ronald, P. and Jeon, J. S. 2009. Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coilnucleotide- binding-leucine-rich repeat genes. Genetics 181:1627-1638. DOI ScienceOn |
58 | Li, Y. B., Wu, C. J., Jiang, G. H., Wang, L. Q. and He, Y. Q. 2007. Dynamic analyses of rice blast resistance for the assessment of genetic and environmental effects. Plant Breed. 126:541-547. DOI ScienceOn |