Browse > Article
http://dx.doi.org/10.5423/PPJ.OA.06.2014.0054

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)
Publication Information
The Plant Pathology Journal / v.31, no.1, 2015 , pp. 12-24 More about this Journal
Abstract
Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1-24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes.
Keywords
blast; marker assisted selection; resistance genes; rice; SSR markers;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
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