Journal of Genetics

, 98:106 | Cite as

Cataloguing of blast resistance genes in landraces and breeding lines of rice from India

  • PAWAN L. KULWALEmail author
Research Article


The rice blast caused by the fungus Magnaporthe oryzae is one of the most devastating diseases of rice and can lead to complete failure of the crop under severe cases. The first step in breeding for blast resistance in rice is therefore to identify the novel sources of resistance and cataloguing different blast resistant genes in these genotypes. In the present study, a set of 37 rice genotypes comprising of landraces, advanced breeding lines and released varieties were first characterized for blast resistance under epiphytotic conditions and subsequently different blast resistant genes were catalogued with the help of markers tightly linked to these genes. A total of 22 different blast resistant genes were catalogued in these genotypes. Lot of diversity was found to be present for different genes in the rice genotypes studied. In addition, a set of 2–3 markers were identified which could distinguish genotypes of a particular geographic area from each other. The results are useful for identifying the right combination of genotypes in the resistance breeding programme.


leaf blast crop improvement molecular markers gene cataloguing diversity. 



Thanks are due to Rice Pathologist, Agricultural Research Station, Lonavala, District Pune, India for providing facilities for screening of the rice genotypes for blast resistance. Thanks are also due to anonymous reviewer for valuable suggestions.


  1. Ballini E., Morel J. B., Droc G., Price A., Courtois B., Notteghem J. L. and Tharreau D. 2008 A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol. Plant Microbe Interact. 21, 859–868.PubMedCrossRefPubMedCentralGoogle Scholar
  2. 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 Breed. 123, 300–302.CrossRefGoogle Scholar
  3. Berruyer R., Adreit H., Milazzo J., Gaillard S., Berger A., Dioh W., et al. 2003 Identification and fine mapping of Pi33, the rice resistance gene corresponding to the Magnaporthe grisea avirulance gene ACE1. Theor. Appl. Genet. 107, 1139–1147.PubMedCrossRefPubMedCentralGoogle Scholar
  4. Borse V. V., Kulwal P. L., Mhase L. B. and Jadhav A. S. 2017 Validation of seed weight-associated SSR markers and their usefulness in distinguishing chickpea genotypes according to seed size. Agric. Res. 6, 130–138.CrossRefGoogle Scholar
  5. Bradbury P. J., Zhang Z., Kroon D. E., Casstevens T. M., Ramdoss Y. and Buckler E. S. 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635.PubMedCrossRefPubMedCentralGoogle Scholar
  6. Chen X. W., Li S. G., Xu J. C., Zhai W. X., Ling Z. Z., Ma B. T. et al. 2004 Identification of two blast resistance genes in a rice variety, Digu. J. Phytopathol. 152, 77–85.CrossRefGoogle Scholar
  7. Cho Y. C., Jeung J. U., Park H. J., Yang C. I., Choi Y. H., Choi I. B. et al. 2008 Haplotype diversity and durability of resistance genes to blast in Korean Japonica rice varieties. J. Crop Sci. Biotech. 11, 205–214.Google Scholar
  8. 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.Google Scholar
  9. Doyle J. J. and Doyle J. L. 1990 Isolation of plant DNA from fresh tissue. Focus 12, 13–15.Google Scholar
  10. 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.CrossRefGoogle Scholar
  11. Fuentes J. L., Correa-Victoria F. J., Escobar F., Prado G., Aricapa G., Duque M. C. et al. 2008 Identification of microsatellite markers linked to the blast resistance gene Pi1(t) in rice. Euphytica 160, 295–304.CrossRefGoogle Scholar
  12. Fjellstrom R., McClung A. M., Conaway-Bormans C. A., Anna M. M., Marchetti M. A et al. 2004 Development of DNA markers suitable for marker assisted selection of three Pi genes conferring resistance to multiple Pyricularia grisea pathotypes. Crop Sci. 44, 1790–1798.CrossRefGoogle Scholar
  13. Fjellstrom R., McClung 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.CrossRefGoogle Scholar
  14. Gowda M., Barman S. R. and Chattoo B. B. 2006 Molecular mapping of a novel blast resistance gene Pi38 in rice using SSLP and AFLP markers. Plant Breed. 125, 596–599.CrossRefGoogle Scholar
  15. 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.Google Scholar
  16. Hua L., Liang L., He X., Wang L., Zhang W., Liu W. et al. 2015 Development of a marker specific for the rice blast resistance gene Pi39 in the Chinese cultivar Q15 and its use in genetic improvement. Biotechnol. Biotechnol. Equip. 29, 448–456.CrossRefGoogle Scholar
  17. 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.CrossRefGoogle Scholar
  18. Jeung J., Kim B., Cho Y., Han S., Moon H., Lee Y. et al. 2007 A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor. Appl. Genet. 115, 1163–1177.PubMedCrossRefPubMedCentralGoogle Scholar
  19. Koide Y., Kobayashi N., Xu D. and Fukuta Y. 2009 Resistance genes and selection DNA markers for blast disease in rice (Oryza sativa L.). Jpn. Agric. Res. Q. 43, 255–280.CrossRefGoogle Scholar
  20. Koide Y., Telebanco-Yanoria M. J., Dela Peña F., Fukuta Y. and Kobayashi N. 2011 Characterization of rice blast isolates by the differential system and their application for mapping a resistance gene, Pi19(t). J. Phytopathol. 159, 85–93.CrossRefGoogle Scholar
  21. Kulkarni K. and Peshwe S. 2019 Screening, isolation and molecular identification of rice pathogen Magnoporthe oryzae. Int. J. Adv. Res. 7, 428–433.CrossRefGoogle Scholar
  22. Kulwal P. L., Thudi M. and Varshney R. K. 2012 Genomics intervention in crop breeding for sustainable agriculture. In Encyclopedia of sustainability science and technology (ed. R. A. Meyers). Springer, New York.Google Scholar
  23. Kumbhar S. D., Kulwal P. L., Patil J. V., Gaikwad A. P. and Jadhav A. S. 2013 Inheritance of blast resistance and identification of SSR marker associated with it in rice cultivar RDN 98-2. J. Genet. 92, 317–321.PubMedCrossRefPubMedCentralGoogle Scholar
  24. Kumbhar S. D., Kulwal P. L., Patil J. V., Sarawate C. D., Gaikwad A. P. and Jadhav A. S. 2015 Genetic diversity and population structure in landraces and improved rice varieties from India. Rice Sci. 22, 99–107.CrossRefGoogle Scholar
  25. Li W., Lei C., Cheng Z., Jia Y., Huang D., Wang J. et al. 2008 Identification of SSR markers for a broad-spectrum blast resistance gene Pi20(t) for marker assisted breeding. Mol. Breed. 22, 141–149.CrossRefGoogle Scholar
  26. Li Y., Wu C., Xing Y., Chen H. and He Y. 2008 Dynamic QTL analysis for rice blast resistance under natural infection conditions. Aust. J. Crop. Sci. 2, 73–82.Google Scholar
  27. Miah G., Rafii M. Y., Ismail M. R., Puteh A. B., Rahim H. A., Asfaliza R. et al. 2013a Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol. Biol. Rep. 40, 2369–2388.PubMedCrossRefPubMedCentralGoogle Scholar
  28. Miah G., Rafii M. Y., Ismail M. R., Puteh A. B., Rahim H. A., Islam K. N. et al. 2013b A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int. J. Mol. Sci. 14, 22499–22528.PubMedPubMedCentralCrossRefGoogle Scholar
  29. Miah G., Rafii M. Y., Ismail M. R., Puteh A. B., Rahim H. A., Ashkani S. et al. 2015 Inheritance patterns and identification of microsatellite markers linked to the rice blast resistance in BC2F1 population of rice breeding. Bragantia 74, 33–41.CrossRefGoogle Scholar
  30. Neeraja C. N., Hariprasad A. S., Malathi S. and Siddiq E. A. 2005 Characterization of tall landraces of rice (Oryza sativa L.) using gene derived simple sequence repeats. Curr. Sci. 88, 149–152.Google Scholar
  31. Qu S., Liu G., Zhou B., Bellizzi M., Zeng L., Dai L. et al. 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.PubMedPubMedCentralCrossRefGoogle Scholar
  32. Rama Devi S., Singh K., Umakanth B., Vishalakshi B., Renuka P., Sudhakar K. V. et al. 2015 Development and identification of novel rice blast resistant sources and their characterization using molecular markers. Rice Sci. 22, 300–308.CrossRefGoogle Scholar
  33. Ramkumar G., Srinivasarao K., Mohan K. M., Sudarshan I., Sivaranjani A. K. P., Gopalakrishna K. et al. 2011 Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pikh). Mol. Breed. 27, 129–135.CrossRefGoogle Scholar
  34. Rathour R., Chopra M. and Sharma T. R. 2008 Development and validation of microsatellite markers linked to the rice blast resistance gene Pi-z of Fukunishiki and Zenith. Euphytica 163, 275–282.CrossRefGoogle Scholar
  35. RoyChowdhury M., Jia Y., Jia M. H., Fjellstrom R. and Cartwright R. D. 2012a Identification of the rice blast resistance gene Pib in the national small grains collection. Phytopathology 102, 700–706.PubMedCrossRefPubMedCentralGoogle Scholar
  36. RoyChowdhury M., Jia Y., Jackson A., Jia M. H., Fjellstrom R. and Cartwright R. 2012b Analysis of rice blast resistance gene Pi-z using pathogenicity assays and DNA markers. Euphytica 184, 35-47.CrossRefGoogle Scholar
  37. Sallaud C., Lorieux M., Roumen E., Tharreau D., Berruyer R., Svestasrani P. et al. 2003 Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy. Theor. Appl. Genet. 106, 794–803.PubMedCrossRefPubMedCentralGoogle Scholar
  38. Sharma T. R., Madhav M. S., Singh B. K., Shanker P., Jana T. K., Dalal V. et al. 2005 High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea. Mol. Genet. Genom. 274, 569–578.CrossRefGoogle Scholar
  39. 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.CrossRefGoogle Scholar
  40. Singh A. K., Singh P. K., Arya M., Singh N. K. and Singh U. S. 2015 Molecular screening of blast resistance genes in Rice using SSR markers. Plant Path. J. 31, 12.CrossRefGoogle Scholar
  41. Shivapriya M. and Hittalmani S. 2006 Detection of genotype-specific fingerprints and molecular diversity of selected Indian locals and landraces of rice (Oryza sativa L.) using DNA markers. Ind. J. Genet. Plant Breed. 66, 1–5.Google Scholar
  42. Siwach P., Jain S., Saini N., Chowdhury V. K. and Jain R. K. 2004 Allelic diversity among Basmati and non-Basmati long-grain indica rice varieties using microsatellite markers. J. Plant Biochem. Biotech. 13, 25–32.CrossRefGoogle Scholar
  43. Susan A., Yadav M. K., Kar S., Aravindan S., Ngangkham U., Raghu S. et al. 2018 Molecular identification of blast resistance genes in rice landraces from northeastern India. Plant Pathol. 68, 537–546.Google Scholar
  44. TeBeest D. O., Guerber C. and Ditmore M. 2007 Rice blast. Plant Health Instr. (
  45. Vasudevan K., Gruissem W. and Bhullar N. K. 2015 Identification of novel alleles of the rice blast resistance gene Pi54. Sci. Rep. 5, 15678.PubMedPubMedCentralCrossRefGoogle Scholar
  46. Vasudevan K., Vera Cruz C. M., Gruissem W. and Bhullar N. K. 2014 Large scale germplasm screening for identification of novel rice blast resistance sources. Front. Plant Sci. 5, 505.PubMedPubMedCentralCrossRefGoogle Scholar
  47. Wang G. L. and Valent B. (ed.) 2009 Advances in genetics, genomics and control of rice blast disease. Springer Netherlands.Google Scholar
  48. Wang X., Fjellstrom R. G., Jia Y., Yan W., Jia M. H., Scheffer B. E. et al. 2010 Characterization of Pita blast resistance gene in an international rice core collection. Plant Breed. 129, 491–501.Google Scholar
  49. Yadav M. K., Aravindan S., Ngangkham U., Raghu S., Prabhukarthikeyan S. R., Keerthana U. et al. 2019 Blast resistance in Indian rice landraces: genetic dissection by gene specific markers. PLoS One 14, e0211061.PubMedPubMedCentralCrossRefGoogle Scholar
  50. Zenbayashi-Sawata K., Ashizawa T. and Koizumi S. 2005 Pi34-AVRPi34: a new gene-for-gene interaction for partial resistance in rice to blast caused by Magnaporthe griseaJ. Gen. Plant Path. 71, 395–401.CrossRefGoogle Scholar
  51. Zhou J. H., Wang J. L., Xu J. C., Lei C. L. and Ling Z. Z. 2004 Identification and mapping of a rice blast resistance gene Pi-g(t) in the cultivar Guangchangzhan. Plant Pathol. 53, 191–196.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.State Level Biotechnology CentreMahatma Phule Agricultural UniversityRahuriIndia
  2. 2.Agricultural Research StationRadhanagariIndia

Personalised recommendations