Skip to main content
SpringerLink
Log in

Candidate screening of blast resistance donors for rice breeding

  • Research Article
  • Published:
Journal of Genetics Aims and scope Submit manuscript

Abstract

Rice blast is one of the most serious diseases in the world. The use of resistant cultivars is the most preferred means to control this disease. Resistance often breaks down due to emergence of new races; hence identification of novel resistance donors is indispensable. In this study, a panel of 80 released varieties from National Rice Research Institute, Cuttack was genotyped with 36 molecular markers that were linked to 36 different blast resistance genes, to investigate the varietal genetic diversity and molecular marker-trait association with blast resistance. The polymorphism information content of 36 loci varied from 0.11 to 0.37 with an average of 0.34. The cluster analysis and population structure categorized the 80 National Rice Research Institute released varieties (NRVs) into three major genetic groups. The principal co-ordinate analysis displays the distribution of resistant and moderately resistant NRVs into different groups. Analysis of molecular variance result demonstrated maximum (97%) diversity within populations and minimum (3%) diversity between populations. Among tested markers, two markers (RM7364 and pi21_79-3) corresponding to the blast resistance genes (Pi56(t) and pi21) were significantly associated and explained a phenotypic variance of 4.9 to 5.1% with the blast resistance. These associated genes could be introgressed through marker-assisted to develop durable blast resistant rice varieties. The selected resistant NRVs could be good donors for the blast resistance in rice crop improvement research.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Barman S., Gouda M., Venu R. and Chatto B. 2004 Identification of a major blast resistance gene in the rice cultivar “Tetep”. Plant Breed. 123, 300–302.

    Article  CAS  Google Scholar 

  • 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 avirulence gene ACE1. Theor. Appl. Genet. 107, 1139–1147.

    Article  CAS  Google Scholar 

  • Bonman J. 1992 Durable resistance to rice blast disease–environmental influences. Euphytica 63, 115–123.

    Article  Google Scholar 

  • Bradbury P. J., Zhang Z., Kroon D. E., Casstevens T. M., Ramdoss Y. and Bucker E. S. 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635.

    Article  CAS  Google Scholar 

  • Chen S., Wang L., Que Z., Pan R. and Pan Q. 2005 Genetic and physical mapping of Pi37(t), a new gene conferring resistance to rice blast in the famous cultivar St. No. 1. Theor. Appl. Genet. 111, 1563–1570.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Dean R. A, Tabot N. J., Ebbole D. J., Farman M. L., Mitchell T. K., Orbach M. J. et al. 2005 The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434, 980–986.

    Article  CAS  Google Scholar 

  • Doyle J. J. and Doyle J. L. 1990 Isolation of plant DNA from fresh tissue. Focus 12, 39–40.

    Google Scholar 

  • Earl D. A. 2012 STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361.

    Article  Google Scholar 

  • Evanno G., Regnaut S. and Goudet J. 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620.

    Article  CAS  Google Scholar 

  • Fjellstrom R., Conawaybormans C. A., Mcclung A. M., Marchetti M. A., Shank A. R. and Park W. D. 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.

    Article  CAS  Google Scholar 

  • Fukuoka S., Saka N., Koga H., Ono K., Shimizu T., Ebana K. et al. 2009 Loss of function of a proline–containing protein confers durable disease resistance in rice. Science 325, 998–1001.

    Article  CAS  Google Scholar 

  • Gowda M., Roy-Barman S. 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Hayashi K., Yasuda N., Fujita Y., Koizumi S. and Yoshida H. 2010 Identification of the blast resistance gene Pit in rice cultivars using functional markers. Theor. Appl. Genet. 121, 1357–1367.

    Article  CAS  Google Scholar 

  • He X., Liu X., Wang L., Wang L., Lin F., Cheng Y. et al. 2012 Identification of the novel recessive gene pi55(t) conferring resistance to Magnaporthe oryzae. Sci. China Life Sci. 55, 141–149.

    Article  CAS  Google Scholar 

  • Huang H., Huang L., Feng G., Wang S., Wang Y., Liu J. et al. 2011 Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi–3150. Phytopathology 101, 620–626.

    Article  Google Scholar 

  • Jiang H., Feng Y., Bao L., Li X., Gao G., Zhang Q. et al. 2012 Improving blast resistance of Jin 23B and its hybrid rice by marker–assisted gene pyramiding. Mol. Breed. 30, 1679–1688.

    Article  CAS  Google Scholar 

  • Kim D. M., Ju H. G., Kang J. W., Han S. S. and Ahn S. N. 2013 A new rice variety ‘Hwaweon 5’ with durable resistance to rice blast. Korean J. Breed Sci. 45, 142–147.

    Article  Google Scholar 

  • Koide Y., Kawasaki A., Telebanco-Yanoria M. J., Hairmansis A., Nguyet N. T., Bigirimana J. et al. 2010 Development of pyramided lines with two resistance genes, Pish and Pib, for blast disease (Magnaporthe oryzae B. Couch) in rice (Oryza sativa L.). Plant Breed. 129, 670–675.

    Article  CAS  Google Scholar 

  • Koide Y., Telebanco–Yanoria M. J., Fukuta Y. and Kobayashi N. 2013 Detection of novel blast resistance genes, Pi58(t) and Pi59(t), in a Myanmar rice landrace based on a standard differential system. Mol. Breed. 32, 241–252.

    Article  CAS  Google Scholar 

  • Kouzai Y., Kaku H., Shibuya N., Minami E. and Nishizawa Y. 2013 Expression of the chimeric receptor between the chitin elicitor receptor CEBiP and the receptor–like protein kinase Pi–d2 leads to enhanced responses to the chitin elicitor and disease resistance against Magnaporthe oryzae in rice. Plant Mol. Biol. 81, 287–295.

    Article  CAS  Google Scholar 

  • Lei C., Hao K., Yang Y., Ma J., Wang S. Wang J. et al. 2013 Identification and fine mapping of two blast resistance genes in rice cultivar 93–11. Crop J. 1, 2–14.

    Article  Google Scholar 

  • Liang Z., Wang L. and Pan Q. 2016 A new recessive gene conferring resistance against rice blast. Rice 9, 47.

    Article  Google Scholar 

  • Liu K. and Muse S. V. 2005 PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21, 2128–2129.

    Article  CAS  Google Scholar 

  • Liu X., Yang Q., Lin F., Hua L., Wang C. Wang L. et al. 2007 Identification and fine mapping of Pi39(t), a major gene conferring the broad–spectrum resistance to Magnaporthe oryzae. Mol. Gen. Genomics 278, 403–410.

    Article  CAS  Google Scholar 

  • 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. Gen. Genomics 274, 394–401.

    Article  CAS  Google Scholar 

  • Liu Y., Liu B., Zhu X., Yang J., Bordeos A. Wang G. et al. 2013 Fine–mapping and molecular marker development for Pi56(t), a NBS–LRR gene conferring broad– spectrum resistance to Magnaporthe oryzae in rice. Theor. Appl. Genet. 126, 985–998.

    Article  CAS  Google Scholar 

  • Ma J., Lei C., Xu X., Hao K., Wang J. Cheng Z. et al. 2015 Pi64, encoding a novel CC–NBS–LRR protein, confers resistance to leaf and neck blast in rice. Mol. Plant Microbe Interact. 28, 558–568.

    Article  CAS  Google Scholar 

  • Matsushita K., Yasuda N., Koizumi S., Ashizawa T., Sunohara Y. Iida S. et al. 2011 A novel blast resistance locus in a rice (Oryza sativa L.) cultivar, Chumroo, of Bhutan. Euphytica 180, 273–280.

    Article  Google Scholar 

  • Neale D. B. and Savolainen O. 2004 Association genetics of complex traits in conifers. Trends Plant Sci. 9. 325–330.

    Article  CAS  Google Scholar 

  • Nei M. 1973 Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA 70, 3321–3323.

    Article  CAS  Google Scholar 

  • Nguyen T. T., Koizumi S., La T. N., Zenbayashi K. S., Ashizawa T. Yasuda N. et al. 2006 Pi35(t), a new gene conferring partial resistance to leaf blast in the rice cultivar Hokkai 188. Theor. Appl. Genet. 113, 697–704.

    Article  CAS  Google Scholar 

  • Okuyama Y., Kanzaki H., Abe A., Yoshida K., Tamiru M. Saitoh H. et al. 2011 A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes. Plant J. 66, 467–479.

    Article  CAS  Google Scholar 

  • Panda G., Sahu C., Yadav M. K., Aravindan S., Umakanta N. Raghu S. et al. 2017 Morphological and molecular characterization of Magnaporthe oryzae from Chhattisgarh. Oryza 54, 330–336.

    Article  Google Scholar 

  • Peakall R. and Smouse P. E. 2012 GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research an update. Bioinformatics 28, 2537–2539.

    Article  CAS  Google Scholar 

  • Pritchard J. X., Stephens M. and Donnelly P. 2000 Inference of population structure using multilocus genotype data. Genetics 155, 945–959.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roy S., Marndi B. C., Mawkhlieng B., Banerjee A., Yadav R. M., Misra A. K. et al. 2016 Genetic diversity and structure in hill rice (Oryza sativa L.) landraces collected from the north–eastern Himalayas of India. BMC Genet. 17, 107.

  • Sahu, C., Yadav M. K., Panda G., Aravindan S., Umakanta N., Raghu S. et al. 2018 Morphological and molecular characterization of Magnaporthe oryzae causing rice blast disease in Odisha. Oryza 55, 467–472.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Shi B. H., Zhang J. H., Zheng Y. M., Liu Y. Q., Cruz C. V. Zheng T. Q. et al. 2012 Identification of a new resistance gene Pi–Da(t) from Dacca6 against rice blast fungus(Magnaporthe oryzae) in Jin23B background. Mol. Breed. 30, 1089–1096.

    Article  CAS  Google Scholar 

  • Silue D., Notteghem J. L. and Tharreau D. 1992 Evidence of a gene or gene relationship in the Oryza sativa–Magnaporthe grisea pathosystem. Phytopathology 82, 577–580.

    Article  Google Scholar 

  • Sun P., Liu J., Wang Y., Jiang N., Wang S. Dai Y. et al. 2013 Molecular mapping of the blast resistance gene Pi49 in the durably resistant rice cultivar Mowanggu. Euphytica 192, 45–54.

    Article  CAS  Google Scholar 

  • Susan A., Yadav M. K., Kar S., Aravindan S., Ngangkham U., Raghu S. et al. 2019 Molecular identification of blast resistance genes in rice landraces from northeastern India. Plant Pathol. 68, 537–546.

    CAS  Google Scholar 

  • Tanksley S. D and Mc Couch S. R. 1997 Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277, 1063–1066.

    Article  CAS  Google Scholar 

  • Vasudevan K., Casiana M., Vera C., Gruissem W. and Navreet K. B. 2014 Large scale germplasm screening for identification of novel rice blast resistance sources. Front. Plant Sci. 505, 1–9.

    Google Scholar 

  • Wang C., Yang Y., Yuan X., Xu Q., Feng Y., Yu H. et al. 2014 Genome–wide association study of blast resistance in indica rice. BMC Plant Biol. 14, 311.

    Article  CAS  Google Scholar 

  • Wang R., Fang N., Guan C., He W., Bao Y. and Zhang H. 2016 Characterization and fine mapping of a blast resistant gene Pi–jnw1 from the japonica rice landrace Jiangnanwan. PLoS One 11, e0169417.

    Article  Google Scholar 

  • Wang Y., Wang D., Deng X., Liu J., Sun P., Liu Y. et al. 2012 Molecular mapping of the blast resistance genes Pi2–1 and Pi51(t) in the durably resistant rice ‘Tianjingyeshengdao’. Phytopathology 102, 779–786.

  • Xu X., Chen H., Fujimura T. and Kawasaki S. 2008 Fine mapping of a strong QTL of field resistance against rice blast, Pikahei–1(t), from upland rice Kahei, utilizing a novel resistance evaluation system in the greenhouse. Theor. Appl. Genet. 117, 997–1008.

  • Xu X., Hayashi N., Wang C. T., Fukuoka S., Kawasaki S., Takatsuji H. et al. 2014 Rice blast resistance gene Pikahei–1(t), a member of a resistance gene cluster on chromosome 4, encodes a nucleotide–binding site and leucine–rich repeat protein. Mol. Breed. 34, 691–700.

    Article  CAS  Google Scholar 

  • Xu Y. and Crouch J. H. 2008 Marker–assisted selection in plant breed: from publications to practice. Crop Sci. 48, 391–407.

    Article  Google Scholar 

  • Yadav M. K., Aravindan S., Ngangkham U., Shubudhi H. N., Bag M. K., Adak T. et al. 2017 Use of molecular markers in identification and characterization of resistance to rice blast in India. PLoS One 12, e0176236.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Yang Q., Lin F., Wang L. and Pan Q. 2009 Identification and mapping of Pi41, a major gene conferring resistance to rice blast in the Oryza sativa subsp. indica reference cultivar, 93–11. Theor. Appl. Genet. 118, 1027–1034.

    Article  CAS  Google Scholar 

  • Zhang W., Sun J., Zhao G., Wang J., Liu H., Zheng H. et al. 2017 Association analysis of the glutelin synthesis genes GluA and GluB1 in a Japonica rice collection. Mol. Breed. 37, 129.

  • Zheng W., Wang Y., Wang L., Ma Z., Zhao J., Wang P. et al. 2016 Genetic mapping and molecular marker development for Pi65(t), a novel broad–spectrum resistance gene to rice blast using next–generation sequencing. Theor. Appl. Genet. 129, 1035–1044.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Zhu M., Wang L. and Pan Q. 2004 Identification and characterization of a new blast resistance gene located on rice chromosome 1 through linkage and differential analyses. Phytopathology 94, 515– 519.

    Article  CAS  Google Scholar 

  • Zhu D., Kang H., Li Z., Liu M., Zhu X., Wang Y. et al. 2016 A genome–wide association study of field resistance to Magnaporthe oryzae in rice. Rice 9, 44.

    Article  Google Scholar 

Download references

Acknowledgements

The authors are extremely grateful to the Director, ICAR-National Rice Research Institute, Cuttack, India, for his support and facilitation in carrying out the research work successfully. This study was funded by the ICAR-National Rice Research Institute, Cuttack.

Author information

Author notes

  1. Manoj Kumar Yadav and S. R. Prabhukarthikeyan contributed equally to this work.

Authors and Affiliations

  1. ICAR-National Rice Research Institute, Cuttack, 753 006, India

    Manoj Kumar Yadav, S. Aravindan, S. R. Prabhukarthikeyan, U. Keerthana, S. Raghu, P. Sanghamitra, T. Adak, Priyanka Priyadarshinee, Mayabini Jena, M. K. Kar & P. C. Rath

  2. ICAR Research Complex for North Eastern Hill Region, Umiam, 793 103, India

    U. Ngangkham

  3. Rice Pathology Laboratory, AICRIP, Gangavathi, University of Agricultural Sciences, Raichur, 584 104, India

    D. Pramesh

  4. Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825 301, India

    A. Banerjee & S. Roy

Authors
  1. Manoj Kumar Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S. Aravindan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. U. Ngangkham
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. S. R. Prabhukarthikeyan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. U. Keerthana
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. S. Raghu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. D. Pramesh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. A. Banerjee
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. S. Roy
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. P. Sanghamitra
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. T. Adak
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Priyanka Priyadarshinee
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Mayabini Jena
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. M. K. Kar
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. P. C. Rath
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Manoj Kumar Yadav.

Additional information

Corresponding Editor: H. A. Ranganath

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (xlsx 13 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yadav, M.K., Aravindan, S., Ngangkham, U. et al. Candidate screening of blast resistance donors for rice breeding. J Genet 98, 73 (2019). https://doi.org/10.1007/s12041-019-1116-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12041-019-1116-z

Keywords

Search

Navigation