Functional & Integrative Genomics

, Volume 13, Issue 3, pp 309–322 | Cite as

Molecular diversity in rice blast resistance gene Pi-ta makes it highly effective against dynamic population of Magnaporthe oryzae

  • S. Thakur
  • Y. K. Gupta
  • P. K. Singh
  • R. Rathour
  • M. Variar
  • S. K. Prashanthi
  • A. K. Singh
  • U. D. Singh
  • D. Chand
  • J. C. Rana
  • N. K. Singh
  • T. R. Sharma
Original Paper


Rice blast is one of the important diseases of rice which can be effectively managed by the deployment of resistance genes. Pi-ta is one of the major blast resistant genes effective against pathogen populations in different parts of India. We analysed allelic variants of Pi-ta from 48 rice lines selected after phenotyping of 529 rice landraces across three eco-geographical blast hot spot regions. Besides, Pi-ta orthologue sequences of 220 rice accessions belonging to wild and cultivated species of rice were also included in the study for a better evodevo perspective of the diversity present in the gene and the selection pressures acting on this locus. We obtained high nucleotide variations (SNPs and insertion–deletions) in the intronic region. We also identified 64 haplotypes based on nucleotide polymorphism in these alleles. Pi-ta orthologues of Indian landraces were scattered in eight major haplotypes indicating its heterogenous nature. We identified a total of 47 different Pi-ta protein variants on the basis of deduced amino acid residues amongst the orthologues. Five unique and novel Pi-ta variants were identified for the first time in rice landraces exhibiting different reaction types against the Magnaporthe oryzae population. A high value of Pinon/syn was observed only in the leucine-rich domain of the alleles cloned from Indian landraces, indicating strong selective forces acting on this region. The detailed molecular analysis of the Pi-ta orthologues provides insights to a high degree of inter- and intraspecific relationships amongst the Oryza species. We identified rice landraces possessing the effective alleles of this resistance gene which can be used in future blast resistance breeding programmes.


Blast resistance gene Haplotypes Rice landraces Magnaporthe oryzae Oryza species Pi-ta Polymorphism 



The financial assistance received from National Agricultural Innovation Project (NAIP) (C4/C1071), ICAR, by TR Sharma is gratefully acknowledged. The authors are thankful to the Officer in Charge, National Phytotron Facility, Indian Agricultural Research Institute, New Delhi, for providing basic facilities for growing and maintaining Indian local landraces. We also thank NCBI and various authors for making available sequence data of various Pi-ta alleles in the public domain.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • S. Thakur
    • 1
    • 6
  • Y. K. Gupta
    • 1
  • P. K. Singh
    • 1
  • R. Rathour
    • 2
  • M. Variar
    • 3
  • S. K. Prashanthi
    • 4
  • A. K. Singh
    • 5
  • U. D. Singh
    • 5
  • D. Chand
    • 6
  • J. C. Rana
    • 7
  • N. K. Singh
    • 1
  • T. R. Sharma
    • 1
  1. 1.National Research Centre on Plant BiotechnologyIARINew DelhiIndia
  2. 2.CSK Himachal Pradesh Agricultural UniversityPalampurIndia
  3. 3.Central Rainfed Upland Rice Research StationCRRIHazaribaghIndia
  4. 4.University of Agricultural SciencesDharwadIndia
  5. 5.Indian Agricultural Research InstituteNew DelhiIndia
  6. 6.Himachal Pradesh UniversityShimlaIndia
  7. 7.NBPGR Regional StationShimlaIndia

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