, Volume 209, Issue 3, pp 725–737 | Cite as

Identification and validation of novel alleles of rice blast resistant gene Pi54, and analysis of their nucleotide diversity in landraces and wild Oryza species

  • G. Ramkumar
  • M. S. Madhav
  • S. J. S. Rama Devi
  • B. Umakanth
  • M. K. Pandey
  • M. S. Prasad
  • R. M. Sundaram
  • B. C. Viraktamath
  • V. Ravindra Babu


Rice blast is a devastating fungal disease, which limits rice production severely. To identify novel alleles of blast resistant gene, Pi54, and to understand its diversity exist among wild Oryza species and landraces sequence-based allele mining strategy was employed. In this study, sixteen Pi54 alleles were sequenced from landraces and wild Oryza species which have genome ranging from AA to EE. Overall analysis confirmed that the alleles derived from wild species had more divergence than the landraces. Among all wild Oryza alleles, Pi54 aus derived from O. australiensis, showed the highest diversity. Comparison of protein domains revealed that LRR region had more variations than NBS region. Haplo-groups among the ecotypes were analyzed based on their Pi54 sequence. Interestingly, four different haplo-groups were identified, that were supported by phylogeny analysis. Among 16 analyzed alleles, two alleles, Pi54 ab, Pi54 btj derived from landraces-Amana Bavo and Boha Thulasi Joha showed superior phenotypic reaction than the reference allele (Pi54 Tetep), and these alleles were validated by allelism test. These alleles have potential application in blast resistance breeding programs and identified SNPs and Indel among the alleles can be useful in development of allele specific markers. The present study helped to gain insights into the evolutionary adaptation of the resistant gene and its allelic distribution and diversity among the Oryza species.


Pi54 Allele mining Rice blast NBS-LRR Land races Oryza sativa 



The Authors thank the Department of Biotechnology, Government of India for providing funds for carrying out the research work.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10681_2016_1666_MOESM1_ESM.doc (106 kb)
Supplementary material 1 (DOC 105 kb)
10681_2016_1666_MOESM2_ESM.xls (122 kb)
Supplementary material 2 (XLS 122 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • G. Ramkumar
    • 1
  • M. S. Madhav
    • 1
  • S. J. S. Rama Devi
    • 1
  • B. Umakanth
    • 1
  • M. K. Pandey
    • 1
  • M. S. Prasad
    • 1
  • R. M. Sundaram
    • 1
  • B. C. Viraktamath
    • 1
  • V. Ravindra Babu
    • 1
  1. 1.Crop Improvement SectionIndian Institute of Rice ResearchHyderabadIndia

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