, Volume 196, Issue 2, pp 199–211 | Cite as

Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers

  • Jahangir Imam
  • Shamshad Alam
  • Nimai P. Mandal
  • Mukund Variar
  • Pratyoosh Shukla


Molecular screening and genetic diversity of major rice blast resistance (R) genes were determined in 32 accessions of rice germplasm from North East and Eastern India with ten gene based single nucleotide polymorphisms and sequence tagged sites (STS) markers, namely z56592, zt56591, k39512, k3957, candidate gene marker, Pita3, YL155/YL87, YL183/YL87, Pb28, 195R-1 which showed close-set linkage to nine major rice blast resistance (R) genes, Piz, Piz-t, Pik, Pik-p, Pik-h, Pita/Pita-2, Pib and Pi9 and one susceptible pita gene. Among the 32 accessions, 13 were positive for Piz gene and six for Piz-t gene. Six accessions were positive for Pik gene, seven for Pik-p and 16 for Pik-h gene. One accession, Atte thima, was positive for three of Pik multiple genes. Out of 32, only two germplasm, Dudhraj and Nepali dhan, were detected with both Pita3 and YL155/YL87 marker for Pita/Pita-2 gene. The Pib gene appeared to be omnipresent and was detected in 31 of 32 germplasm with marker Pb28. The gene specific STS marker, 195R-1, for Pi9 gene produced positive bands in only two germplasm, Kalchatti and Bachi thima. The Uniform Blast Nursery (UBN) analysis showed that out of 32, six germplasm was resistant, ten moderately resistant and 16 germplasm were susceptible. Presence of Piz-t, Pita/Pita-2 and Pi9 gene ensured a resistant reaction in outdoor blast nursery whereas germplasm carrying Pib was susceptible when present alone. Presence of multiple genes, however, contributed to slow blasting resistance in the field. These results are useful in identification and incorporation of resistant genes from the germplasm into elite cultivars through marker assisted selection in rice breeding programs.


Indian rice germplasm R genes screening Blast resistance SNP markers Marker assisted selection 







Single nucleotide polymorphisms


Sequence tagged sites


Uniform blast nursery


Moderately resistant




Marker assisted selection


North East


Standard evaluation system


Days of sowing



The authors acknowledge the National Agriculture Innovative Project- Component 4, Indian Council of Agricultural Research (ICAR), on Allele mining blast resistance genes for financial support for this research. This work was performed at the Central Rainfed Upland Rice Research Station, Hazaribag, Jharkhand, India.


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Jahangir Imam
    • 1
    • 2
  • Shamshad Alam
    • 1
  • Nimai P. Mandal
    • 1
  • Mukund Variar
    • 1
  • Pratyoosh Shukla
    • 2
  1. 1.Central Rainfed Upland Rice Research Station (CRRI)HazaribaghIndia
  2. 2.Enzyme Technology and Protein Bioinformatics Laboratory, Department of MicrobiologyMaharshi Dayanand UniversityRohtakIndia

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