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Mining of rice blast resistance gene Pi54 shows effect of single nucleotide polymorphisms on phenotypic expression of the alleles

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Abstract

The rice blast resistance gene Pi54 (formerly Pi-k h) isolated from indica rice line Tetep confers broad spectrum resistance to different strains of Magnaporthe oryzae in India. In this study, we performed PCR based allele mining for blast resistance gene Pi54 from six cultivated rice lines and eight wild rice species to understand its structural variation and its impact on the phenotypes. Sequence analysis indicates presence of more variation between cultivated and wild species (35–90 %) than variation found among cultivated species (1–20 %). Structural analysis of alleles showed presence of variable number of Open Reading Frames (0–2) principally having point mutations in the leucine rich repeats (LRR) regions. The Ka/Ks ratio of LRR region was >1, which shows the effect of selection pressure at this domain. The Pi54 alleles have 142 polymorphic sites with average nucleotide diversity of 0.04522. The Ka/Ks ratio of coding region ranged from 0 to >1 and Tajima’s D test showed negative as well as Darwinian selection within the alleles, which corresponded well with their phenotypic reaction to M. oryzae. The results obtained in this study shows divergent nature of Pi54 allele in wild species and land races of rice. The resistance alleles identified in this study can be used in effective management of rice blast disease through gene pyramiding.

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Abbreviations

NBS-LRR:

Nucleotide binding site-leucine rich repeat

R-gene:

Resistance gene

SNPs:

Single-nucleotide polymorphisms

InDel:

Insertion/Deletion

ORFs:

Open reading frames

SOCS:

Suppressor of cytokine signalling

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Acknowledgments

T R Sharma is thankful to the National Agriculture Innovative Project (Indian Council of Agricultural Research) project code C4/1701 and the Department of Biotechnology, Govt. of India (projects: BT/AB/FG-2 (PHII)/2009-3A and BT/HRD/34/04/2008) for financial assistance. BND is thankful to the Council of Scientific and Industrial Research, Govt. of India for senior research fellowship. We thank the incharge National Phytotron Facility at IARI, New Delhi for providing facilities to maintain wild species of rice.

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Authors and Affiliations

  1. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Room No 39, LBS Centre, Pusa Campus, New Delhi, 110012, India

    A. Kumari, B. N. Devanna, S. Thakur, P. K. Singh, N. K. Singh & T. R. Sharma

  2. Division of Crop Improvement, Indian Institute of Pulses Research, Kanpur, 208 024, Uttar Pradesh, India

    A. Das

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  1. A. Kumari
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Correspondence to T. R. Sharma.

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A. Kumari, A. Das and B. N. Devanna contributed equally.

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Kumari, A., Das, A., Devanna, B.N. et al. Mining of rice blast resistance gene Pi54 shows effect of single nucleotide polymorphisms on phenotypic expression of the alleles. Eur J Plant Pathol 137, 55–65 (2013). https://doi.org/10.1007/s10658-013-0216-5

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