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Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice

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Abstract

Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplification showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice.

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Abbreviations

BB:

bacterial blight

dNTP:

deoxyribonucleotide triphosphate

EST:

expressed sequence tag

GAI:

gibberellic acidinsensitive

InDel:

insertion-deletion

IRGSP:

International Rice Genome Sequencing Project

NBS-LRR:

nucleotide-binding site leucinerich repeat

NCBI:

National Center for Biotechnology Information

PCR:

polymerase chain reaction

PGIP:

polygalacturonase-inhibiting protein

RGA:

resistance gene analogue

R-gene:

resistance gene

SNP:

single-nucleotide polymorphism

TBE:

tris-borate-EDTA

TIR:

toll/interleukin-1 receptor

TNL:

toll/interleukin-1 receptor NBS-LRR

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Author notes

  1. Irfan A. Ghazi

    Present address: Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046, India

Authors and Affiliations

  1. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012, India

    Irfan A. Ghazi, Vivek Dalal, Kishor Gaikwad, Tilak R. Sharma, Nagendra K. Singh & Trilochan Mohapatra

  2. Department of Biotechnology, Faculty of Science, Jamia Hamdard, New Delhi, 110 062, India

    Irfan A. Ghazi & Prem S. Srivastava

  3. Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110 012, India

    Ashok K. Singh

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  1. Irfan A. Ghazi
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Correspondence to Trilochan Mohapatra.

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Supplementary tables pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/june09/pp251-261-suppl.pdf

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Ghazi, I.A., Srivastava, P.S., Dalal, V. et al. Physical mapping, expression analysis and polymorphism survey of resistance gene analogues on chromosome 11 of rice. J Biosci 34, 251–261 (2009). https://doi.org/10.1007/s12038-009-0029-z

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  • DOI: https://doi.org/10.1007/s12038-009-0029-z

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