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High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea

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Abstract

In order to understand the molecular mechanisms involved in the gene-for-gene type of pathogen resistance, high-resolution genetic and physical mapping of resistance loci is required to facilitate map-based cloning of resistance genes. Here, we report the molecular mapping and cloning of a dominant gene (Pi-k h) present in the rice line Tetep, which is associated with resistance to rice blast disease caused by Magnaporthe grisea. This gene is effective against M. grisea populations prevalent in the Northwestern Himalayan region of India. Using 178 sequence tagged microsatellite, sequence-tagged site, expressed sequence tag and simple sequence repeat (SSR) markers to genotype a population of 208 F2 individuals, we mapped the Pi-k h gene between two SSR markers (TRS26 and TRS33) which are 0.7 and 0.5 cM away, respectively, and can be used in marker-assisted-selection for blast-resistant rice cultivars. We used the markers to identify the homologous region in the genomic sequence of Oryza sativa cv. Nipponbare, and a physical map consisting of two overlapping bacterial artificial chromosome and P1 artificial chromosome clones was assembled, spanning a region of 143,537 bp on the long arm of chromosome 11. Using bioinformatic analyses, we then identified a candidate blast-resistance gene in the region, and cloned the homologous sequence from Tetep. The putative Pi-k h gene cloned from Tetep is 1.5 kbp long with a single ORF, and belongs to the nucleotide binding site-leucine rich repeat class of disease resistance genes. Structural and expression analysis of the Pi-k h gene revealed that its expression is pathogen inducible.

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Acknowledgements

Financial assistance received from the Indian Council of Agricultural Research and the Department of Biotechnology, Government of India by TRS is gratefully acknowledged. We are thankful to Prof. K.R. Koundal, Project Director of National Research Centre on Plant Biotechnology and the incharges Phytotron Facility, Indian Agricultural Research Institute for providing facilities for phenotyping the mapping population and to R. Rathour, for providing pathogen culture. We are thankful to NCBI, FGENESH and RGP for making their databases and genome analysis tools publicly available.

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Sharma, T.R., Madhav, M.S., Singh, B.K. et al. High-resolution mapping, cloning and molecular characterization of the Pi-k h gene of rice, which confers resistance to Magnaporthe grisea . Mol Genet Genomics 274, 569–578 (2005). https://doi.org/10.1007/s00438-005-0035-2

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