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Analysis of natural variation of the rice blast resistance gene Pike and identification of a novel allele Pikg

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Abstract

Plant major resistance (R) genes are effective in detecting pathogen signal molecules and triggering robust defense responses. Investigating the natural variation in R genes will allow identification of the critical amino acid residues determining recognition specificity in R protein and the discovery of novel R alleles. The rice blast resistance gene Pike, comprising of two adjacent CC-NBS-LRR genes, namely, Pike-1 and Pike-2, confers broad-spectrum resistance to Magnaporthe oryzae. Here, we demonstrated that Pike-1 determined Pike-specific resistance through direct interaction with the pathogen signal molecule AvrPik. Analysis of natural variation in 79 Pike-1 variants in the Asian cultivated rice Oryza sativa and its wild relatives revealed that the CC and NBS regions, particularly the CC region of the Pike-1 protein were the most diversified. We also found that balancing selection had occurred in O. sativa and O. rufipogon to maintain the genetic diversity of the Pike-1 alleles. By analysis of amino acid sequences, we identified 40 Pike-1 variants in these rice germplasms. These variants were divided into three major groups that corresponded to their respective clades. A new Pike allele, designated Pikg, that differed from Pike by a single amino acid substitution (D229E) in the Pike-1 CC region of the Pike protein was identified from wild rice relatives. Pathogen assays of Pikg transgenic plants revealed a unique reaction pattern that was different from that of the previously identified Pike alleles, namely, Pik, Pikh, Pikm, Pikp, Piks and Pi1. These findings suggest that minor amino acid residues in Pike-1/Pikg-1 determine pathogen recognition specificity and plant resistance. As a new blast R gene derived from rice wild relatives, Pikg has potential applications in rice breeding.

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Acknowledgements

The authors thank Dr. Zhijian Xu (Guangxi Academy of Agricultural Sciences of China) for providing the wild rice accessions used in the present study. Also thank Dr. Cailin Lei (Chinese Academy of Agricultural Sciences), Prof. Weiren Wu (Fujian Agriculture and Forestry University) for providing rice blast resistance gene monogenic lines, and Dr. Dazhao Yu (Hubei Academy of Agricultural Sciences of China) for providing some of the M. oryzae isolates inoculated in the present study. This work was financed by the Special Transgenic Program of the Ministry of Agriculture in China (No. 2016ZX08001004-002), National Natural Science Foundation of China (No.31901522) and Collaborative Innovation Center of Hubei Province for Hybrid Rice.

Funding

This work was financed by the Special Transgenic Program of the Ministry of Agriculture in China (No. 2016ZX08001004-002), National Natural Science Foundation of China (No.31901522) and Collaborative Innovation Center of Hubei Province for Hybrid Rice.

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Fen Meng, Yonggang He, Jing Chen, Xia Long, He Wang, Menghao Zhu, Shaojia Liu, Qiang Cai & Zhihong Zhang

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  1. Fen Meng
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  2. Yonggang He
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Contributions

FM, YH and ZZ conceived and designed research. FM conducted experiments and analysed data. YH, JC, XL, HW, MZ and SL contributed to the experiment and data analysis. FM, QC and ZZ wrote and revised the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Zhihong Zhang.

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Meng, F., He, Y., Chen, J. et al. Analysis of natural variation of the rice blast resistance gene Pike and identification of a novel allele Pikg. Mol Genet Genomics 296, 939–952 (2021). https://doi.org/10.1007/s00438-021-01795-w

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