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Identification of SNP for rice blast resistance gene Pike and development of the gene-specific markers

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Abstract

Rice blast disease caused by Magnaporthe oryzae is an important limiting factor to rice production in the world. Introgression of blast resistance genes into improved germplasm by marker-assisted selection has been considered as an effective and environmentally beneficial means to control this disease. Pike, a broad-spectrum blast resistance gene, was cloned by map-based strategy recently in our laboratory. Two adjacent CC-NBS-LRR genes (designated as Pike-1 and Pike-2) were required for Pike-mediated resistance. In the current study, sequence alignment of the SNP G1328C and the SNP-surrounding region let us find that the Pik DNA variants of the studied rice lines appear to be divided into G-, C-, T- and G’-types. Based on the four genotypes, a Pike-specific marker system consisting of three PCR-based markers CP-G1328C, CP-G1328T and CP-G1328G’ was developed and used to effectively differentiate G-type allele from each of the others. Using this marker system, we investigated distribution of the Pik DNA variants in a set of 326 rice varieties or breeding lines and found that there were 2, 130, 135 and 59 rice lines identified to carry G-, C-, T- and G’-type alleles, respectively. In addition, with sequence data of the SNP G1328C-containing genomic region derived from 56 rice lines, we constructed a phylogenetic tree with three major clades which just corresponded to the types of the Pik DNA variants described above.

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Acknowledgements

The authors thank Dr. Cailin Lei of the Chinese Academy of Agricultural Sciences for providing rice blast R gene monogenic lines. This work was financed by The Special Transgenic Program of the Ministry of Agriculture, China (Nos. 2014ZX0800902B-002 and 2016ZX08001004-002).

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Authors and Affiliations

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

    Yonggang He, Fen Meng, Shuiqing Quan, Wenjun Ji, Anmin Liang, Jing Chen, Wenchao Huang & Zhihong Zhang

  2. Yichang Academy of Agricultural Sciences, Yichang, 443000, China

    Jinshan Tian

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  1. Yonggang He
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  2. Fen Meng
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  3. Shuiqing Quan
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Correspondence to Zhihong Zhang.

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Fig. S1

Design strategy of PCR primers for the Pike-specific markers developed in the current study. Locations and orientations of the primers were indicated by black arrows. The SNP G1328C was indicated by boldface letter (TIFF 14358 kb)

Fig. S2

Unrooted Neighbor-Joining phylogenetic tree based on DNA sequence data of the SNP G1328C-containing genomic region of 56 rice cultivars and breeding lines. The numbers at the branch nodes represent the percentage of 1000 bootstrap replications. The weighted sequence divergence was represented by the scale bar. The allele type of each cultivar was indicated in the figure, and the G, C, T and G’ in the brackets were corresponding to G-, C-, T- and G’-type, respectively (TIFF 20615 kb)

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He, Y., Meng, F., Quan, S. et al. Identification of SNP for rice blast resistance gene Pike and development of the gene-specific markers. Euphytica 213, 61 (2017). https://doi.org/10.1007/s10681-017-1841-4

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