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Identification of SNP for rice blast resistance gene Pike and development of the gene-specific markers
- He, Yonggang, Meng, Fen, Quan, Shuiqing, Ji, Wenjun, Liang, Anmin, Chen, Jing, Huang, Wenchao, Tian, Jinshan, Zhang, Zhihong
- Euphytica 2017 v.213 no.3 pp. 61
- DNA, Magnaporthe oryzae, Oryza sativa, alleles, blast disease, breeding lines, crop production, disease resistance, genetic resistance, genotype, germplasm, introgression, marker-assisted selection, phylogeny, plant breeding, polymerase chain reaction, rice, sequence alignment, single nucleotide polymorphism
- 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.