Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus
Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus
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DOI：
10.1007/s00122-003-1553-0
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发表时间：
2004-05-01
影响因子：
5.4
通讯作者：
Ashikawa, I
中科院分区：
文献类型：
--
作者：
Hayashi, K;Hashimoto, N;Ashikawa, I
本研究探讨了单核苷酸多态性（SNPs）和小片段插入/缺失多态性（InDels）作为DNA标记在水稻遗传分析和育种中的应用。为此，我们调查了含有Piz和Piz-t稻瘟病抗性基因的染色体区域中的SNPs和InDel，并开发了用于分型SNPs的基于PCR的标记。对来自一个对稻瘟病敏感的日本品种和两个各自含有这些基因之一的品种的序列的分析显示，在Piz和Piz-t区域中SNP是丰富的（平均每248 bp一个SNP），但InDel的数量要低得多。SNP的密集分布促进了基因附近SNP标记的产生。为了分型这些SNPs，我们使用了一种改良的等位基因特异性PCR方法。在49个候选等位基因特异性标记中，33个明确且可重复地区分两个等位基因。我们使用的标记映射的Piz和Piz-t基因和评估的DNA片段的大小渗入从日本近等基因系含有Piz的Piz供体品种。我们的研究结果表明，由于它能够在一个目标区域内产生大量的标记，并在测定基因型的简单性，SNP基因分型等位基因特异性PCR是一个有价值的工具，基因定位，图位克隆，标记辅助选择作物，特别是水稻。
We assessed the utility of single-nucleotide polymorphisms (SNPs) and small insertion/deletion polymorphisms (InDels) as DNA markers in genetic analysis and breeding of rice. Toward this end, we surveyed SNPs and InDels in the chromosomal region containing the Piz and Piz-t rice blast resistance genes and developed PCR-based markers for typing the SNPs. Analysis of sequences from a blast-susceptible Japanese cultivar and two cultivars each containing one of these genes revealed that SNPs are abundant in the Piz and Piz-t regions (on average, one SNP every 248 bp), but the number of InDels was much lower. The dense distribution of SNPs facilitated the generation of SNP markers in the vicinity of the genes. For typing these SNPs, we used a modified allele-specific PCR method. Of the 49 candidate allele-specific markers, 33 unambiguously and reproducibly discriminated between the two alleles. We used the markers for mapping the Piz and Piz-t genes and evaluating the size of DNA segments introgressed from the Piz donor cultivar in Japanese near-isogenic lines containing Piz. Our findings suggest that, because of its ability to generate numerous markers within a target region and its simplicity in assaying genotypes, SNP genotyping with allele-specific PCR is a valuable tool for gene mapping, map-based cloning, and marker-assisted selection in crops, especially rice.