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单核苷酸多态性(SNP)广泛分布于水稻基因组中,SNP分型已成为水稻遗传作图、关联分析、资源鉴定和分子标记辅助选择等研究的重要技术。本文选择水稻可溶性淀粉合酶基因SSIIIa的12个SNP位点,研究了利用等位基因特异性PCR法检测SNP的可行性。按照等位基因特异性PCR原理设计引物3’末端碱基,并根据每个SNP位点引物3’端的错配类型,在上游引物3’末端第3位引入不同的错配碱基,结果均获得了很好的扩增特异性,PCR检测结果与测序结果吻合。表明,等位基因特异性PCR是一种简便、快捷、可靠和低成本的SNP分型方法,可有效应用于水稻可溶性淀粉合酶基因的种质资源鉴定和分子标记辅助选择育种等相关研究。
Single nucleotide polymorphisms (SNPs) are widely distributed in the rice genome. SNP typing has become an important technique in the research of genetic mapping, association analysis, resource identification and molecular marker-assisted selection in rice. In this paper, we selected 12 SNP sites of SSIIIa of rice soluble starch synthase gene and studied the feasibility of SNP detection using allele-specific PCR. According to the principle of allele-specific PCR, the 3’-terminal base of the primer was designed and different mismatched bases were introduced at the 3’-end of the upstream primer according to the mismatch pattern at the 3’-end of each SNP site. Good amplification specificity was obtained. PCR results were in good agreement with sequencing results. It is indicated that allele-specific PCR is a simple, rapid, reliable and low-cost SNP typing method that can be effectively applied to related studies on germplasm identification and molecular marker-assisted selection breeding of rice soluble starch synthase genes.