利用等位基因特异性PCR检测水稻可溶性淀粉合酶基因的单核苷酸多态性

Identification of Single Nucleotide Polymorphism of Soluble Starch Synthase Genes of Rice with Allele-specific PCR

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 polymorphism（SNP） is widely distributed in rice genome.Identification of SNPs has become a very important technique for linkage mapping,association mapping,gene resources identification and molecular marker assisted selection.In this study,12 SNPs of rice soluble starch synthase SSIIIa gene were selected to study the technical feasibility of allele-specific PCR to SNPs identification.The result showed that all the 12 SNPs could be specifically identified by designing 3′end specific base of primers according to the principle of allele-specific PCR and introducing an artificially mismatched base into the third base in the 3′end area of the upstream primers according to the different types of mismatched base at 3′ end.The results from the PCR assay were consistent with those of sequencing.This PCR assay is simple,quick,reliable and economical.Implementation of this PCR assay will greatly enhance the efficiency of germplasm characterization and marker-assisted selection of soluble starch synthase genes in rice.