Shirasawa Kenta, Maeda Hiroaki, Monna Lisa, Kishitani Sachie, Nishio Takeshi
Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan.
Theor Appl Genet. 2007 Nov;115(8):1067-74. doi: 10.1007/s00122-007-0632-z. Epub 2007 Sep 6.
Identification of single nucleotide polymorphisms (SNPs) in a large number of genes will enable estimation of the number of genes having different alleles in a population. In the present study, SNPs between 21 rice cultivars including 17 Japanese cultivars, one upland rice, and three indica cultivars were analyzed by PCR-RF-SSCP. PCR-RF-SSCP analysis was found to be a more efficient method for detecting SNPs than mismatch-cleavage analysis, though both PCR-RF-SSCP and mismatch-cleavage are useful for screening SNPs. The number of DNA fragments showing polymorphism between Japanese cultivars was 134 in the 1,036 genes analyzed. In 137 genes, 638 DNA polymorphisms were identified. Out of 52 genes having polymorphisms in the exons, one had a frame-shift mutation, three had polymorphism causing amino acid insertions or deletions, and 16 genes had missense polymorphisms. The number of genes having frame-shift mutations and missense polymorphisms between the 17 Japanese cultivars was estimated to be 41 and 677 on average, respectively, and those between japonica and indica to be 425 and 6,977, respectively. Chromosomal regions of cultivars selected in rice breeding processes were identified by SNP analysis of genes.
鉴定大量基因中的单核苷酸多态性（SNP）将有助于估计群体中具有不同等位基因的基因数量。在本研究中，通过PCR-RF-SSCP分析了包括17个日本品种、1个旱稻品种和3个籼稻品种在内的21个水稻品种之间的SNP。虽然PCR-RF-SSCP和错配切割都可用于筛选SNP，但发现PCR-RF-SSCP分析是检测SNP比错配切割分析更有效的方法。在所分析的1036个基因中，日本品种之间表现出多态性的DNA片段数量为134个。在137个基因中，鉴定出638个DNA多态性。在52个外显子具有多态性的基因中，1个发生了移码突变，3个具有导致氨基酸插入或缺失的多态性，16个基因具有错义多态性。估计17个日本品种之间平均具有移码突变和错义多态性的基因数量分别为41个和677个，粳稻和籼稻之间分别为425个和6977个。通过对基因的SNP分析确定了水稻育种过程中所选品种的染色体区域。
