Single nucleotide polymorphisms in randomly selected genes among japonica rice (Oryza sativa L.) varieties identified by PCR-RF-SSCP.
Single nucleotide polymorphisms in randomly selected genes among japonica rice (Oryza sativa L.) varieties identified by PCR-RF-SSCP.
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DOI：
10.1093/dnares/11.4.275
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发表时间：
2004
期刊：
影响因子：
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通讯作者：
K. Shirasawa;L. Monna;S. Kishitani;T. Nishio
中科院分区：
文献类型：
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作者：
K. Shirasawa;L. Monna;S. Kishitani;T. Nishio
采用聚合酶链式反应-限制性片段-单链构象多态性（PCR-RF-SSCP）技术对水稻品种中随机选择的基因进行DNA多态性分析。通过测试的 1000 个引物对中的 671 个引物对，从日本晴品种的基因组 DNA 中扩增出单个 DNA 片段。使用 671 个引物对进行 PCR-RF-SSCP 分析，检测出 17 个粳稻品种之间的 108 个 DNA 片段的多态性。任何一对粳稻品种之间平均有 36.9 个 DNA 片段显示出多态性。确定了45个基因的50个等位基因以及日本晴等位基因的多态性DNA片段的核苷酸序列。在这些基因中，鉴定出 142 个 SNP 和 32 个插入/缺失。在这 174 个序列变异中，71 个位于外显子，78 个位于内含子，25 个位于未指定区域。有28个等位基因在外显子中存在序列变异。一个等位基因在外显子中存在 1 bp 缺失，导致移码突变，15 个等位基因具有错义突变，其他 12 个等位基因在 3' 非翻译区具有同义变化和/或序列变异。本文讨论了水稻品种之间具有序列变异的基因数量以及所鉴定的 SNP 的功能含义。
DNA polymorphism of randomly selected genes in rice cultivars was analyzed by the polymerase chain reaction-restriction fragment-single strand conformation polymorphism (PCR-RF-SSCP) technique. Single DNA fragments were amplified from genomic DNA of the Nipponbare cultivar by 671 primer pairs among the 1000 primer pairs tested. PCR-RF-SSCP analysis using the 671 primer pairs detected polymorphism in 108 DNA fragments between 17 japonica paddy-rice cultivars. An average of 36.9 DNA fragments showed polymorphism between any pair of japonica paddy-rice cultivars. The nucleotide sequences of the polymorphic DNA fragments were determined for 50 alleles of 45 genes together with Nipponbare alleles. In these genes, 142 SNPs and 32 insertions/deletions were identified. Among these 174 sequence variations, 71 were in exons, 78 in introns, and 25 in unassigned regions. There were 28 alleles which had sequence variations in the exons. One allele had a 1-bp deletion in the exon causing a frame-shift mutation, 15 alleles had missense mutations, and the other 12 alleles had synonymous changes and/or sequence variations in 3' untranslated regions. The number of genes having sequence variations between the rice cultivars and the functional implications of the identified SNPs are herein discussed.