Journal Article

Single Nucleotide Polymorphisms in Randomly Selected Genes among <i>japonica</i> Rice (<i>Oryza sativa</i> L.) Varieties Identified by PCR-RF-SSCP

Kenta Shirasawa, Lisa Monna, Sachie Kishitani and Takeshi Nishio

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 11, issue 4, pages 275-283
Published in print January 2004 | ISSN: 1340-2838
Published online January 2004 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/11.4.275

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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 identi.ed. 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.

Keywords: DNA polymorphism; marker-aided selection; point mutation

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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