Authors: Kenta Shirasawa Hiroaki Maeda Lisa Monna Sachie Kishitani Takeshi Nishio
Publish Date: 2007/09/06
Volume: 115, Issue: 8, Pages: 1067-1074
Abstract
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 1036 genes analyzed In 137 genes 638 DNA polymorphisms were identified Out of 52 genes having polymorphisms in the exons one had a frameshift mutation three had polymorphism causing amino acid insertions or deletions and 16 genes had missense polymorphisms The number of genes having frameshift 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 6977 respectively Chromosomal regions of cultivars selected in rice breeding processes were identified by SNP analysis of genesWe are grateful to Ms Y Sugiyama for her technical assistance This work was supported in part by Research project for utilizing advanced technologies in agriculture forestry and fisheries K Shirasawa is a recipient of a research fellowship from the Japan Society for the Promotion of Science for Young Scientists
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