title: Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers.
abstract: We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars 'Nipponbare' and 'Koshihikari' can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice.
authors.affiliation: Plant Genome Center, 1-25-2 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
authors.forename: Shinobu
authors.initials: S
authors.lastname: Nasu
authors.forename: Junko
authors.initials: J
authors.lastname: Suzuki
authors.forename: Rieko
authors.initials: R
authors.lastname: Ohta
authors.forename: Kana
authors.initials: K
authors.lastname: Hasegawa
authors.forename: Rika
authors.initials: R
authors.lastname: Yui
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Kitazawa
authors.forename: Lisa
authors.initials: L
authors.lastname: Monna
authors.forename: Yuzo
authors.initials: Y
authors.lastname: Minobe
mesh_terms: D005819:Genetic Markers; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers