Detection of SNPs between Tainung 67 and Nipponbare rice cultivars

Single nucleotide polymorphisms (SNPs) are known as the most detectable variations among related genomes. We estimated the SNPs between Tainung 67 (TNG67), an elite cultivar of rice (Oryza sativa) in Taiwan, and Nipponbare, the cultivar used for rice genome sequencing by the international consortium. More than 6,000 expressed sequence tag (EST) sequences from developing panicles of TNG67 were compared with the annotated gene sequences of Nipponbare. The estimated SNP rate is about 0.3% to 0.4% between the two cultivars, with most of the insertions or deletions (indels) occurring on the 5 ́ or 3 ́ untranslated regions (UTRs). The rate of transition substitutions on the 3 ́ UTR and the third codon positions is higher than that of transversions but lower on 5 ́ UTR and first codon positions. The synonymous (Ks) and non-synonymous (Ka) substitution distances are also calculated, and most of the Ka/Ks ratios are less than 1. Because the SNP density is higher than that of other traditional markers, detection of SNPs in this report with subsequent development of markers will allow genetic mapping and positional cloning between TNG67 and Nipponbare.