Computational Analysis of Single-Nucleotide Polymorphisms in Proximal Promoter Region of Rice (Oryza sativa L.)

The term promoter is used to designate a region in the genome sequence upstream of a gene transcription start site (TSS). Most promoter elements regulating TSS are localized in the proximal promoter, is a region of several hundreds nucleotides around the TSS. If the SNP occurs within coding sequence, which may or may not alter amino acid sequence. Where as, SNPs occur within the proximal promoter region has more impact on gene expression. The publication of whole genome sequences for the japonica (Nipponbare) and indica (93-11) types of rice enables the determination of common SNPs occurring between them. In present study we used 31 non-redundant proximal promoter sequences in rice, from previous studies which are experimentally determined transcription start site for RNA polymerase II. When proximal promoters of japonica were compared with the corresponding proximal promoters of indica using BLAST alignment programme, a total of 69 SNPs were identified. Out of these 32 SNPs (46.3%) were transitions (A/G, T/C) and 37 SNPs (53.6 %) were transversions (A/C, A/T, G/C, G/T). Maximum frequency of SNPs was found in the region -50 to -150 (61.2 %). Minimum frequency found in region -151 to -201(9.6 %). It demonstrate that functional cis-regulatory polymorphisms segregate within sub species of rice and there is abundant SNP present in proximal promoter region. SNPs in proximal promoter may one of the causes of fictional variation. In addition, study indicates that SNPs are not evenly distributed. Selection pressure is always more for a region having more fictional impact and theoretically should have conserved, in contrast nonfunctional regions acting as reservoir of mutation.