Genome-Wide Analysis of SNPs in Promoter Regsions of Oryza sativa

3,000 rice genomes project provides a unique scientific resource for plant researchers. We have analyzed distribution of 29 million SNPs in Oryza sativa genome identified by the 3000 rice genome project (The 3,000 Rice Genomes Project, 2014) near transcription and translation start and end sites, promoters, 5’ and 3’ UTRs, and exon/intron junctions. We present analysis of nucleotide diversity in regulatory regions of Oryza sativa genome, focusing on core promoters and transcription factor binding sites. Generally, regulatory regions are significantly more conserved compared to the intergenic regions. We demonstrate reduced position-specific nucleotide diversity characteristic of certain classes of transcription factor bidning sites and certain gene families.