agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species

Abstract

Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (Brassica napus, Helianthus annuus, Hordeum vulgare, Oryza glaberrima, Oryza glumipatula, Oryza sativa Indica, Oryza sativa Japonica, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Triticum turgidum, Vitis vinifera, and Zea mays). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise.

Keywords

• regulatory SNP
• transcription factor
• transcription factor binding site
• gene regulation
• GWAS
• database