agReg-SNPdb

agReg-SNPdb catalogs regulatory single nucleotide polymorphisms (rSNPs) that alter transcription factor binding sites (TFBSs) across cattle, pig, chicken, sheep, horse, goat, and dog to enable analysis of genetic effects on gene regulation.

Key Features:

• Species coverage: Includes rSNP data for seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog.
• Extensive SNP cataloging: Contains 10,623,512 rSNPs identified within TFBSs across the covered species.
• TFBS-centered rSNP identification: Focuses on SNPs located within transcription factor binding sites to assess regulatory variation.
• Impact on transcription factor binding: Annotates SNPs that alter transcription factor binding affinity and thereby may affect gene expression.
• Systematic promoter analysis: Represents a systematic analysis of promoter-region SNPs in livestock with reported effects on TF binding affinities.

Scientific Applications:

• Genetic research: Identification of rSNPs that affect gene regulation supports studies of trait heritability and disease mechanisms in agricultural animals.
• Breeding and trait selection: Highlights regulatory variants that can be evaluated for associations with desirable traits or disease resistance in breeding programs.
• Functional genomics: Enables exploration of how genetic variation within TFBSs impacts gene expression and contributes to phenotypic diversity.

Methodology:

Development used a bioinformatics pipeline that collected genomic data from the seven species, mapped known transcription factor binding sites across these genomes, and analyzed SNPs within those regions to determine their impact on TF binding affinity.