Bovine Genome Variation Database (BGVD)

Bovine Genome Variation Database (BGVD) provides a searchable archive of cattle genomic variation derived from next-generation sequencing to support characterization of population genetic diversity and identification of genomic regions under selection.

Key Features:

• Gene Search: Locate specific genes in the bovine genome and retrieve associated gene-related variation information.
• Variation Search: Explore single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and copy number variation (CNV) regions across 432 cattle samples, encompassing approximately 60.44 million SNPs, 6.86 million indels, and 76,634 CNV regions.
• Genomic Signature Search: Identify and analyze signatures of selective sweeps indicative of natural or artificial selection pressures.
• Genome Browser: Integrate variation and selection data as tracks alongside resources from NCBI, UCSC Genome Browser, and AnimalQTLdb for genomic context.
• Alignment Search Tools: Align sequences against reference genomes to support comparative genomics analyses.
• Genome Coordinate Conversion Tool: Convert genomic coordinates between ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1 reference assemblies.
• Breed Distribution Data: Provide distribution patterns of genomic variations for 54 cattle breeds via a breed origin map.
• Visualization: Display signals of selection using Manhattan plots and Genome Browser tracks.

Scientific Applications:

• Population Genetics: Characterize global population genetic diversity across 54 cattle breeds using genome-wide variation data.
• Selection Mapping: Detect and interpret regions under natural or artificial selection through selective sweep signatures and visualization.
• Comparative Genomics: Compare sequences and structural variation by aligning samples to bovine reference genomes.
• Cattle Biology and Breeding Analyses: Enable data mining for genotype–phenotype associations and breeding-related genomic investigations.

Methodology:

Data derived from next-generation sequencing; sequence alignment against reference genomes; genome coordinate conversion among ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1; integration of NCBI, UCSC Genome Browser, and AnimalQTLdb tracks; visualization via Manhattan plots and Genome Browser tracks.