BarleyVarDB

BarleyVarDB provides a repository of genomic variation in barley (Hordeum vulgare L.) to support genetic diversity analysis and crop improvement.

Key Features:

• Extensive Variation Data: Contains 57,754,224 single nucleotide polymorphisms (SNPs) and 3,600,663 insertions/deletions (InDels) identified from high-coverage whole-genome sequencing of 21 barley germplasm, including eight wild accessions from three evolutionary centers and thirteen landraces.
• Microsatellite Data (SSRs): Includes 522,212 microsatellites/simple sequence repeats (SSRs) identified within the reference barley pseudo-molecular genome sequence for genetic mapping and marker development.
• Reference Genome Integration: Variations are represented in the context of the International Barley Genome Sequencing Consortium (IBSC) barley reference genome and its annotation.
• JBrowse: Provides genome browser-based visualization of genomic features and variant tracks.
• BLAST: Offers sequence alignment and similarity searches against the barley reference genome.
• Primer3: Supplies PCR primer design capabilities for validation and genotyping of polymorphic variants.

Scientific Applications:

• Molecular Breeding: Enables use of ultra-high-density SNP and InDel markers for marker-assisted selection and genetic mapping.
• Gene Discovery: Supports identification of functional genes associated with agronomic traits in barley.
• Comparative Genomics: Facilitates comparative analyses within Hordeum species and across cereal genomes.

Methodology:

Variants (SNPs and InDels) were identified from high-coverage whole-genome sequencing of 21 barley germplasm; SSRs were identified within the reference barley pseudo-molecular genome sequence; the database uses the IBSC barley reference genome and annotation.