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Metabolomic Analysis of Barley by Gas Chromatography/Mass Spectrometry
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BarleyVarDB: a database of barley genomic variation.
Cong Tan1, Brett Chapman1, Penghao Wang1
1Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.
Database : the Journal of Biological Databases and Curation
|November 28, 2020
Summary
BarleyVarDB is a new database offering extensive genomic variation data for barley (Hordeum vulgare L.). It provides millions of single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) to aid barley genetic research and breeding.
Area of Science:
- Agricultural Science
- Genomics
- Bioinformatics
Background:
- Barley (Hordeum vulgare L.) is a globally significant cereal crop vital for human and animal consumption.
- Understanding barley's genomic variation is crucial for crop improvement and genetic research.
Purpose of the Study:
- To develop and present BarleyVarDB, a comprehensive database for barley genomic variation.
- To provide researchers with easy access to a large collection of genetic markers and the barley reference genome.
Main Methods:
- Whole genome sequencing of 21 barley germplasm, including wild accessions and landraces.
- Identification and compilation of single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and microsatellites/simple sequence repeats (SSRs).
- Integration of the latest barley genome reference and annotation data from the International Barley Genome Sequencing Consortium (IBSC).
Main Results:
- BarleyVarDB contains over 57 million SNPs and 3.6 million InDels from diverse barley germplasm.
- The database includes over 522,000 whole genome-wide microsatellites/simple sequence repeats (SSRs).
- Web-based tools like JBrowse, BLAST, and Primer3 are integrated for user-friendly data access and analysis.
Conclusions:
- BarleyVarDB serves as a valuable resource for the barley research community.
- It offers an ultra-high density of SNP and InDel markers for molecular breeding and functional gene discovery.
- The database facilitates enhanced genetic research and the identification of genes related to important agronomic traits in barley.
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