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BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures
Ningbo Chen1, Weiwei Fu1, Jianbang Zhao2
1Key Laboratory of Animal Genetics, Breeding and Reproduction Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
Genomics, Proteomics & Bioinformatics
|June 17, 2020
Summary
The Bovine Genome Variation Database (BGVD) offers efficient storage and analysis of cattle genomic data, including millions of variations and selection signatures. This resource aids in understanding cattle biology and breeding globally.
Area of Science:
- Genomics
- Bioinformatics
- Animal Science
Background:
- Next-generation sequencing generates extensive cattle genomic data.
- Challenges exist in storing, querying, and visualizing large cattle genomic datasets.
- Characterizing population genetic diversity and identifying selection regions is crucial.
Purpose of the Study:
- To develop a comprehensive database for cattle genomic variation and selection data.
- To provide efficient tools for data storage, querying, and visualization.
- To support in-depth data mining and analysis for cattle biology and breeding.
Main Methods:
- Development of the Bovine Genome Variation Database (BGVD).
- Integration of genomic variations (SNPs, indels, CNVs) and selection signatures.
- Implementation of functionalities including gene search, variation search, Genome Browser, and coordinate conversion.
Main Results:
- BGVD contains ~60.44M SNPs, ~6.86M indels, 76,634 CNV regions, and selection signatures from 432 cattle samples.
- Interactive breed origin map facilitates distribution pattern retrieval for 54 breeds.
- Genome Browser integrates variation, selection data, and external resources (NCBI, UCSC, Animal QTLdb).
Conclusions:
- BGVD serves as a valuable archive for comprehensive cattle genomic data analysis.
- The database supports global-scale data mining for cattle biology and breeding research.
- BGVD enhances the accessibility and utility of large-scale cattle genomic datasets.
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