GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

Weiwei Fu; Rui Wang; Jiantao Yu; Dexiang Hu; Yudong Cai; Junjie Shao; Yu Jiang

doi:10.1016/j.jgg.2021.03.003

Volume 48 Issue 3

Mar. 2021

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Article Navigation > Journal of Genetics and Genomics > 2021 > 48(3): 248-256

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GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions

doi: 10.1016/j.jgg.2021.03.003

a
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
b
College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China

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Corresponding author: E-mail address: yu.jiang@nwafu.edu.cn (Yu Jiang)
Received Date: 2020-11-06
Accepted Date: 2021-03-13
Rev Recd Date: 2021-03-12

Available Online: 2021-04-09

Publish Date: 2021-03-20

Abstract

Abstract

Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database (GGVD). GGVD hosts a total of ∼41.44 million SNPs, ∼5.14 million indels, 6,193 selected loci, and 112 introgression regions. Users can freely visualize the frequency of genomic variations in geographical maps, selective sweeps in interactive tables, Manhattan plots, or line charts, as well as the heatmap patterns of the SNP genotype. Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early, middle, and late stages. For facilitating access to sequence features, the UCSC Genome Browser, BLAT, BLAST, LiftOver, and pcadapt are also integrated into GGVD. GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs, and it is publicly available at http://animal.nwsuaf.edu.cn/GoatVar.
- Goat,
- Genetic structure,
- Variation,
- Selective signature,
- Introgression,
- Database

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References(48)

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