Many genome projects have generated a deluge of whole-genome data from modern domesticated goats, ancient goats, and their wild relatives, to identify genetic diversity, selective regions and historic introgression events that involved in domestication, subsequent intensive breeding, or climate-driven adaptation. Nevertheless, there is no dedicated database integrating these resource. Here we used a uniform pipeline to develop the first comprehensive database (GGVD) which focuses on high-quality SNPs, indels, selective regions, and introgression from 208 modern domestic goats, 24 bezoars, 46 ibex, and 82 ancient goats. A total of ~41.44 M SNPs and ~5.14 M indels were identified in modern goat samples. Selected loci were implemented through eight statistical tests (FST, Pi ratio, XP-EHH, Pi, Hp, Tajima’s D, CLR, and iHS). Introgression regions between ibex species and domestic goats were also integrated into database. Users can freely visualize the frequency of genomic variations in geographical maps, selective regions in interactive tables, Manhattan plots or line charts, and especially, the SNP genotype patterns in heatmaps. Ancient goats were used to track the spatiotemporal trajectories of each genetic variant. Moreover, we have introduced the UCSC Genome Browser, BLAT, BLAST, and LiftOver into database. GGVD allows users to identify breeding-associated candidate genes and variants, and track the state of variants before, during and following selection and introgression events. GGVD will be a useful archive for future genetic studies and goat breeding.

Related articles:

1. Zheng Z., Wang X., Li M., Li Y., ... Chen Y & Jiang Y. (2020) The origin of domestication genes in goats. Science Advances, 6, eaaz5216.
2. Cai Y., Fu W., Cai D., Heller R., Zheng Z., ... Jiang Y & Wang X. (2020) Ancient genomes reveal the evolutionary history and origin of cashmere producing goats in China. Molecular Biology and Evolution, 37, 2099-2109.