Welcome to PGVD

Pig have had a central role in the evolution of human cultures and are the most economically important of domesticated animal species. Until now, it formed nearly eight hundred of breeds with various traits. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD) for providing six main functionalities: Gene Quick Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools (BLAT/BLAST) and Genome Coordinate Conversion Tool (LiftOver). In current version, BGVD contains 60,439,391 SNPs, 6,859,056 indels, and 76,634 CNV regions derived from 432 animals. And selective signatures were evaluated for eight cattle groups by using six methods (Pi, H_p, iHS, F_ST, XP-CLR and XP-EHH). Many external databases, such as NCBI, the UCSC Genome Browser, AnimalQTLdb, AmiGO 2 and KEGG were integrated into our browser. BGVD will be a useful archive for in-depth analysis in cattle biology and cattle breeding.

Features

• Basic information of 448 pig accessions.
• Variations including SNPs and Indels are provided in PGVD.
• We provide two ways to view variations, one is interactive tables and graphs and the other is Gbrowse format.
• We provide a parallel search for variations, such as dbSNP rsid, gene symbol, and genomic region in one versions of the pig genome (Sscrofa11.1/susScr11).
• We provide allele frequency distribution pattern of each SNP or indel in 61 globally representative pig breeds or six "core" pig groups.
• We provide copy number distribution in 448 individuals representing 61 cattle populations.
• We provide selection scores for six groups of Asia_wild, Europe_wild, Europe, North_China, South_China and Tibetan by using six statistical terms.
• We integrate variations, selection scores, gene annotation, QTL and conserved elements into Gbrowse to facilitate global presentation.

For publication of results please cite the following article:

Wen, J., Zheng, Z., Gong, M. et al. Ancient genomes reveal the genetic inheritance and recent introgression in Chinese indigenous pigs. Sci. China Life Sci. 65, 842–845 (2022).