BbGSD: Black-boned Sheep Genome SNP Database.

Abstract

Lanping black-boned (LPBB) sheep are a unique and rare ruminant species, characterized by black pigmentation in the skin and internal organs. Thus far, LPBB are the only known animal with heritable melanin characteristics besides the black-boned chicken, and the only mammal known to contain a large amount of melanin in the body. LPBB have therefore attracted substantial research attention, due to their potential contribution to medicine. However, long periods of grazing freely and crossbreeding with Lanping normal sheep (LPN) have diluted LPBB breeding resources, posing a challenge to the protection of species. To ensure the effective conservation and management of LPBB genetic resources, the construction of a large-scale database of genotypic information is therefore very important. To achieve this, we established the first LPBB-specific SNP database, named Black-boned Sheep Genome SNP Database (BbGSD, http://202.203.179.115:3838/oarsnpdb) using sheep genotype data (100 LPBB and 50 LPN) across 46 894 242 SNP sites. In this database, we implemented four main function modules: (i) the "LD heatmap" module, which uses a heatmap to enable the interactive visualization of pairwise linkage disequilibrium (LD) measurements between SNPs; (ii) the "SNP distribution" module, which allows users to interactively visualize tabular genotype data as heat maps; (iii) the "Phylogenetics" module which enables phylogenetic analysis to explore the evolutionary history or genetic relationships of the LPBB sheep; and the "Diversity" module, which can be used to calculate and display the nucleotide diversity among sheep populations in user-specified genomic regions. BbGSD is essential for accelerating studies on the functional genomics and screening of molecular markers of molecular-assisted breeding in black-boned sheep. Database URL: http://202.203.179.115:3838/oarsnpdb.