Soybean knowledge base (SoyKB): Bridging the gap between soybean translational genomics and breeding

Many genome-scale data are available in soybean including genomic sequence, transcriptomics (microarray, RNA-seq), proteomics and metabolomics datasets, together with growing knowledge of soybean in gene, microRNAs, pathways, and phenotypes. This represents rich and resourceful information which can provide valuable insights, if mined in an innovative and integrative manner and thus, the need for informatics resources to achieve that. Towards this we have developed Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for soybean translational genomics and breeding. SoyKB handles the management and integration of soybean genomics and multi-omics data along with gene function annotations, biological pathway and trait information. It has many useful tools including Affymetrix probelD search, gene family search, multiple gene/metabolite analysis, motif analysis tool, protein 3D structure viewer and download/upload capacity for experimental data and annotations. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, breeders and consumers. SoyKB has new innovative tools for soybean breeding including a graphical chromosome visualizer targeted towards ease of navigation for breeders. It integrates QTLs, traits, germplasm information along with genomic variation data such as single nucleotide polymorphisms (SNPs) and genome-wide association studies (GWAS) data from multiple genotypes, cultivars and G. soja. QTLs for multiple traits can be queried and visualized in the chromosome visualizer simultaneously and overlaid on top of the genes and other molecular markers as well as multi-omics experimental data for meaningful inferences. SoyKB can be publicly accessed at http://soykb.org.