Soybean Knowledge Base (SoyKB): A Web Resource for Integration of Soybean Translational Genomics and Molecular Breeding

Soybean Knowledge Base (SoyKB, http://soykb.org) is a comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information.

SoyKB has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies (GWAS) data, from multiple soybean cultivars and Glycine soja. SoyKB also has many new data analysis and visualization tools for RNA-seq and proteomics expression datasets including heat-maps, scatter plots and hierarchical clustering. Various new types of data including DNA methylation, fast neutron mutations, phosphorylation, genotype by sequencing (GBS) data for molecular breeding and phenotypic inferences have also been incorporated.

SoyKB is now powered by the iPlant Cyber-Infrastructure. The website is hosted on the iPlant’s advanced computing infrastructure established to leverage the data analysis capabilities. The infrastructure is being utilized for bioinformatics analyses of next-generation resequencing data for the 108 soybean germplasm lines. These GBS data are also incorporated into SoyKB and utilized for trait discovery and GWAS analyses.