Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Jan;42(Database issue):D1245-52.
doi: 10.1093/nar/gkt905. Epub 2013 Oct 16.

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

Trupti Joshi  1 , Michael R Fitzpatrick, Shiyuan Chen, Yang Liu, Hongxin Zhang, Ryan Z Endacott, Eric C Gaudiello, Gary Stacey, Henry T Nguyen, Dong Xu
Affiliations

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

Trupti Joshi et al. Nucleic Acids Res. 2014 Jan.

Abstract

Soybean Knowledge Base (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 multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base 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 data, from multiple soybean cultivars and Glycine soja.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Germplasm Browser of the In Silico Breeding Program suite of tools showing phenotypic descriptors for ∼19 000 PI lines.
Figure 2.
Figure 2.
Example of QTL viewer in the In Silico Breeding Program suite of tools showing multiple traits in Gm01 along with underlying genes, GBS, SNP array and insertions/deletions data on the bottom panels, respectively.
Figure 3.
Figure 3.
Protein BioViewer for protein Glyma04g36000 showing the primary sequence, secondary structures, amino acid characteristics and domain positions.
Figure 4.
Figure 4.
Heatmap and hierarchical clustering tool for viewing RNA-seq expression data for multiple genes.
See this image and copyright information in PMC

References

    1. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463:178–183. - PubMed
    1. Grant D, Nelson RT, Cannon SB, Shoemaker RC. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010;38:D843–D846. - PMC - PubMed
    1. Shultz JL, Kurunam D, Shopinski K, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal AJ, et al. The soybean genome database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res. 2006;34:D758–D765. - PMC - PubMed
    1. Joshi T, Patil K, Fitzpatrick MR, Franklin LD, Yao Q, Cook JR, Wang Z, Libault M, Brechenmacher L, Valliyodan B, et al. Soybean knowledge base (SoyKB): a web resource for soybean translational genomics. BMC Genomics. 2012;13(Suppl. 1):S15. - PMC - PubMed
    1. Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, et al. The iPlant collaborative: cyberinfrastructure for plant biology. Front. Plant Sci. 2011;2:34. - PMC - PubMed

Publication types