SoyBase, the USDA-ARS Soybean Genetics and Genomics Database
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1 SoyBase, the USDA-ARS Soybean Genetics and Genomics Database David Grant Victoria Carollo Blake Steven B. Cannon Kevin Feeley Rex T. Nelson Nathan Weeks
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3 SoyBase Site Map and Navigation
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6 Video Tutorials: Using SoyBase and Community How-Tos
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9 Search all of SoyBase for a specif ic item or a general term. All items related to search term will be returned. Tools for extracting and downloading all or subsets of the data in SoyBase. BLAST sequence similarity search against the Wm82.a2 genome sequence. The Full BLAST link allows sequence similarity searches against more than 30 selected subsets of soybean sequences. Jump directly to viewer for a specif ic Linkage Group (genetic map) or Chromosome (genome sequence). Search the SoyBase SoyCyc metabolism database. Comprehensive overview of the data, map and sequence browsers, and analysis and reporting tools at SoyBase. Short video tutorials on using SoyBase.
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16 Gene models on Genome build Wm82.a2.v1 Chromosome Gm11 from to bp Gene Model Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Start Stop
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18 Feature Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Glyma.11g Source KOG PFAM Panther Panther AT PFAM AT PFAM AT PFAM AT PFAM AT KOG PFAM AT PFAM AT PFAM AT GO GO GO PFAM PFAM PFAM Panther Annotation ID KOG2473 PF09734 PTHR13230 PTHR13230:SF5 AT3G PF03087 AT4G PF03087 AT4G PF03087 AT4G PF03087 AT4G KOG4473 PF01988 AT3G PF03087 AT4G PF03087 AT4G GO: GO: GO: PF00145 PF00385 PF01426 PTHR10629 Annotation Text RNA polymerase III transcription factor (TF)IIIC subunit RNA polymerase III transcription factor (TF)IIIC subunit GENERAL TRANSCRIPTION FACTOR IIIC, POLYPEPTIDE 5 GENERAL TRANSCRIPTION FACTOR 3C POLYPEPTIDE 5 Transcription factor IIIC, subunit 5 Arabidopsis protein of unknown function Arabidopsis protein of unknown function (DUF241) Arabidopsis protein of unknown function Arabidopsis protein of unknown function (DUF241) Arabidopsis protein of unknown function Arabidopsis protein of unknown function (DUF241) Arabidopsis protein of unknown function Arabidopsis protein of unknown function (DUF241) Uncharacterized membrane protein VIT family Vacuolar iron transporter (VIT) family protein Arabidopsis protein of unknown function Arabidopsis protein of unknown function (DUF241) Arabidopsis protein of unknown function Arabidopsis protein of unknown function (DUF241) DNA binding DNA methylation methyltransferase activity C-5 cytosine-specif ic DNA methylase Chromo (CHRromatin Organisation MOdif ier) domain BAH domain CYTOSINE-SPECIFIC METHYLTRANSFERASE
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25 Some Traits Analyzed by GWAS Al tolerance Chlorophyll content Chlorophyll f luorescence ABS/RC Chlorophyll f luorescence ETo/ABS Chlorophyll f luorescence ETo/TR Chlorophyll f luorescence Fv/Fm Chlorophyll f luorescence Piabs Days from f lowering to maturity Days to f lowering Days to maturity Drought tolerance Iron def ci iency chlorosis Pod weight, fresh Pods per plant SCN race 1 SCN race 3 Seed free amino acids Seed length Seed length to thickness ratio Seed length to width ratio Seed oil Seed protein Seed sucrose Seed thickness Seed weight Seed weight, fresh Seed width Seed width to thickness ratio Seed yield Seeds per plant Soybean mosaic virus
26 View GWAS QTL in Context of Genetic Map
27 View GWAS QTL in Context of Genome Sequence
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29 Genome Browser Available for Both Wm82.a1 and Wm82.a2
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37 SoySNP50K SNPs in Genome Browser
38 Markers in Genome Browser
39 RNA-seq Expression Data on the Genome Sequence
40 Show Large-scale Genome Structure Relationships
41 Transposable Element Insertions and Fast Neutron-induced Indels Displayed in Genome Browser
42 This shows the primary entry to the Fast Neutron Mutant Population page. From here mutants can be selected by sample name, gene model, locus name or indel name1, pedigree2, visual3 or biochemical4 phenotype, or sequence similarity to a query sequence
43 A list of gene or locus names can be submitted to determine if any are covered by an indel.
44 One or more FASTA sequences can be BLASTed against the indel sequences to determine if any are covered by an indel.
45 Genes Covered by an Indel
46 Selected Examples of Data Sets and Tools BLAST GO Enrichment Tool Data Downloads Searching SoyBase
47 Full BLAST Search
48 BLAST Targets at SoyBase * * * *
49 BLAST Results
50 View BLAST Alignments
51 View BLAST Hit in Genome Browser
52 View All BLAST Hits for Whole Genome
53 GO Term Enrichment Tool
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57 Data Downloads
58 Search All of SoyBase for Cadmium
59 Summary of Search Results
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61 Questions? We value your opinion!! Please take our quick six question survey using the link on the SoyBase home page or at
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