SoyBase
SoyBase transitions to NEW site on 10/1/2024
Integrating Genetics and Genomics to Advance Soybean Research
SoyBase
SoyBase transitions to NEW site on 10/1/2024
| Bi-Parental QTL | ||||||
|---|---|---|---|---|---|---|
Total growth duration | ||||||
| QTL Name | LG (GmComposite2003) | Start (cM) | End (cM) | |||
| Trailing growth 1-1 | F | 106.30000 | 108.30 | |||
| Total growth duration 1-2 | C1 | 78.65000 | 80.62 | |||
| Total growth duration 1-3 | L | 59.52000 | 70.36 | |||
| Total growth duration 1-4 | C2 | 112.19000 | 115.09 | |||
| Total growth duration 1-5 | O | 71.09000 | 93.37 | |||
| Total growth duration 2-1 | C2 | 113.10000 | 115.10 | |||
| Total growth duration 2-2 | O | 103.50000 | 105.50 | |||
| Total growth duration 2-3 | B1 | 60.10000 | 62.10 | |||
| Total growth duration 2-4 | H | 37.40000 | 39.40 | |||
| GWAS QTL Related by Ontology | |||||||
|---|---|---|---|---|---|---|---|
| Lodging | |||||||
| Lodging 1 | |||||||
| Lodging 3 | |||||||
| Pubescence Color | |||||||
| Pubescence color 1 | |||||||
| Pubescence color 2 | |||||||
| Pubescence color 4 | |||||||
| Pubescence Density | |||||||
| Pubescence density 1 | |||||||
| Pubescence Form | |||||||
| Pubescence form 1 | |||||||
| R8 Full Maturity | |||||||
| R8 full maturity 10 | |||||||
| R8 full maturity 2 | |||||||
| R8 full maturity 3 | |||||||
| R8 full maturity 4 | |||||||
| R8 full maturity 5 | |||||||
| R8 full maturity 8 | |||||||
| R8 full maturity 9 | |||||||
| Reproductive Period | |||||||
| Reproductive period 2 | |||||||
| Reproductive period 3 | |||||||
| Reproductive period 4 | |||||||
| Reproductive Stage Length | |||||||
| Reproductive stage length 1 | |||||||
| Reproductive stage length 4 | |||||||
| Stem Determination | |||||||
| Stem determination 1 | |||||||
| Stem Termination Type | |||||||
| Stem termination type 1 | |||||||
| Stem termination type 2 | |||||||
| Genes Related by Ontology | |
|---|---|
| ENOD2 | |
| GmENOD13 | |
| GmENOD2A | |
| GmENOD2B | |
| GmENOD40 | |
| GmENOD40-1 | |
| GmENOD40-2 | |
| GmENOD55 | |
| GmENOD55-1 | |
| GmENOD55-2 | |
| ADO3 | |
| AOMT | |
| E9-1 | |
| Em | |
| FKF1 | |
| FKF2 | |
| GI1A | |
| GI2 | |
| GI3 | |
| MAT1 | |
| MAT9 | |
| MER3 | |
| TFL1-1 | |
| TFL1-2 | |
| TFLa | |
| TFLb | |
| TSF1 | |
| TSF2 | |
| Papers | |
|---|---|
| Wang et al. 2021 "Increased copy number of Gibberelin 2-oxidase 8 genes reduced trailing growth and shoot length during soybean domestication" | |
Results of a search at SoyBase are presented in two complementary ways.
The user-submitted search term is used to find exact lexical matches to the name or description of data objects in SoyBase (QTL, genes, etc.). If an exact match is not found, and when the search term was two or more words, then a further search is done using the individual words. These text-based matches are reported in the Text column of the results table.
The goal of the ontology search is to identify data objects in SoyBase that are related to the search term but which might not have the exact search word(s) in their name or description. Data in SoyBase are tagged using a soybean-specific ontology termed a SOYnumber (SOY#). The user-submitted search term is used to search this SoyBase ontology for an exact match. If an exact match is not found, and when the search term was two or more words, the individual words are used in an additional search. Once a match is found its SOY# is used to traverse the ontology tree to identify related terms. These terms are then used to find SoyBase objects that are related to those directly identified by the search term. These ontology-based matches are reported in the Ontology column of the results table.
Occasionally unrelated SoyBase data objects will be reported in the Ontology-based results along with the correctly identified ones. This is an unavoidable consequence of the the way we have structured the underlying trait, structure and development ontologies at SoyBase. For example a search for 'protein' also returns 'oil'-related objects since both are seed components.
| Data Category | Search Was Performed Against |
|---|---|
| Genetic Marker | Genetic Markers (SNPs, SSRs, etc.). |
| Gene | Gene records (ex. Glyma.15g026400, Fad2-1). |
| QTL | Bi-Parental QTL and GWAS QTL collections. |
| Germplasm Collections | The Induced Mutant and Uniform Field Trial records. |
| Publications | Paper records and abstracts held within the Soybase data set. |
| Sitemap, News & Tutorials | SoyBase Sitemap, News archive, Upcoming meetings and Tutorials. |
As an example of how these two searching capabilities can be helpful, a search for 'oil' will return those QTL that contain the word 'oil' in their name ('Seed oil', 'Seed oil to protein ratio', etc.) in the QTL line of the Text column. The Ontology column will contain these QTL along with the related QTL 'Seed palmitate', 'Seed oleic', etc.
Note: Because of the idiosyncratic ways that authors name phenotypic and developmental traits it is always advisable to look through the Ontology-based results, even when the submitted search term seems unambiguous. This can reveal additional SoyBase objects that might have been missed using exact text matching.
| Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA | ||
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