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 | ||||||
|---|---|---|---|---|---|---|
Neutral detergent fiber, R6 | ||||||
| QTL Name | LG (GmComposite2003) | Start (cM) | End (cM) | |||
| Neutral detergent fiber, R6 1-1 | H | 81.03000 | 88.62 | |||
| Neutral detergent fiber, R6 1-2 | F | 94.61000 | 118.26 | |||
| Neutral detergent fiber, R6 1-3 | L | 64.63000 | 66.13 | |||
| Neutral detergent fiber, R6 1-4 | H | 70.52000 | 81.00 | |||
| Neutral detergent fiber, R6 1-5 | F | 86.02000 | 89.81 | |||
| Neutral detergent fiber, R6 1-6 | F | 92.32000 | 94.61 | |||
| Neutral detergent fiber, R6 1-7 | L | 46.10000 | 66.13 | |||
| Neutral detergent fiber, R6 1-8 | L | 71.18000 | 89.22 | |||
| GWAS QTL Related by Ontology | |||||||
|---|---|---|---|---|---|---|---|
| Carbon Isotope Discrimination | |||||||
| Carbon isotope discrimination 1 | |||||||
| Carbon isotope discrimination 10 | |||||||
| Carbon isotope discrimination 11 | |||||||
| Carbon isotope discrimination 2 | |||||||
| Carbon isotope discrimination 3 | |||||||
| Carbon isotope discrimination 4 | |||||||
| Carbon isotope discrimination 5 | |||||||
| Carbon isotope discrimination 6 | |||||||
| Carbon isotope discrimination 7 | |||||||
| Carbon isotope discrimination 8 | |||||||
| Carbon isotope discrimination 9 | |||||||
| Leaf Carotenoid Content | |||||||
| Leaf carotenoid content 1 | |||||||
| Seed Amino Acids | |||||||
| Seed amino acids 1 | |||||||
| Seed Protein | |||||||
| Seed protein 10 | |||||||
| Seed protein 7 | |||||||
| Seed protein 8 | |||||||
| Genes Related by Ontology | |
|---|---|
| Lba | |
| Lbc1 | |
| Lbc2 | |
| Lbc3 | |
| Lhcb1-7 | |
| FT1a | |
| FT1b | |
| FT2a | |
| FT2b | |
| FT3a | |
| FT3b | |
| FT4 | |
| FT5a | |
| FT5b | |
| FT6 | |
| FTL1 | |
| FTL2 | |
| FTL3 | |
| FTL4 | |
| FTL5 | |
| FTL6 | |
| FTL7 | |
| Lbc2A | |
| LGB1 | |
| PHYA1 | |
| PHYA2 | |
| PHYA3 | |
| PHYA4 | |
| PHYB1 | |
| PHYB2 | |
| PHYE1 | |
| PHYE2 | |
| Papers | |
|---|---|
| Asekova et al. 2016A "Novel Quantitative Trait Loci for Forage Quality Traits in a Cross between PI 483463 and ÔHutchesonÕ in Soybean" | |
| Keim et al. 1997 "A high-density soybean genetic map based upon AFLP markers" | |
| Patel et al. 2000 "Investigation of the haem-nicotinate interaction in leghaemoglobin role of hydrogen bonding" | |
| Stombaugh et al. 2004 "Quantitative Trait Loci Associated with Cell Wall Polysaccharides in Soybean Seed" | |
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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