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SoyBase has added a tool to convert gene names between Glyma.Wm82.a1.v1.1 (genome assembly 1 annotation version 1.1) and Glyma.Wm82.a2.v1(genome assembly 2 annotation version 1). It can be accessed from the Genome
and Analysis Tools
QTL names on the Composite Genetic Map (Comp2003) have been revised both to make it clearer exactly what trait was measured and to use names that allow related QTL to be easily recognized. The previous QTL names have been retained as alternatives and can still be used with the SoyBase search tools.
The Wm82.a2 soybean genome sequence (aka the 2nd assembly) is now the default BLAST target from our quick BLAST tool on the front page. The associated gene calls and peptide sequences are available in our advanced BLAST page, as are the Wm82.a1 genome and gene sequences.
We have fixed the error that resulted in incorrect SoySNP50K data being downloaded from SoyBase. To summarize, the downloadable file for the entire data set was correct. However, data for individual cultivars, ie. the tab-delimited file with SNP rows and cultivar columns (snp_id_position_and_value), contained incorrect values. Please contact David Grant (firstname.lastname@example.org; 515-294-1205) with any questions.
We have identified a problem with the SoySNP50K data in SoyBase. The file provided for the entire data set was correct. However, data for individual cultivars or SNPs downloaded using the SoyBase tool were incorrect. Please contact David Grant (email@example.com; 515-294-1205) with any questions. An update will be posted once this problem has been resolved.
Video tutorials for various aspects of SoyBase searches and tool functionalities have been developed. The tutorials page can be accessed from the Resources
tab at SoyBase.
Registration will open on Sunday, November 10, 2013 for the joint 6th International Food Legumes Research Conference & 7th International Conference on Legume Genetics and Genomics to be held in Saskatoon, Saskatchewan, Canada from July 7 - 11, 2014.Conference website
The 2017 World Soybean Research Conference, hosted by the University of Georgia, will be held in Savannah, Georgia. More details will be posted once the plans for this meeting are finalized.
SoyBase staff will present a tutorial on using SoyBase including search, download and analysis tools. There will be two sessions, each limited to 25 participants: Sunday 2/10 1-3P and Monday 2/11 10-noon. Attendees must register
. Participants are encouraged to bring suggestions for improving SoyBase and/or questions on effectively using the web site.
The 2nd Annual Soybean Mutant Finder and Precision Genomics Workshop will be held in July 8-10, 2013 at the University of Missouri. July 8-9: Participants will view fast neutron-derived mutant plants growing in the field, can screen these mutants and can request seed of those that may be of research interest. Other demonstrations will also occur. July 9-10: Precision Genomics Workshop (in conjunction with Dr. Bob Stupar, Univ. of Minnesota, and Dr. Steve Whitham, Iowa State Univ.,) Participants will learn about viral induced gene silencing and engineered nuclease technology (Zn finger, TALENS) and how both methods can be used in soybean for the investigation of gene function. A tutorial on the gene knockout-related parts of SoyBase will be presented. Contact Gary Stacey
for more information.
Seed for cultivars whose PVP registration has expired is now available at the National Center for Genetic Resources Preservation (NCGRP) in Ft. Collins, CO. This spreadsheet
contains a list of private varieties with expired PVP certificates. If you are interested in requesting any of these varieties (50 seeds/sample), please send your requests to Esther Peregrine
Learn about engineered nuclease technology
and how it can be used in soybean:
Site-directed structural variation (deletions, inversions, etc.)
Contact Bob Stupar
for more information.
The 1st Soybean Mutant Finder Field Day
will be held in July 17-18, 2012 at the University of Minnesota. Participants will view fast neutron-derived mutant plants growing in the field and can request seed of those that may be of research interest. A tutorial on the gene knockout-related parts of SoyBase will be presented. Contact Carroll Vance
or Bob Stupar
for more information.
Progress made by the soybean community on the 2012-2016 Soybean Genomics Research Strategic Plan is being compiled by George Graef, Katy Rainey and Rich Wilson. Please see the Strategic Plan website
for details on how to contribute to the report.
The number of QTL on the genetic maps has dramatically increased as the SoyBase staff continues to incorporate QTL experiments from the literature. This has resulted in displays that are increasingly crowded and potentially difficult to use. To address this we have split the QTL into 4 classes (seed composition & yield, disease & stress, plant architecture, and other traits) with each of these classes presented as a separate column in the CMap genetic map displays. We hope that this will enhance the usefulness of the genetic maps. As always, comments on these changes are encouraged.
In March 2011 a group of scientists met to develop a research plan to address the emerging problem of a complex of pod-attacking stink bugs. A Strategic Research Plan
The Gene Ontology (GO) terms associated with the Wm82 gene calls are being updated. The gene calls associated with enzymes involved in metabolism have been revised, and we expect the remainder to be finished soon.
A unified downloads page
has been developed where various collections of genetic and sequence data can be retrieved. Please let us know if there are other data types or subsets that you would like added.
A Minimum Tiling Path (MTP) for the Wm82 BAC-based physical map has been developed by Jungmin Ha and Scott Jackson (Purdue University). A track for this MTP is available in the SoyBase genome sequence browser
We have reworked and expanded the search capabilities for SoyBase. The new search page (SoyBase -> Search menubar entry or here
) allows the submission of terms in one or more categories. The search results page shows the number and types of data in SoyBase that relate to the search terms, with links from this page to the complete search results. The examples shown on the search page can be used for testing by clicking on the term.
PDF files of the presentations made at the 2011 Soybean Breeders Workshop (2/21-23/2011 in St. Louis, MO) have been added to SoyBase
. PDF files of the 2010 presentations are also available, and we expect to continue to post similar files from future Workshops.
A document outlining Soybean Genomics Research: A Strategic Plan for 2012-2016 has been released. Word and PDF versions are available here
A new whole genome display option has been added to the BLAST tool at SoyBase. When chosen, the results of the BLAST are shown for all chromosomes with links to individual zoomed views in the SoyBase sequence viewer.
A collection of photos taken by Rich Wilson at the 13th Biennial Molecular & CellularBiology of the Soybean held in Durham, NC in August 2010 has been posted
Information about the gene models has been updated with improved annotations and enhanced sequence browser views
and text reports
. Additionally it is now possible to download the mRNA, CDS or predicted protein sequences for a gene model and all of its splice isoforms from the text page returned by clicking on a gene model name in the SoyBase Genome Browser.
The Soybean Genetics Newsletter has ceased publication. An archive of the site has been set up at SoyBase and is accessible from the Soybean Genetics Newsletter link on the Resources
We have added a selection of preconfigured views to the SoyBase Genome Browser
.Choosing one of the Example Views in the Search section at the top of the page will turn on a set of related tracks in the viewer. These examples show some of the kinds of data available in the genome viewer and can be used as a starting point forconstructing a customized set of tracks.
Explore soybean metabolic pathways using the SoyCyc
metabolic pathway interface.This interface allows users to explore soybean metabolic pathways that have beenelectronically annotated with the Glyma 1.01 gene calls from JGI.
BARCSOYSSR 1.0, a collection of 33,065 potential SSRs identified by Qijian Songand Perry Cregan from the Wm82 genomic sequence has been released. These SSRs arenow available as a track in the SoyBase Genome Browser
. The whole dataset is availablefor download
Soybean data at PLEXdb. PLEXdb
is now home to 13 more soybean data series imported from NCBI-GEO. There are now 16 publicly visible experiments associated with the Soybean Affymetrix chip.
SoyBase Soybean ontologies
are available from the SoyBase site under "Soybean Ontologies" in the SoyBase sub-nav bar. These ontologies cover soybean growth and development. Input from the community is actively encouraged.
The SoyBase and Soybean physical map websites have undergone a user interface upgrade. Please tell us your impressions. You can contact us HERE
The Glyma1.0 chromosome-based assembly and annotation of soybean is now available, replacing the preliminary contig-based assembly and annotation.
The SoyBase RSS feed is now available. See here