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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 1st Soybean Mutant Finder Field Day will be held in late July, 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.
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 was produced.
GO terms updatedDavid GrantThu, 05 May 2011 16:31:59 -0500
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.
SoyBase Newsdgrant2010-10-14 14:34:09
SoyBase Newsdgrant2010-09-28 13:39:57
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.
SoyBase Newsdgrant2010-09-03 14:13:58
SoyBase Newsdgrant2010-08-17 14:24:47
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.
SoyBase Newsdgrant2010-05-25 17:26:14
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.
SoyBase Newsdgrant2010-07-13 10:43:56
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 page.
SoyBase Newsdgrant2010-04-12 13:46:59
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.
SoyBase Newsdgrant2010-03-18 13:59:07
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.
SoyBase Newsdgrant2010-03-01 16:19:34
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.
SoyBase Newsdgrant2009-10-02 10:43:15
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 NewsDavid Grant2008-08-15 12:00:01
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.
SoyBase NewsDavid Grant2008-08-15 12:00:00
The SoyBase and Soybean physical map websites have undergone a user interface upgrade. Please tell us your impressions. You can contact us
HERESoyBase NewsDavid Grant2008-07-30 12:00:00
SoyBase NewsDavid Grant2008-12-08 12:00:00
The Glyma1.0 chromosome-based assembly and annotation of soybean is now available, replacing the preliminary contig-based assembly and annotation.
SoyBase NewsAndrew Denner2009-05-22 13:41:36
The SoyBase RSS feed is now available. See
here for details.
SoyBase NewsDavid Grant2009-05-21 12:39:17
