News This is our newsfeed Copyright 2018, en-us USDA-ARS Thu, 22 February 2018 22:39:11 -0600 David Grant SoyBase News /soynews/newsview.php#SoyBase+News Try the new SoyBase whole genome <a href=>sequence browser</a> 2009-05-21 12:39:17 Andrew Denner SoyBase News /soynews/newsview.php#SoyBase+News The SoyBase RSS feed is now available. See <a href="">here </a> for details. 2009-05-22 13:41:36 David Grant SoyBase News /soynews/newsview.php#SoyBase+News The Glyma1.0 chromosome-based assembly and annotation of soybean is now available, replacing the preliminary contig-based assembly and annotation. 2008-12-08 12:00:00 David Grant SoyBase News /soynews/newsview.php#SoyBase+News A table is now available to <a href="">convert the soybean linkage group names to chromosome numbers</a>. The table was compiled by Perry Cregan's group at the USDA-ARS Soybean Genomics and Improvement Laboratory. 2008-07-30 12:00:00 David Grant SoyBase News /soynews/newsview.php#SoyBase+News The SoyBase and Soybean physical map websites have undergone a user interface upgrade. Please tell us your impressions. You can contact us <a href="" title="SoyBase contact link">HERE</a> 2008-08-15 12:00:00 David Grant SoyBase News /soynews/newsview.php#SoyBase+News SoyBase Soybean <a href="" title="SoyBase soybean ontologies">ontologies</a> 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. 2008-08-15 12:00:01 dgrant SoyBase News /soynews/newsview.php#SoyBase+News Soybean data at PLEXdb. <a href="">PLEXdb</a> 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. 2009-10-02 10:43:15 dgrant SoyBase News /soynews/newsview.php#SoyBase+News 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 <a href="">SoyBase Genome Browser</a>. The whole dataset is availablefor <a href="">download</a>. 2010-03-01 16:19:34 dgrant SoyBase News /soynews/newsview.php#SoyBase+News Explore soybean metabolic pathways using the <a href="">SoyCyc</a> 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. 2010-03-18 13:59:07 dgrant SoyBase News /soynews/newsview.php#SoyBase+News We have added a selection of preconfigured views to the <a href="">SoyBase Genome Browser</a>.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. 2010-04-12 13:46:59 dgrant SoyBase News /soynews/newsview.php#SoyBase+News 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 <a href="">Resources</a> page. 2010-07-13 10:43:56 dgrant SoyBase News /soynews/newsview.php#SoyBase+News Information about the gene models has been updated with improved annotations and <a href=";stop=50160000;ref=Gm01;cache=on;drag_and_drop=on;show_tooltips=on;grid=on;label=centromere:overview-pericentromere:overview-Glyma1">enhanced sequence browser views</a> and <a href=" ">text reports</a>. 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. 2010-05-25 17:26:14 dgrant SoyBase News /soynews/newsview.php#SoyBase+News 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 <a href=""> posted</a>. 2010-08-17 14:24:47 dgrant SoyBase News /soynews/newsview.php#SoyBase+News A Progress Report has been completed by Rich Wilson and DavidGrant based onresponses to a survey sent out in early 2010. A PDFversion of the report, <a href="">SoyGenStratPlan2008-2012-Accomplishments v1.6</a>, isavailable. 2010-09-03 14:13:58 dgrant SoyBase News /soynews/newsview.php#SoyBase+News 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. 2010-09-28 13:39:57 dgrant SoyBase News /soynews/newsview.php#SoyBase+News The first in a <a href="">series of tutorials on SoyBase and soybean genetics and genomics</a> has been posted. This video will walk you through the needed supplies and proper methods in soybean cross-pollination. 2010-10-14 14:34:09 David Grant Soybean Genomics Research: A Strategic Plan for 2012-2016 /soynews/newsview.php#Soybean+Genomics+Research%3A+A+Strategic+Plan+for+2012-2016 A document outlining Soybean Genomics Research: A Strategic Plan for 2012-2016 has been released. Word and PDF versions are available <a href="">here</a>. Mon, 01 November 2010 David Grant Soybean Breeders Workshop presentations posted /soynews/newsview.php#Soybean+Breeders+Workshop+presentations+posted PDF files of the presentations made at the 2011 Soybean Breeders Workshop (2/21-23/2011 in St. Louis, MO) have been added to <a href="">SoyBase</a>. PDF files of the 2010 presentations are also available, and we expect to continue to post similar files from future Workshops. Mon, 28 February 2011 16:03:20 -0600 David Grant Improved searching at SoyBase /soynews/newsview.php#Improved+searching+at+SoyBase We have reworked and expanded the search capabilities for SoyBase. The new search page (SoyBase -> Search menubar entry or <a href="">here</a>) 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. Thu, 05 May 2011 16:25:25 -0500 David Grant MTP for Wm82 physical map /soynews/newsview.php#MTP+for+Wm82+physical+map 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 <a href="">SoyBase genome sequence browser</a>. Thu, 05 May 2011 16:29:40 -0500 David Grant Improved data downloading from SoyBase /soynews/newsview.php#Improved+data+downloading+from+SoyBase A <a href="">unified downloads page</a> 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. Thu, 05 May 2011 16:30:31 -0500 David Grant GO terms updated /soynews/newsview.php#GO+terms+updated 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. Thu, 05 May 2011 16:31:59 -0500 David Grant A Strategy for Prioritizing Research Goals and Outreach Plans to Reduce Soybean Production Losses Caused by Stink Bugs and Related Insect Pests /soynews/newsview.php#A+Strategy+for+Prioritizing+Research+Goals+and+Outreach+Plans+to+Reduce+Soybean+Production+Losses+Caused+by+Stink+Bugs+and+Related+Insect+Pests 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 <a href="">Strategic Research Plan</a> was produced. Thu, 12 May 2011 09:59:03 -0500 David Grant SoyBase and other plant databases at the Plant Biology 2011 Outreach Booth /soynews/newsview.php#SoyBase+and+other+plant+databases+at+the+Plant+Biology+2011+Outreach+Booth If you plan to be at <a href="">ASPB</a> (Aug. 6-10), please stop by and see <a href="">SoyBase and other plant databases</a> at the Plant Biology 2011 Outreach Booth. Thu, 04 August 2011 10:14:06 -0500 David Grant Improved Genetic Maps Display /soynews/newsview.php#Improved+Genetic+Maps+Display 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. Mon, 14 November 2011 08:54:57 -0600 David Grant Soybean Genomics Research Strategic Plan Updates /soynews/newsview.php#Soybean+Genomics+Research+Strategic+Plan+Updates 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 <a href="">Strategic Plan website</a> for details on how to contribute to the report. Wed, 01 February 2012 15:27:35 -0600 David Grant Soybean Mutant Finder Field Day /soynews/newsview.php#Soybean+Mutant+Finder+Field+Day The <a href="">1st Soybean Mutant Finder Field Day</a> 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 <a href="">Carroll Vance</a> or <a href="">Bob Stupar</a> for more information. Thu, 22 March 2012 13:32:11 -0500 David Grant Soybean Precision Genomics Workshop /soynews/newsview.php#Soybean+Precision+Genomics+Workshop Learn about <a href="">engineered nuclease technology</a> and how it can be used in soybean:<br>&nbsp;&nbsp;Site-directed mutagenesis<br>&nbsp;&nbsp;Site-directed structural variation (deletions, inversions, etc.)<br>&nbsp;&nbsp;Gene editing<br>Contact <a href="">Bob Stupar</a> for more information. Thu, 22 March 2012 13:42:08 -0500 David Grant Seed available for cultivars with expired PVP's /soynews/newsview.php#Seed+available+for+cultivars+with+expired+PVP%27s 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 <a href=" PVP's at NSSL 051512.xls">spreadsheet</a> 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 <a>Esther Peregrine</a>, USDA-ARS. Fri, 18 May 2012 13:45:00 -0500 David Grant 2nd Annual Soybean Mutant Finder and Precision Genomics Workshop /soynews/newsview.php#2nd+Annual+Soybean+Mutant+Finder+and+Precision+Genomics+Workshop 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 <a>Gary Stacey</a> for more information. Fri, 07 September 2012 13:27:49 -0500 David Grant SoyBase tutorial at the Soybean Breeders Workshop /soynews/newsview.php#SoyBase+tutorial+at+the+Soybean+Breeders+Workshop 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 <a href="">register</a>. Participants are encouraged to bring suggestions for improving SoyBase and/or questions on effectively using the web site. Wed, 12 December 2012 11:02:11 -0600 David Grant 2017 World Soybean Research Conference /soynews/newsview.php#2017+World+Soybean+Research+Conference 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. Mon, 15 April 2013 11:20:40 -0500 David Grant 6th International Food Legumes Research Conference & 7th International Conference on Legume Genetics and Genomics /soynews/newsview.php#6th+International+Food+Legumes+Research+Conference+%26+7th+International+Conference+on+Legume+Genetics+and+Genomics 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.<br><a href="">Conference website</a> Tue, 12 November 2013 14:29:53 -0600 David Grant SoyBase video tutorials now available /soynews/newsview.php#SoyBase+video+tutorials+now+available Video tutorials for various aspects of SoyBase searches and tool functionalities have been developed. The tutorials page can be accessed from the <a href="">Resources</a> tab at SoyBase. Tue, 25 February 2014 09:19:34 -0600 David Grant VERY IMPORTANT NOTICE ABOUT SoySNP50K DATA /soynews/newsview.php#VERY+IMPORTANT+NOTICE+ABOUT+SoySNP50K+DATA 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 (; 515-294-1205) with any questions. An update will be posted once this problem has been resolved. Thu, 10 April 2014 10:04:32 -0500 David Grant SoySNP50K data problem FIXED /soynews/newsview.php#SoySNP50K+data+problem+FIXED 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 (; 515-294-1205) with any questions. Mon, 14 April 2014 09:57:52 -0500 David Grant Wm82.a2.v1 genomic sequence now searchable by BLAST /soynews/newsview.php#Wm82.a2.v1+genomic+sequence+now+searchable+by+BLAST 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. Fri, 27 June 2014 13:25:20 -0500 David Grant Revised QTL nomenclature /soynews/newsview.php#Revised+QTL+nomenclature 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. Mon, 30 June 2014 08:38:51 -0500 David Grant Gene name correspondence lookup tool /soynews/newsview.php#Gene+name+correspondence+lookup+tool 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 <a href="">Genome</a> and <a href="">Analysis Tools</a> pages. Thu, 28 August 2014 13:00:14 -0500 David Grant SoyNAM seed available /soynews/newsview.php#SoyNAM+seed+available Seed of the 41 SoyNAM parents is now available. Please see <a href="">here</a> for details. A brief description of the SoyNAM Project is available <a href=" NAM presentation - 2015 Breeders Workshop (abbrev. vers.).pdf">here</a>. Fri, 27 March 2015 13:40:18 -0500 KHF 6K SNP Infinium Chip update /soynews/newsview.php#6K+SNP+Infinium+Chip+update Illumina has lowered the consortia price of the Soy6K SNP Infinium Chips to $20/sample USD for consortia members and $25/sample USD for non-consortia members. These prices are available immediately from your Illumina regional sale rep. Fri, 17 April 2015 08:44:06 -0500 KHF University of Missouri Soybean Sequencing Effort /soynews/newsview.php#University+of+Missouri+Soybean+Sequencing+Effort A project led by Henry Nguyen will sequence 350 diverse soybean lines. Details and the list of lines is available <a href="">here</a>. 2015-06-29 10:03:00 David Grant Uniform Trial Entries Parentage Database /soynews/newsview.php#Uniform+Trial+Entries+Parentage+Database A <a href="">soybean parentage database</a> is available at SoyBase. It provides parentage information gleaned from the Soybean Uniform Tests for the Northern and Southern states and other published sources. The database lists the parentage of entries in the Uniform Tests as they were supplied by the cooperators and where possible the parentage of each strain was traced back to PI accessions or named strains. Searches are performed by strain names and can be filtered by region. If you have suggestions on extending or making the interface better or have corrections to the parentage information please let us know by clicking on the "Contact Us" links and describing your suggestions or providing corrections to the parentage information. Thu, 17 December 2015 10:15:40 -0600 David Grant Uniform Trial Data now available /soynews/newsview.php#Uniform+Trial+Data+now+available An experimental database summarizing the results of the <a href="">2012 and 2013 Soybean Uniform Tests: Northern Region</a> is available at SoyBase. We are making these data available to the community to solicit suggestions for improvements to the data display and functionality of the database. These tables are the summary data taken from the Uniform Tests for those years. For a full report, including methodology and comments, see the <a href="">Northern Test report publications</a>. The database could be expanded to include earlier years if there is an interest from the community, so please let us know by leaving us comments through the "Contact Us" links. Thu, 17 December 2015 10:16:17 -0600 DG SoyGEC elections /soynews/newsview.php#SoyGEC+elections An election will be held to replace four SoyGEC members whose terms will expire December 31, 2016. Terms of each elected position will be three years and will begin January 1, 2017. Serving SoyGEC members can be re-elected without limit.<br />Candidates are needed for each of the four disciplines represented in the SoyGEC:<ul><li>Genetics</li><li>Genomics/Informatics</li><li>Breeding</li><li>Biochemistry/Physiology</li></ul> 2016-09-27 10:14:37 DG SoyGEC elections /soynews/newsview.php#SoyGEC+elections Four new members have been elected to the SoyGEC. Terms of each elected position will be three years and will begin January 1, 2017. See the <a href="">SoyGEC page</a> for details. Wed, 11 January 2017 13:23:56 -0600 DG NCBI GEO gene expression data at SoyBase /soynews/newsview.php#NCBI+GEO+gene+expression+data+at+SoyBase Gene expression data from the NCBI GEO repository have been added to SoyBase. Samples can be chosen either by <a href="">GEO Experiment</a> or <a href="">tissue/treatment/developmental stage</a> and displayed in the <a href="">SoyBase Genome Browser</a>. Wed, 11 January 2017 13:23:56 -0600 DG New QTL added to SoyBase /soynews/newsview.php#New+QTL+added+to+SoyBase 278 QTL from 19 papers have been added to SoyBase. Look for them using the <a style="color:red">New</a> tag at <a href=""> SoyBase QTL List</a> Mon, 17 July 2017 16:07:04 -0500 DG Searching GRIN phenotype descriptors /soynews/newsview.php#Searching+GRIN+phenotype+descriptors We have released an improved user interface for searching <a href="">GRIN phenotype descriptor</a> data. Fri, 20 July 2017 16:07:04 -0500 DG Template for submitting cultivar pedigree data to SoyBase /soynews/newsview.php#Template+for+submitting+cultivar+pedigree+data+to+SoyBase A soybean pedigree <a href="">worksheet</a> has been added to our data submission page to enable breeders to submit the pedigrees of Soybean Uniform Test entries or newly registered cultivar/lines. Mon, 17 July 2017 16:07:04 -0500 DG GWAS QTL added to SoyBase /soynews/newsview.php#GWAS+QTL+added+to+SoyBase Over 1250 <a href="">GWAS QTL</a> from 16 studies have been added to SoyBase. The same nomenclature rules used for biparental QTL were followed with the exception of a 'g' as part of each GWAS QTL name, i.e. Seed oil 3-g2. These GWAS QTL are shown in both the <a href=";ref_map_set_aid=GmComposite2003&ref_map_aids=GmComposite2003_D1a&comparative_map_left=GmGWAS_D1a">Genetic</a> and <a href=";stop=999999999;ref=Gm04;width=1024;version=100;flip=0;grid=on;l=genome_wide_association_qtl%1Egene_models_wm82_a2_v1">Genome</a> viewers. Thu, 11 January 2018 14:45:51 -0600 DG New Reference Genome Assemblies /soynews/newsview.php#New+Reference+Genome+Assemblies <a href="">High-quality genome assemblies</a> for the soybean cultivar <a href="">Lee</a> and the Glycine soja accession <a href="">PI 483463</a> have been released. These should provide useful complements to the primary reference assembly for Glycine max cv. Williams 82 (Wm82.a2). Wed, 7 February 2018 14:45:51 -0600