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Assistant Soybean Germplasm Curator, Dr. Esther Peregrine, is retiring after many years with the USDA-ARS Soybean Collection. We thank Esther for her service and wish her the best in retirement. Dr. Adam Mahan (Adam.Mahan@usda.gov), is the new USDA-ARS Soybean Germplasm Curator.
Anyone interested in pooling requests for the soybean Illumina 3K SNP chip for volume pricing should contact Qijian Song at Qijian.Song@usda.gov
The presentations from the 2021 Virtual Soybean Breeder's Workshop are now available. They can be accessed from the 2021 Soybean Breeder's Workshop
Registration page.
The
Genome Context Viewer (GCV) is a web-app that visualizes genomic data using functional annotations to assist in the genome comparison. The GCV is a micro-synteny and macro-synteny viewer that enables comparative analysis of genomic data.
The 2021 Soybean Breeder's Workshop Feb. 22-24 will be virtual this year. Poster presentations will also be virtual. Registration will only be $10. For more information on the meeting contact
Bo Zhang. For registration information see our
2021 Soybean Breeder's Registration page.
The Expression Explorer tool is available to explore the expression of soybean genes in a wide variety of tissues. The tool is designed to facilitate the identification of candidate genes for GWAS and biparental QTL's. A
video tutorial on its use is available in the Video Tutorial section of SoyBase.
The GCViT tool allows users to see SNPs from large scale diversity experiments in the context of the 20 soybean chromosomes. The tool also allows users to compare the distribution of SNPs between cultivars in a number of display options. A video
tutorial is available demonstrating its use.
Due to the continuing spread of COVID-19 around the country, the organizers have reluctantly decided to postpone this year’s (2020) scheduled Soybean Breeders Tour in NC, until 2021. If you have any questions or concerns, please email ben.fallen@usda.gov.
SOY2020 CancelledRTNMon, 13 April 2020 18:28:37 -0500
The biennial Conference on Molecular and Cellular Biology of Soybean has been cancelled. The meeting has been tentatively rescheduled for 2022. For more information contact Blake Meyers(BMeyers@danforthcenter.org) or Ivan Baxter (IBaxter@danforthcenter.org)
GSE33155 "Transcript profiling reveals expression differences in wild-type and glabrous soybean lines" is now viewable on the SoyBase Genome Viewer. This experiment profiles gene expression in wild-type and glabrous Clark isolines. The experiment can be viewed
HERE under the label "Normal and glabrous Clark isolines"
The Soybean Crop Germplasm Committee is currently seeking nominees to serve on the Committee. There are currently two positions open for three year terms. The positions being filled are a Soybean Pathologist or Nematologist, Entomologist or Pathologist. The function of the Soybean Crop Germplasm Committee is to serve soybean commodity groups and provide expert advice to individuals or organizations such as the Agricultural Research Service (ARS), State Agricultural Experiment Stations (SAES), and others on technical matters relating to plant germplasm, its collection, preservation, and effective utilization. Members involvement includes participation in an annual meeting which meets during the Soybean Breeders Workshop in St. Louis. Sub-committees may be formed to address needs during the year. Please send nominations to Thomas Hoffman at thom.hoffman@corteva.com, indicating the position for which the individual is being nominated.
Gene model expression data is now available in the SoyBase gene model report page. Images of tissue expression is supplied by eFP and
ePlant at the University of Toronto. Tabular data are also available for many GEO datasets.
Due to various reasons, the 2020 Soybean Breeders’ Workshop is rescheduled for Mar 2nd to 4th, 2020 in Sheraton Westport Chalet Hotel St. Louis, MO. The theme of the 2020 Workshop will be “Plant Physiology and Agronomy”. Details will be coming soon. USB Seed composition Workshop will be announced separately. For more details contact: Zenglu Li (zli@uga.edu)
From the Pangenome search page you can compare your sequence or sequences of interest to a number of other De Novo sequenced soybean cultivars (G. max or G. soja). This type of analysis will allow users the ability to see how sequences evolved (were eliminated or were retained) in the various soybean cultivars.
GSE42550 "Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling" is now browsable on the SoyBase Genome Viewer. This experiment profiles gene expression in cotyledons at 7 developmental stages. The experiment can be browsed
HERE under the label of "Expression profiling Williams cotyledon development".
GSE42871 "Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity" is now viewable on the SoyBase Genome Viewer. This experiment profiles gene expression from seed fertilization to maturity. The experiment can be browsed
HERE under the label of "Expression profiling of seed development in Williams". Seed expression was sampled at 7 developmental stages in duplicate.
The parentage information from the 2018 Uniform Soybean Tests: Southern Region have been added to the Soybean Parentage database.
The registration deadline for the 2019 Precision Genomics and Soybean Mutant Finder Day Workshop in Lincoln, Nebraska is July, 4th.
SoyBase Curator Dr. David Grant, PhD. retired April 30, 2019 after 23 years with the USDA-ARS and SoyBase. We thank him for his insightful service guiding the development of the database and wish him the best in retirement. Dr. Rex Nelson PhD. will continue on as SoyBase Curator. Any questions or comments regarding SoyBase tools or activities should be directed to the
SoyBase Curator.
GSE54903 "RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts" is now browsable on the SoyBase Genome Viewer. This experiment profiles gene expression in seed coat of Clark and Harosoy with a defective phenotype. The experiment can be viewed
HERE under the label "Profiling of defective seed coat mutants of Clark and Harsoy".
Data from "Mutations in Argonaute5 illuminate epistatic interaction of the K1 and I loci leading to saddle seed color patterns in Glycine max" is now available in the SoyBase Genome Browser. The experiment can be seen
HERE under the label "Epistatic Interactions of K1 and I in saddle color patterns"
Pedigrees from the 2017 Uniform Soybean Tests: Northern Region strains and their parents have been added to the
Soybean Parentage Database .
High-quality genome assemblies for the soybean cultivar
Lee and the Glycine soja accession
PI 483463 have been released. These should provide useful complements to the primary reference assembly for Glycine max cv. Williams 82 (Wm82.a2).
Over 1250
GWAS QTL 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
Genetic and
Genome viewers.
A soybean pedigree
worksheet 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.
278 QTL from 19 papers have been added to SoyBase. Look for them using the
New tag at
SoyBase QTL ListSoyGEC electionsDGWed, 11 January 2017 13:23:56 -0600
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
SoyGEC page for details.
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.
Candidates are needed for each of the four disciplines represented in the SoyGEC:
- Genetics
- Genomics/Informatics
- Breeding
- Biochemistry/Physiology
An experimental database summarizing the results of the
2012 and 2013 Soybean Uniform Tests: Northern Region 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
Northern Test report publications. 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.
A
soybean parentage database 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.
A project led by Henry Nguyen will sequence 350 diverse soybean lines. Details and the list of lines is available
here.
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.
SoyNAM seed availableDavid GrantFri, 27 March 2015 13:40:18 -0500
Seed of the 41 SoyNAM parents is now available. Please see
here for details. A brief description of the SoyNAM Project is available
here.
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 pages.
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.
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. 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.
The 2017 World Soybean Research Conference, hosted by the University of Georgia, will be held in Savannah, Georgia.
The 2nd Annual Soybean Mutant Finder and Precision Genomics Workshop will be held in July 8-10, 2013 at the University of Missouri.
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
Adam Mahan, USDA-ARS.
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 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 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 NewsDavid Grant2009-05-21 12:39:17
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