August 2020: New tracks at the Barley cv Morex v2 genome browser by IPK

The following tracks were provided by Dr. Martin Mascher's groups at IPK and created as tracks in the Barley cv Morex v2 genome browser:

July 2020: Dormancy gene classes curated from Wheat Gene Catalog

The following gene classes have been added to, or updated at GrainGenes based on the information in the Wheat Gene Catalogue (WGC). This includes all genes, along with any associated alleles, references, loci, germplasm sources etc.
GrainGenes maintains an Ongoing List of genes curated from the WGC.
For more information on the Wheat Gene Catalogue, please visit the GrainGenes Wheat Gene Catalogue Main Page

July 2020: Oat germplasm records linked to T3 and GRIN

The Triticeae Toolbox for Oat oat.triticeaetoolbox.org has enabled the POOL Pedigree Viewing Tool for germplasm records.
For example, see Noble at T3/Oat.

July 2020: GrainGenes new BLAST Service Release

GrainGenes is proud to introduce a new BLAST service (beta) for our wheat, barley, oat and rye collections. The new BLAST service harnesses the latest NCBI BLAST+ 2.10.0 with all our databases provided in the new version 5 database format and processing is load-balanced by multithreading. The new interface provides a drag-and-drop interface, multiple database selections with multiple query sequence support.

July 2020: New YouTube Tutorials for GrainGenes Genome Browsers

Two new GrainGenes video tutorials are now available via the 'GrainGenes Official' site on YouTube.

1. Navigating between GrainGenes Database Records and Genome Browsers

2. Saving Information from Genome Browsers in GrainGenes

Please Subscribe to the GrainGenes Official to keep updated on future tutorials.

June 2020: PepsiCo OT3098 Hexaploid Oat Genome Assembly and Annotation Release in collaboration with GrainGenes

Please see the PepsiCo press release at our "Hot Topic" page at https://wheat.pw.usda.gov/GG3/node/922 for the release of OT3098 hexaploid oat genome assembly and annotation by PepsiCo in collaboration with GrainGenes.

The OT3098 hexaploid oat genome is available at https://wheat.pw.usda.gov/jb/?data=/ggds/oat-ot3098-pepsico.

June 2020: Exome-Capture Variants track on the Barley Morex (2017) genome browser

The exome-Capture Variants (Morell et al, 2019) track was added to the Barley Morex (2017) genome browser.

The dataset: Using exome capture resequencing of 21 barley 6-row spring breeding lines, the study identified 3,855 dSNPs among 497,754 total SNPs.

Citation: Morrell, Peter L; Smith, Kevin P; Vonderharr, Emily E; Kono, Thomas John Y; Fay, Justin C; Koenig, Daniel. (2019). Supporting data for The Fate of Deleterious Variants in a Barley Genomic Prediction Population.

May 2020: Avena atlantica and Avena eriantha genome browsers and probe pages

Genome browsers for Avena atlantica and Avena eriantha are available at GrainGenes displaying genomic features mapped on the 7 pseudomolecules.

The browsers can be reached from the GrainGenes genome browser page at https://wheat.pw.usda.gov/GG3/genome_browser.

May 2020: Barley cv. Morex, version MorexV2 by TRITEX Genome Browser and Probe/Locus pages

Barley cv. Morex, version MorexV2 by TRITEX genome browser is available at GrainGenes at https://wheat.pw.usda.gov/jb/?data=%2Fggds%2Fbar-morex2.

The pseudomolecules and track information are taken from Monat et al. 2019.

We also created probe and locus pages with cross-links to and from the genome browser. For example:

April 2020: New Curated Genes for Chlorophyll Abnormalities

30April2020

The following genes have been added to GrainGenes. These were curated from the Catalog of Wheat Symbols for Wheat (WGC) and current literature.

GrainGenes maintains an Ongoing List of updated genes from the WGC.

Visit the new navigation page for .pdfs of the full releases and supplements of the WGC.

April 2020: 2019 Uniform Regional Scab Nursery for Spring Wheat Parents report is available

2019 Uniform Regional Scab Nursery for Spring Wheat Parents report is available at https://wheat.pw.usda.gov/GG3/germplasm in the table "Uniform Regional Hard Red Spring Wheat Nursery."

March 2020: New GrainGenes Content at WheatIS (QTL, genes, physical and genetic maps)

WheatIS is an International Wheat Information System to support the wheat research community.
The main objective is to provide a single-access web base system to access to the available data resources and bioinformatics tools including GrainGenes.

GrainGenes links at WheatIS are formated from existing curated data with a goal of quarterly updates that will be announced here.

GrainGenes data at WheatIS consists of the following.

February 2020: New curated genes for Brittle rachis and Brittle culm

5March2020

The following genes have been added to GrainGenes. All except brc5 were curated from the Catalog of Wheat Symbols for Wheat (WGC).

GrainGenes maintains an Ongoing List of updated genes from the WGC.

Visit the new navigation page for .pdfs of the full releases and supplements of the WGC.

February 2020: TILLING, HAPMAP, and WHEALBI tracks on the IWGSC Chinese Spring v1 genome browser

The following tracks were added to the IWGSC Chinese Spring v1 genome browser .

February 2020: Links to expVIP and KnetMiner from the IWGSC Chinese Spring genome browser

We created links to expVIP (http://www.wheat-expression.com) and KnetMiner (https://knetminer.rothamsted.ac.uk/KnetMiner/) from the IWGSC Chinese Spring genome browser v1 for the v1.0 (expVIP) and v1.1 (expVIP and KnetMiner) annotations.

February 2020: Barley Genetics Newsletter v48 (2018) is released

Barley Genetics Newsletter v48 (2018) is released and available at the Barley Genetics Newsletter site at GrainGenes.

January 2020: KASP markers for yield QTL on GrainGenes

Data including 15 yield-related QTL, 4 maps, 26 KASP probes with primer information, and germplasm were added to GrainGenes for Yang et al. (2019) TAG 133: 857. QTL mapping for grain yield-related traits in bread wheat via SNP-based selective genotyping. All data are available via the mapdata page: Wheat-2019-KASP_YldQTL.

January 2020: IBSC barley Morex RefSeq v1.0 Functional Annotations on GrainGenes

Functional annotations for the High Confidence genes from the IBSC barley Morex RefSeq 1.0 have been loaded onto GrainGenes as probe records providing external links to Pfam, InterPro, and AmiGo.

Please see HORVU1Hr1G051970 for an example.

January 2020: IWGSC RefSeq v1.0 Functional Annotations on GrainGenes

Functional annotations from the High Confidence genes from the IWGSC Chinese Spring RefSeq 1.0 have been loaded onto GrainGenes. Probe records for the collection provide external links to Pfam, InterPro, and AmiGo.

Please see TraesCS1A01G002500 for an example.

December 2019: Google Search was added to search GrainGenes pages

We added Google Search to our "Browse GrainGenes" page: https://wheat.pw.usda.gov/cgi-bin/GG3/browse.cgi.

Our users can now either search the whole website text with Google or use our classic data type-specific search tool that search our back-end database.

GrainGenes Updates