December 2021: Wheat Fielder genome browser and BLAST are available

Wheat Fielder genome browser and BLAST service were created at GrainGenes based on Sato et al. 2021.

Wheat Fielder genome browser: https://wheat.pw.usda.gov/jb/?data=/ggds/whe-fielder
Wheat Fielder BLAST service: https://wheat.pw.usda.gov/blast/

October 2021: PepsiCo releases annotated gene set and associated files for OT3098 v2 genome in partnership with GrainGenes

Please see the more detailed Hot Topic description here
PepsiCo is releasing a set of predicted transcripts and translated protein sequences mapped to OT3098 v2 reference. Researchers are able to access the annotation file as a track on the genome browser. Additional files including a GFF, gene nucleotide fasta, ORF translated peptide fasta, and a text file with top BLAST hits are also available via the download site on GrainGenes.

October 2021 : More MASWheat Quality Genes Curated

Genes for 'Quality and Yield' traits with protocols at MASWheat were curated for:

October 2021: Aegilops tauschii Aet v5.0 genome browser and BLAST are available

Aegilops tauschii Aet v5.0 genome browser and BLAST service were created at GrainGenes based on Wang et al., G3, 2021

Aet v5.0 genome browser: https://wheat.pw.usda.gov/jb?data=/ggds/whe-aet5
Aet v5.0 BLAST service: https://wheat.pw.usda.gov/blast/

BLAST database can be found at https://wheat.pw.usda.gov/blast/ under "Wheat D Collections."

September 2021: Black awns gene class curated from Wheat Gene Catalogue

Black awns Gene Class

September 2021: WAPO1, a candidate 'spikelet number per spike' gene.

WAPO1 (Triticum) has been curated with links to the MASWheat page describing the protocol to distinguish alleles.

September 2021: Polyphenol oxidase genes updated with links to MASWheat and the WGC

"Polyphenol oxidase (PPO) activity is a main factor in the darkening of unfermented wheat flour dough. The presence of active PPO leads to the discoloration through the formation of o-quinones (JFB-8-134), causing the formation of dark pigments and ultimately leading to perceived quality loss."

September 2021: Quick Links on GrainGenes' homepage are enriched

We updated the Quick Links on GrainGenes' homepage (https://wheat.pw.usda.gov). We added icons for
1) Job listings
2) How to cite GrainGenes, and
3) Video Tutorials

August 2021: Historical (1960-1969) hard red spring wheat performance nursery reports added

Historical (1960-1969) hard red spring wheat performance nursery reports added to GrainGenes on the Gerplasm page (https://wheat.pw.usda.gov/GG3/germplasm). You can reach these reports by following 1960-2001 link on the page under "Uniform Regional Hard Red Spring Wheat Nursery" heading.

August 2021: Glume color genes curated from the WGC

This group of gene classes describes the accumulated research into the basis of the variation in glume color phenotypes which spans red, black, brown and grey colors.

August 2021: Lipoxygenase genes updated with links to MASWheat and the WGC

"Lipoxygenases constitute a family of enzymes that catalyze the breakdown of lipids, resulting in products that may have undesirable effects. These enzymes can affect pasta color and cause off-flavors." Hessler et al., CRS-42-1695. A deletion in Lpx-B1 on 4B is useful in wheat breeding efforts to improve pasta quality.

August 2021: Grain Protein Content genes and QTL updated with links to MASWheat and the WGC

From MASWheat:

August 2021: MacGene files were added to the Wheat Gene Catalogue collection

MacGene files were added to the Wheat Gene Catalogue collection in GrainGenes at https://wheat.pw.usda.gov/GG3/Wheat_Gene_Catalog_Documents. These are the files that were usually distributed in CDs in wheat conferences.

To reach our WGC page in GrainGenes with links to WGC curation in GrainGenes and to Komugi, please go to https://wheat.pw.usda.gov/GG3/wgc.

August 2021: Wheat hardness (Ha) locus genes curated from the WGC

Grain hardness in wheat is determined by the alleles at the Ha locus on 5D.

Three genes are involved, two purindolines (Pina and Pinb) and a 'grain softness protein' (Gsp-1). Please see the gene record to access the alleles noted below.

July 2021: Starch branching enzyme gene sets curated from the Wheat Gene Catalog

The activity of starch branching enzymes in wheat grain results in the content of amylose, i.e. starch resistant to digestion in the gut.

Two orthologous gene sets were curated, SbeI and SbeII.

June 2021 Glaucousness Gene Class curated from the Wheat Gene Catalogue

Glaucousness is the visual expression of waxiness on the leaves and stem, and is the preferred term. Plants may be either 'waxy, glaucous' (the normal situation), 'waxy, non-glaucous' (e.g., Mentana), or 'low-wax, non-glaucous' (e.g., AUS 2598). The expression of glaucousness depends on the arrangement of wax deposits rather than the amount of wax (Johnson et al., 1983).

June 2021: Links to MASWheat updated for all pathology gene protocols

Marker Assisted Selection in Wheat (MASWheat) is a highly-curated site for PCR protocols in wheat research.

All pathology genes in GrainGenes with protocols at MASWheat are now up to date with links to the site. These are listed below. Please note that some pathology genes have several names reflecting their role in disease resistance. These are all listed, with links pointing to the first gene in the group.

June 2021: Links to wheat-expression.com (expVIP) added to GG records for the IWGSC RefSeq 1.0

Links to the Wheat Expression Browser have been available via the gene records in the JBrowse genome browser, and now they are also linked to the 'probe' records in the GrainGenes database.

For example see TraesCS1A01G000100 (tRNA (cytidine(34)-2'-O)-methyltransferase)

June 2021: 4 new Aegilops tauschii Genome Browsers and BLAST

4 new Aegilops tauschii genome browsers and BLAST service were created at GrainGenes based on Zhou et al., Nature Plants, 2021.

June 2021: New G4 tracks available for Barley cv Morex V3, PepsiCo OT3098 v2, and Rye Lo7

The following G-quadruplex (G4) tracks are available at GrainGenes Genome Browsers. These G4 data were created using the methodology that was published in Cagirici et al., G3, 2020 (https://doi.org/10.1534/g3.120.401288) and Cagirici et al., Sci. Rep. 2021 (https://doi.org/10.1038/s41598-021-86838-3).

GrainGenes Updates