GrainGenes Updates

February - April 2019: Durum QTL added to GrainGenes

The Durum cv. Svevo Browser includes a QTL track with ~2100 encoded quantitative trait loci with abundant primary curation (i.e. references, traits, significant markers, and population information). At GrainGenes, these QTL are undergoing a 'secondary curation' after reviewing the primary reference.  The encoded QTL are linked to synonyms that are created to align with original names if possible, or with GrainGenes QTL nomenclature (i.e.

February 2019: Durum Wheat (cv. Svevo) RefSeq Release 1.0 is available at GrainGenes

In collaboration with the International Durum Wheat Genome Sequencing Consortium, GrainGenes is releasing the Durum Wheat (cv. Svevo) RefSeq Rel. 1.0 and its annotations.

The manuscript for the Svevo genome reference is accepted for publication in Nature Genetics. Please cite the manuscript for your publications.

October 2018: Spring Wheat Nested Association (NAM) Maps are in GrainGenes.

The Spring Wheat Nested Association Mapping (NAM) population based on 2100 recombinant inbred lines from 28 families was used to construct 588 chromosome-specific genetic maps. With each population reporting ~50,000 markers, this work contributes ~1,400,000 markers to the GrainGenes collection. Many of these markers were previously entered as probes / sequences for the IWA and IWB marker collection. GrainGenes curators will be working in the coming weeks to connect these markers and fill in the data for new markers.

September 2018: Germplasm from the Global Tetraploid Wheat Collection added to GrainGenes and WheatIS

1872 germplasm records were added or updated in GrainGenes and WheatIS representing the Global Tetraploid Wheat Collection. Collection and/or development data is included and accessions are linked to GRIN when possible.
These accessions include Triticum turgidum ssp. durum, dicoccum, dicoccon, turanicum, polonicum, carthlicum, dicoccoides, aethiopicum, petropavlovskyi, ispahanicum, and karamyschevii.

July 2018: Genome browser at GrainGenes for the IWGSC Chinese Spring Browser is now publicy available

The International Wheat Genome Sequencing Consortium is pleased to announce that all data related to the reference sequence of bread wheat, IWGSC RefSeq v1.0, are available without restriction.

Please find the Hot Topic about the release at GrainGenes: https://wheat.pw.usda.gov/GG3/node/674

The genome browser at GrainGenes for the IWGSC Chinese Spring Browser: https://wheat.pw.usda.gov/GG3/jbrowse_Chinese_Spring

June 2018: Oat 2018 Consensus map added to GrainGenes

An update of the hexaploid Oat consensus map set containing 99,846 markers was added to GrainGenes. Working closely with Nick Tinker and Charlene Wight at Agriculture and Agri-Food Canada (AAFC), a Google doc was created for collaboration and all markers were carefully curated, including 93,560 avgbs (Avena GBS) markers. A review of legacy markers in this project (RFLP, SSR, SNP, genes) initiated a massive locus reconciliation project for GrainGenes that resulted in the update of over 100,000 additional markers.

May 2018: Barley, USDA Core Collection, 2014 Consensus Maps

Maps from Munoz-Amatriain M et al. (2014) The USDA Barley Core Collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS ONE 9:e94688 have been added to GrainGenes. These contain markers from the POPA collections that were not advanced to the BOPA sets as well as the BOPA1 and BOPA2 marker sets. To reconcile the rich history of marker naming for these SNPs, synonyms were created for all markers that link to all other forms of the marker name. Common probe links will enable all map sets utilizing these markers to correspond via CMap.

May 2018: GrainGenes gene pages link directly to MASWheat protocols.

MASWheat is an extensively curated site maintained at UC Davis by Jorge Dubcovsky and Marcelo Soria, assisting small grains researchers in the use marker-assisted selection for a wide range of traits. Its presentation in "natural language" is being translated into the GrainGenes relational schema for genes, markers, traits, references and germplasm.

The list below will grow as more GrainGenes reports are enriched with MASWheat's curated information and direct links to the protocols described there.

Leaf Rust

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