GrainGenes Updates

October 2018: Spring Wheat Nested Association 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

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

April 2018 : GrainGenes Germplasm and MapData added to WheatIS

The GrainGenes node at WheatIS has added links to 120 Mapping Data records and 14,411 germplasm records for Triticum aestivum and its close relatives.

Mapping data records at GrainGenes are the hubs for mapping projects and contain metadata and links to the maps in the CMap tool.

Records at WheatIS are enriched with text from comments in GrainGenes, including parents of mapping populations, country of origin for germplasm and titles of the original publications; all completely searchable.

March 2018 : A Track for Transcription Factors and Protein Kinases added to the Barley Morex IBSC Genome Browser

High-confidence protein sequences from Beier et al. (https://www.ncbi.nlm.nih.gov/pubmed/28448065) went through the iTAK bioinformatics pipeline to identify transcription factors, transcriptional regulators and protein kinases. The iTAK pipeline annotated 1455 protein kinases, 1882 transcription factors, and 457 transcriptional regulators.

February 2018: The Three-Pistil (Pis1) QTL in Wheat

A map for the QTL containing the three-pistil gene (Pis1) recently published by Yang et al (2017) BMC Genomics 18:567, including 127 predicted protein-coding genes flanked by KASP markers has been added to GrainGenes. The Pis1 gene is expressed in the mutant line CM28TP originating from Chuanmai 28, directing the plant to produce three seeds where normal wheat produces one seed. The causative gene for this mutation has not been identified yet, but the QTL contains 10 loci that are candidate genes for this trait. This lays the groundwork for map-based cloning of the Pis1 Gene.

December 2017: Aegilops umbellulata 2017 Consensus Maps

The high-density consensus map consists of both markers with known genetic map position and SNP markers placed on the linkage maps using minimum recombination frequency values. Two F2 Ae. umbellulata populations were used for linkage map construction. The first consisted of 140 F2 individuals that were derived from a cross made between two accessions of Ae. umbellulata: PI 298905, from Manisa, Turkey, and resistant to wheat stem rust pathogen P. graminis f. sp. tritici race TTTTF (isolate 01MN84A-1-2), and PI 542369, from Usak, Turkey, and susceptible to race TTTTF.

December 2017: GrainGenes QTLs can be searched at WheatIS

Wheat Information System (WheatIS) operating under the Wheat Initiative is a platform that provides a single-access site to wheat data distributed at different databases. GrainGenes created a WheatIS node, and made wheat QTL data searcahble through the WheatIS site at URGI: https://urgi.versailles.inra.fr/wheatis/#result/term=graingenes

Posted on: December 15, 2017

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