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. These results were added as a track to the Barley Morex IBSC Genome Browser at /GG3/jbrowse_Morex_Hv_2017.

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.

January 2018: The Salzberg Chinese Spring assembly is BLASTable at GrainGenes

You can now BLAST your sequences against the Salzberg Chinese Spring assembly at GrainGenes (choose NCBI WGA 3.1, 2017 from the drop-down menu).

The link to the paper at the journal site Zimin et al., 2017.

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: Pc Genes mapped in Oat from Wight, et al.

To launch a collaboration between the USDA and the AAFC, curators added two new oat (Avena sativa) map data sets to GrainGenes.
These include sets from the Pendek 39 x Pendek 48 population Oat-2004-P39xP48 and a Pendek 48 x Pendek 38 population Oat-2004-P48xP38.
Visit the original paper at Springer-Link

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

November 2017: Carotenoid Genes in Wheat from Colasuonno et al.

Fifteen carotenoid biosynthetic and catabolic genes in wheat coupled with 41 quality-related QTL from Colasuonno et al. has been added to GrainGenes and is available here.

November 2017: Barley Genetics Newsletter v46 (2016) is available at GrainGenes

Barley Genetics Newsletter v46 (2016) is available at GrainGenes as a pdf document. Please follow the following links for all the available Barley Genetics Newsletter issues: /ggpages/bgn/. Thanks to Phil Bregitzer and Udda Lundqvist for their hard work and dedication.

August 2017: New genome browsers at GrainGenes

We created a page to reach genome browsers available at GrainGenes. The genomes uploaded to the genome browsers include Morex (barley), Zavitan (wheat), and Lo7 (rye), as well a wheat pangenome.

The GrainGenes genome browsers will help evolve GrainGenes into a repository with a genome-centric focus.

You can reach the page here: /GG3/genome_browser

July 2017: Stripe Rust Genes and QTL

A summary map of known stripe rust genes and QTL from the Maccaferri et al. (2015) genome-wide association study of stripe rust resistance in a diverse collection of hexaploid wheat (Triticum aestivum L.) is now available in the GrainGenes CMap viewer.

June 2017: Wheat Landrace Consensus Map

The Wheat Landrace Consensus Map from the 2017 study by Wingen et al. has been added to GrainGenes. The landrace consensus map was constructed from a NAM panel of crosses between a reference variety, the spring bread wheat cultivar 'Paragon' , and 60 bread wheat landraces or cultivars. Single seed descendants from a landrace accession from the A.E. Watkins collection (Wingen et al.

May 2017: Wild Emmer Wheat (genotype Zavitan) assembly and annotations are available to BLAST at GrainGenes

In collaboration with the International Wild Emmer Wheat Genome Sequencing Consortium, GrainGenes is providing pre-publication BLAST service for the Wild Emmer Genome Assembly (Zavitan WEWSeq v.1.0).

For further information, please go to: /GG3/wildemmer
For our BLAST service, please go to: /GG3/wildemmer_blast

May 2017: Tetraploid Wheat Consensus Map

The consensus map for tetraploid wheat (Triticum turgidum) from the Maccaferri et al. 2015 study has been added to GrainGenes and is available here.

March 2017: Barley 9K iSelect SNP Data

Mapping, marker, and sequence data from the Barley 9K iSelect SNP Chip is now available in GrainGenes. The array is from the Comadran et al. 2012 study. It contains 7,842 SNPs in total, including a combination of 2,832 existing barley OPA (POPA) SNPs and 5,010 new SNPs found through next-generation sequencing. In all, 3,968 of the SNP markers were genetically mapped.

March 2017: Hexaploid Oat Consensus Map

The consensus map for hexaploid oat (Avena sativa L.) from Chaffin et al. 2016 has been added to GrainGenes.

February 2017: Seed Dormancy Data from Chao et al. 2015

QTL and phenotypic data from the Chao et al. 2015 study of pre-harvest sprouting in durum wheat are now available at GrainGenes. Chao et al. developed a population from a cross between Langdon and a deletion line, LDN(521-2B), and used it to identify two QTLs on chromosome 2B that are associated with seed dormancy.

February 2017: A new Tutorials page

GrainGenes is preparing video tutorials to train our users how to best use GrainGenes' data and tools. The tutorial link is in the "Community Services" section on our front page. Here is the direct link to the Tutorials page: /GG3/tutorials.

February 2017: 2016 Uniform Regional Hard Red Spring Wheat Nursery

The 2016 Uniform Regional Hard Red Spring Wheat Nursery data has been added. Please follow the link provided below:

January 2017: MAS Wheat Data Added

Information on markers for disease resistance, agronomic, and processing quality traits from the UC Davis MAS Wheat website (http://maswheat.ucdavis.edu) has been added to the GrainGenes database. This data includes genes, loci, QTLs, markers and PCR probes. Several new genetic maps of these markers are viewable in our CMap map viewer. This data is helpful to wheat researchers and breeders who wish to use marker-assisted selection for these traits.

GrainGenes Updates