News

Gramene will be present at next week's Plant and Animal Genome (PAG) XX meeting in San Diego, CA from January 14-18, 2012. On Tuesday, January 17, we will present a workshop from 3:50 PM-6:00 PM in the California Room. We will also participate in a Plant Genomics Outreach booth (#423) with other members of the plant community to answer your questions about furthering your research with our resources.

Responsibilities: Advances in biochemistry, metabolomics, and metabolic engineering, and the availability of genomic sequences for food crop species are opening new and valuable research opportunities for plant breeding. This molecular breeding position will have responsibility for conducting innovative research exploring genetic/epigenetic/quantitative variation in plants and the association with phenotypic variation in traits relating to human and animal health and nutrition made accessible by the latest technologies.

The developers of Flapjack have released a new version (1.11.12.13). Flapjack is a tool for visualizing genotypic and haplotype data that "can handle the large data volumes generated by high throughput SNP and comparable genotyping technologies." Gramene's diversity data sets are available in Flapjack format. We encourage you to extend your analysis of our data using tools like Flapjack.

The first draft of the pigeonpea (Cajanus cajan) geneome of the variety ‘Asha’ was published last week in two separate but similar reports.

The Gramene team is happy to announce the 34th major release of the site. In our Ensembl genome browser, six genomes have been updated and we have added Glycine max (soybean), Selaginella moellendorffii, Chlamydomonas reinhardtii bringing us to 22 genomes.

We are pleased to announce the release of the BrachyCyc database. Developed by the Gramene database project, BrachyCyc is a catalog of predicted metabolic pathways from Brachypodium distachyon. Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene on the version 1.2 of the gene models and release 1.0 of the Brachypodium distachyon inbred line Bd21 genome. The database was created using the Pathway Tools PathoLogic module developed by Peter D.

Gramene members contributed to a new paper entitled "QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice in the journal Database. "The QlicRice database is designed to host publicly accessible, abiotic stress responsive quantitative trait loci (QTLs) in rice (Oryza sativa) and their corresponding sequenced gene loci." You can try out the new interface.

Gramene was happy to contribute to a recently published paper entitled "BioMart Central Portal: an open database network for the biological community." Gramene's BioMart installation is a resource for our users to download plant sequences, QTLs, variations, markers, and more.

To facilitate collaborative international research in the area of rice genetics and genomics, funds have been granted from USDA National Institute of Food and Agriculture to support the participation of graduate students, postdoctoral fellows and junior faculty from the USA to attend the 9th International Symposium of Rice Functional Genomics (ISRFG 9) which will be held in Taipei, Taiwan on November 7-9, 2011.

UniProtKB-GOA are pleased to announce the inclusion in their database of electronic GO annotations created by EnsemblPlants/Gramene. The annotations are created by projection of GO annotations from Arabidopsis thaliana or Oryza sativa proteins onto proteins from one or more target species based on gene orthology obtained from Ensembl Compara.