Flapjack, a software tool from SCRI for “graphical genotyping and haplotype visualization”, is now available at their download page. Gramene’s genetic diversity modules offers SNP data in Flapjack format.

Two recent papers have cited Gramene. In 2009, Yamamoto et al. acknowledged Gramene’s QTL resources in a paper in DNA Research entitled “Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?”, and in 2010, a paper published in BMC Plant Biology entitled “Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress” noted Gramene’s usefulness to understanding rice transcription factors.

Today Gramene announces an interim release (Build 30a) with the following updates:

Data

• Updated variation database for Arabidopsis thaliana with indels from Mott (Wellcome Trust Centre for HumanGenetics) and Kover (University of Bath); and updated Affymetrix data from Nordborg (see this page for information)
• Updated variation database for Vitis vinifera to include read coverage data
• Updated BioMart
• Software migrated to Ensembl 56

Software updates

Ensembl Release 56 re-introduces the following multi-species views:

• Alignments (image), formerly alignsliceview, shows pairwise or multiple alignments from the Ensembl Compara database, highlighting any gaps in the alignment. The display can only show one pairwise alignment at a time. EXAMPLE
• Multi-species view, formerly known as multicontigview, displays pairwise alignments without gaps; multiple pairwise alignments can be configured to create a multiple alignment display. EXAMPLE

Fine mapping and characterization of the Wheat Ph1 gene, a suppressor of crossing over between homologous chromosomes reported by Sidhu et al. PNAS April 15, 2008 vol. 105 no. 15 5815-5820 extensively used Gramene database for analysis and confirming their results. An excellent example of Gramene database usage and its contribution to advancement of plant biology research.

A member of the Gramene team attended The Rice Technical Working Group’s (RTWG) 33rd Meeting in Biloxi, MS February 22-25, 2010 and presented a talk titled “Rice genotype, phenotype, and germplasm data in the Gramene database” at the RTWG Applied Genomics Workshop. The goal of this presentation was to discuss the features and goals of the Gramene Genetic Diversity module for a group of rice breeders and geneticists interested in rice SNP data projected for release in 2010. Genevieve also presented a poster titled, “The Gramene Genetic Diversity module: A resource for genotype-phenotype association analysis in grass species.” The poster provided an overview of the datasets housed in and tools offered by the Gramene Genetic Diversity module.

Several of Gramene’s personnel were present at the 2010 Plant and Animal Genome (PAG) conference in San Diego, CA. We presented posters on metabolic pathway networks for cereal plants, genome visualization tools, and using our genetic diversity data for genotype-phenotype association analysis in grass species as well as flowering time variation across three plant species. We additionally presented an hour-long demonstration of using the Gramene website as a genomics and genetics resource for rice and other grasses. We also had the pleasure to participate in an outreach booth manned by many other plant databases including CottonDB, GDR, GrainGenes, LIS, MaizeGDB, Maizesequence.org, Oryzabase, PlantGDN, SGN, SCRI, Soybase, and SGN. It was a welcome opportunity to interact directly with our users and researchers wishing to add to and use Gramene.

The January 14th edition of Nature contains an article describing the whole-genome shotgun sequencing of the soybean genome. It has been “sequenced and integrated with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly” (Schmutz et al.).

Florida Institute of Technology an independent, technological university located on Florida’s east coast invites applications for an assistant or associate professor position beginning in Fall 2010. Candidates must have expertise in plant biology and biochemistry, a Ph.D. degree, and relevant postdoctoral experience. Successful candidates are expected to participate in undergraduate and graduate (M.S./Ph.D.) teaching, and will be expected to establish an active, externally-funded research program. We also seek a colleague who will support our growing M.S. Biotechnology program. Review of applications will commence immediately. Women and minorities are strongly encouraged to apply. Interested candidates should submit a cover letter, detailed C.V., statements of research interests and teaching philosophy, and contact information for three references to:

Prof. Alan C. Leonard
Dept. of Biological Sciences
Florida Institute of Technology
150 W. University Blvd.
Melbourne, FL 32901-6975

Florida Institute of Technology is an Equal Opportunity/Affirmative Action Employer.

Gramene is hiring a Programmer/Analyst and a Database Biologist at Cornell University! Please see the links for more information or come find us at PAG this week to talk to us.

Gramene will be present at the Plant and Animal Genome (PAG) conference in San Diego, California, from January 9-14. You can find us at one of our posters (P817, P822, P835, P843, P859), at our computer demonstration, and at a outreach consortium booth we will share with several other plant databases.