News

Release #31 of Gramene brought new data sets and features in the Genetic Diversity module. Gramene Diversity now features five large-scale SNP genotype data sets generated by recent re-sequncing projects in rice, maize, and Arabidopsis from the OryzaSNP, Panzea, Arabidopsis 2010 and 1001 Genomes projects.

Genome sequencing continues to become less expensive and faster which is great news for researchers; however, manipulating and storing vast amounts of sequence data has become a challenge. Version 4.0 of the Genomic Diversity and Phenotype Data Model (GDPDM) database schema has a solution. Instead of storing individual SNP values, the 4.x version stores long haplotypes as Binary Large OBjects (BLOBs). Each SNP value only requires four bits of memory. Additionally, BLOBs are used to store physical positions and indel lengths. Version 4.1 added another BLOB to store SNP id values.

A while ago, Gramene instantiated a Distributed Annotation System (DAS) for serving some of our rice genome annotations directly from our markers and sequences database. We soon found that the size and design of our database was not optimized for type of real-time queries necessary to serve DAS.

We are pleased to announce the 31st release of the Gramene database which includes updates to our genomes, diversity, maps, pathways, and web services. Our genome browser has been updated to Ensembl version 57 and hosts fourteen genomes with new annotations, Fgenesh gene predictions, gene trees, whole genome alignments, and synteny views. The genetic diversity databases for rice, Arabidopsis, and maize have new data sets; there are helpful links to start external tools such as TASSEL and Flapjack from our website; and our SNP query tool now shows gene loci overlapping SNP positions.

Co-PI Pankaj Jaiswal and Gramene were profiled in the latest edition of Oregon State University's Terra magazine.

Gramene would like our users to be aware of the scholarship program with OpenHelix for under-represented groups in science. For more information, please see the press release.

The International Peach Genome Initiative (IPGA) has released version 1.0 of the peach genome sequence.

Gramene users might be interested in the paper "Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines", by S. Atwell et al., published in Nature, March 24, 2010.

By Doreen Ware

Last week I had the pleasure of attending the 52nd Maize Genetics meeting that took place from March 18-21, 2010, in Riva del Garda, Italy. This is the first time the meeting has taken place in Italy. The science and venue set a very high bar for the future maize genetics meetings.

The iPlant Collaborative (www.iplantcollaborative.org) announces free, 2-day workshops to introduce DNA Subway, iPlant's first educational Discovery Environment. Instruction and workshop materials, lunches and coffee breaks are provided, as well as a stipend of $100 are provided. Further support for travel or other related expenses cannot be provided. DNA Subway was developed to make high-level genome analysis broadly available to students and educators.