News

With 870 million people still hungry (FAOSTAT, 2011), the publication of the most comprehensive analysis to date of two of the most elusive cereal genomes – wheat and barley – opens a realm of possibilities for optimizing the supply of these vital crops.

Gramene and MaizeGDB project teams publish work on MaizeCyc, a network of maize metabolic genes and pathways.

Gramene is looking forward to participating at the annual Plant and Animal Genome (PAG) meeting in the Town & Country Hotel of San Diego, CA from January 12-16, 2013.  We invite the community of plant researchers and breeders to learn how to get the most out of our resources by joining our workshop, stopping by the plant bioinformatics outreach booth, attending a talk or one of our posters.

The speed, cost, and accessibility of DNA sequencing has been transformed in recent years by new technologies, opening up exciting opportunities for disease diagnosis, therapeutic intervention, and studying complex trait variations. Chief among these are genome wide association studies, frequently referred as GWAS, where researchers look for SNP genetic polymorphisms that give raise to phenotypic variation or are in linkage disequilibrium with the causative genetic variants.

The Gramene Team is happy to announce its 36th release.

Figure 1: Gramene homepage

I.   Introduction to Gramene’s Ensembl Genome Browsers

Last week, Hurricane Sandy battered the mid-Atlantic region causing coastal flooding, knocking down trees and power lines, and literally leaving more than eight million people in the dark, and in some cases a quite cold scene. The main campus of Cold Spring Harbor Laboratory (CSHL), home of the servers that support the Gramene website and databases, was no exception. As a preventive measure, Gramene was shut down by 11:00 am EST on Monday, October 29, 2012.

Questions about simple sequence repeats (SSRs) make up a significant portion of the questions we get. A user just yesterday asked about finding the markers matching a particular repeat motif. While Gramene doesn't have a specific tool for finding this, it's possible to figure it out a number of ways:

A user wrote in asking about the rice QTL positions we have projected onto the O. sativa japonica genome. Our method uses a QTL's closely linked marker positions mapped via ePCR or through the BLAT alignments of shared or source sequences.

Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and two plant agribusinesses gathered in Corvallis, Oregon, September 13th-15th, 2012 for a Crop Plant Trait Ontology Workshop. The workshop was hosted by the Plant Ontology and the Trait Ontology, and co-organized by TransPlant, European Bioinformatics Institute, GARNet, Generation Challenge Program, Sol Genomics Network, and SoyBase.