News

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.

Cold Spring Harbor, NY – With research in plant biology “at a tipping point,” in the words of a leading investigator, two pathbreaking efforts by scientists interested in making comparisons across and within sequenced plant genomes have been given a significant funding boost and vote of confidence from the National Science Foundation (NSF).

The NSF has announced that it will make a new research award to fund a project called Gramene for a 5-year period. The previous two awards to Gramene by the NSF were in 4-year cycles. In conjunction with the new award NSF will make new funds available to the Gramene project for developing a Plant Reactome, which serves to increase Gramene’s functionality. The Plant Reactome will be modeled based on the Human Reactome project framework developed for the human genome, and funded by the National Institutes of Health (NIH), which will join NSF in supporting this portion of the work.

The B vitamins and the cofactors derived from them are essential for all forms of life. B vitamin synthesis in plants is therefore crucial to plants themselves as well as to humans and animals, which cannot make most B vitamins themselves and so must obtain them from the diet.

A user wrote in asking how "to find the GRMZ corn ids that correspond to microarray ids on the Affymetrix Commerical Maize array." Gramene's BioMart tool is the way to get this information. Start by selecting "Gramene Mart" from our home page. "CHOOSE DATABASE" to be "Plant Genes" and then "CHOOSE DATASET" to be "Zea mays genes." Go to "Filters" and open the "GENE" box.

American Journal of Botany

New search tools give scientists better ways of managing data

The BBSRC funded Wheat Improvement Strategic Programme (WISP, http: //www.wheatisp.org ) aims to identify new and useful genetic variation to support the vital contribution of wheat breeding to food security.  The aim of this course is to offer training in the genetic analysis methodologies employed in WISP at the John Innes Centre.  The participants will gain the skills necessary to apply these methodologies in their own research.

Gramene release 35 includes variation data for Zea mays (maize) and Oryza glaberrima (African rice). The new maize variation data corresponds to the HapMap v2 set and comprises 55 million SNPs and indels identified in a collection of 103 pre-domesticated and domesticated Zea mays varieties, including a representative from the sister genus, Tripsacum dactyloides (Eastern gamagrass).

Putative gene split models are available for 18 plant reference genomes hosted at Gramene. The split gene models are commonly related to an annotation artifact wherein a single gene is annotated as two or more genes due to incomplete evidence, but could also result from legitimate evolutionary processes. The Compara Gene Tree method predicts a special class of within-species paralogs called "contiguous_gene_split". A contiguous_gene_split is called when the two apparently paralogous genes lie on the same strand and in close proximity (<1MB) but have no (or little) overlapping sequence.

Left to right: Donghui Li (TAIR), Laurel Cooper (Plant Ontology), Sylva Donaldson (BAR), Steve Goff (iPlant), Kate Dreher (PMN), Eva Huala (TAIR), Doreen Ware (Gramene), and Ken Youens-Clark (Gramene). Josh Stein (Gramene & iPlant) who contributed this blog, is missing in this group photo.