Gramene participating at the 14th ISRFG Conference, 26-29 Sept 2016

Representing Gramene, Dr. Sushma Naithani and Dr. Joshua Stein, will be available during the upcoming 14th International Symposium on Rice Functional Genomics in Montpellier, France on September 26-29, 2016. Dr. Naithani will present general updates to the Gramene Database and detailed navigation of the Plant Reactome database, a resource for comparative plant pathway analysis in the Bioinformatics Workshop ISRFG2016 on September 28th (Workshop Organizer: Dr. Francois Sabot).  Dr. Stein will describe his research work on coupled R-gene disease resistance systems in 11 species of the Oryzeae tribe.  We welcome our users to seek help from Dr. Naithani and Dr. Stein during the workshop and throughout the conference.

Below are abstracts for Dr. Stein's and Dr. Naithani's presentations.


Coupled R-gene disease resistance systems in 11 species of the Oryzeae tribe

Joshua C. Stein, Kapeel Chougule, Sharon Wei, Rod Wing, Doreen Ware

Disease pathogens, such as rice blast (Magnaporthe oryzae), severely impact rice production and may pose an increasing threat as climate change alters the geographical range of pests in the future. Breeding for natural host resistance is a proven strategy for protecting crop yield but is limited by sources of variation.  Wild relatives of rice collected from around the world provide an untapped reservoir of resistance (R-gene) haplotypes needed to sustain breeding programs. Taking advantage of an 11-species set of reference genomes, including Asian and African rice progenitors and more distantly related AA, BB, FF and Leersia representatives, we discovered over 4500 NB-ARC-domain R-genes (NLR) in 28 families. Most NLR were positionally clustered, often forming complex arrangements of distantly related genes. Despite this complexity, and evidence of local gene expansion and loss, clear orthologous relationships and evidence of conserved underlying haplotype structures could be drawn, even to the most distantly related (~17 MY) species of Leersia.  Adjacent heterogenous pairs, with head-to-head arrangement, showed disproportionate prevalence, conservation, and association with unusual domains, suggesting function as coupled R-gene pairs. Striking variation in domain structure suggests that swapping of various unusual domains contributes to the evolution of haplotype diversity and resistance specificity, and adds new support for the integrated decoy hypothesis. This study has opened a treasure trove of potentially novel R-gene resistance functions, whose evolutionary relationships traceable to today’s economically important R-gene systems may help in the development and sustainability of disease resistant crops in the future. We gratefully acknowledge funding from NSF awards #1026200 and #1127112.


Plant Reactome: A resource for comparative plant pathway analysis  

The Gramene Plant Reactome database portal ( hosts metabolic, genetic, developmental and signaling pathways for several model and crop plant species. The Reactome data model organizes gene products, small molecules, macromolecules and their interactions into reactions and pathways using the structural framework of a plant cell. Plant Reactome features Oryza sativa (rice) as a reference species and currently consists of  222 curated pathways (release 50). To develop the rice Reactome, we imported the RiceCyc metabolic network and added new curated metabolic, signaling, developmental and genetic pathways. In addition, Plant Reactome contains orthology-based pathway projections for 62 plant species. Plant Reactome links to numerous external reference resources, including the gene pages of Gramene, Phytozome, SoyBase, Legume Information System, PeanutBase, Uniprot, ChEBI, PubMed and GO. Plant Reactome allows users to i) search and browse various components of the database; ii) compare projected pathways with the reference pathways to identify potential gaps in projection or biological differences; iii) visualize curated baseline and differential gene expression data in the context of pathways fetched remotely from EMBL-EBI’s Expression Atlas; and iv) upload and analyze genome-scale expression datasets to identify differentially expressed pathways and genes. Users can download our data in various formats from our web site and via APIs. The presentation will discuss development of the Plant Reactome portal, curation of reference rice pathways, phylogeny-based analyses of projected pathway annotations and tools for Omics data analysis and pathway comparisons. The project is supported by the Gramene database award (NSF IOS-1127112) and the Human Reactome award (NIH: P41 HG003751, ENFIN LSHG-CT-2005-518254, Ontario Research Fund, and EBI Industry Programme).