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Publication on Rice Metabolic Network called RiceCyc.

Nearly half of the world's population acquires their staple calories from rice. While the Green revolution has witnessed substantial increases in the production, availability and global per capita consumption of rice, FAO estimates 870 million of the world population to be still hungry. To increase production and especially to alleviate effect of climate change on rice production it is imperative that rice breeding moves beyond the Green Revolution and incorporate modern genomics based methods. Such crop improvement requires understanding how a genome sequence or a genotype is translated to a phenotype. Computationally derived and experimentally strengthened reconstruction of metabolic and regulatory networks provides the basis for understanding the manifestation of a phenotype in terms of physiology, development and environmental interactions. The reconstruction of a genome scale metabolic network for rice developed and hosted by the Gramene team was recently reported in the Journal Rice (http://www.thericejournal.com/content/6/1/15/). It describes the RiceCyc version 3.3 featuring 316 pathways and 6,643 peptide-coding genes mapped to 2,103 enzyme-catalyzed and 87 protein-mediated transport reactions, and provide insight to network development and its usage. To illustrate its significance as a platform for synthesizing new knowledge the authors analyzed the regulation of the amino acid tryptophan, the growth hormone auxin and the serotonin biosynthetic pathways under biotic stress in the context of the circadian clock. The co-examination of diurnal and pathogen response activation showed strong evidence of a link between circadian control and activation of core tryptophan pathway and derivative serotonin biosynthesis genes under pathogen treatment, which is a novel finding and demonstrates the significance of RiceCyc as a platform for building novel hypothesis for experimental validation.

The development and analysis of the rice metabolic network was co-authored by researchers from the Oregon State University, Cornell University and the Cold Spring Harbor Laboratory. This work was supported by the National Science Foundation (NSF) awards IOS #0703908 and #1127112.

Publication citation:
Palitha Dharmawardhana, Liya Ren, Vindhya Amarasinghe, Marcela Monaco, Jim Thomason, Dean Ravenscroft, Susan McCouch, Doreen Ware and Pankaj Jaiswal (2013). A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice 2013, 6:15, doi:10.1186/1939-8433-6-15 [View Publication]

RiceCyc Database Access:
http://www.gramene.org/pathway/

Author: Palitha Dharmawardhana, OSU