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Plant Reverse Genetics pp 247–275Cite as

Gramene Database: A Hub for Comparative Plant Genomics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 678))

Abstract

The rich collection of known genetic information and the recent completion of rice genome sequencing project provided the cereal plant researchers a useful tool to investigate the roles of genes and genomic organization that contribute to numerous agronomic traits. Gramene (http://www.gramene.org) is a unique database where users are allowed to query and explore the power of genomic colinearity and comparative genomics for genetic and genomic studies on plant genomes. Gramene presents a wholesome perspective by assimilating data from a broad range of publicly available data sources for cereals like rice, sorghum, maize, wild rice, wheat, oats, barley, and other agronomically important crop plants such as poplar and grape, and the model plant Arabidopsis. As part of the process, it preserves the original data, but also reanalyzes for integration into several knowledge domains of maps, markers, genes, proteins, pathways, phenotypes, including Quantitative Trait Loci (QTL) and genetic diversity/natural variation. This allows researchers to use this information resource to decipher the known and predicted interactions between the components of biological systems, and how these interactions regulate plant development. Using examples from rice, this article describes how the database can be helpful to researchers representing an array of knowledge domains ranging from plant biology, plant breeding, molecular biology, genomics, biochemistry, genetics, bioinformatics, and phylogenomics.

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Acknowledgments

This work was initially supported (2001–2004) by the USDA Initiative for Future Agriculture and Food Systems (IFAFS) (grant no. 00-52100-9622) and USDA-Agricultural Research Service specific cooperative agreement (grant no. 58-1907-0-041). For the years 2004–current, this work is supported by National Science Foundation (NSF) awards #0321685 and 0703908. We are thankful to our project team members and numerous collaborators and data contributors for help in curation, sharing the datasets and tools. For a full list of our collaborators, please visit http://www.gramene.org/collaborators.

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Authors and Affiliations

  1. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA

    Pankaj Jaiswal

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  1. Pankaj Jaiswal
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Editors and Affiliations

  1. , Virginia Bioinformatics Institute, Virginia Tech, Washington Street, Blacksburg, 24061, Maryland, USA

    Andy Pereira

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Jaiswal, P. (2011). Gramene Database: A Hub for Comparative Plant Genomics. In: Pereira, A. (eds) Plant Reverse Genetics. Methods in Molecular Biology, vol 678. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-682-5_18

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  • DOI: https://doi.org/10.1007/978-1-60761-682-5_18

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-681-8

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