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A resource on rice and other grass genomes

Tutorial and training materials by OpenHelix

Learn to use Gramene, a publicly available data resource for comparative genome analysis of grasses with genome browsers for many species, species information pages, various databases, an advanced search and more. Gramene contains genome browsers for Oryza sativa indica and japonica, O. glaberrima, O. rufipogon, Zea mays, Sorghum bicolor, Arabidopsis thaliana, Arabidopsis lyrata, Vitis vinifera and Populus trichocarpa. There are also tools to search for genetic markers, traits and biochemical pathways. Gramene's purpose is to provide added value to the many data sets available from public grass genomics studies and other projects.


You'll learn:

  • to perform effective searches and understand the genome browser displays
  • to access advanced searches enabling multifaceted queries
  • to access and use the various databases of markers, proteins, traits, gene diversity, and biochemical pathways
  • to perform BLAST sequence searches of the genomes

Related tutorials

This tutorial is a part of the tutorial group Gramene-associated resources. You might find the other tutorials in the group interesting:

  • GBrowse: GBrowse User Introductory Tutorial
  • BioMart: Management and querying of many types of biological data


View additional tutorials for resources in

Recent BioMed Central research articles citing this resource

Biselli Chiara et al., Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining Regular submissions. Rice (2014) doi:10.1186/1939-8433-7-1

Chen Jia-Shing et al., Development of a microarray for two rice subspecies: characterization and validation of gene expression in rice tissues. BMC Research Notes (2014) doi:10.1186/1756-0500-7-15

Licciardello Concetta et al., Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck Genetics and crop biotechnology. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-39

Oldach H Klaus et al., Genetic analysis of tolerance to the root lesion nematode Pratylenchus neglectus in the legume Medicago littoralis Genetics and crop biotechnology. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-100

Westengen T Ola et al., Modern maize varieties going local in the semi-arid zone in Tanzania Speciation and evolutionary genetics. BMC Evolutionary Biology (2014) doi:10.1186/1471-2148-14-1

More about the resource:

Gramene is a collection of databases, tools and resources for research on various plant genomes. Some of the species included in this resource are rice, maize, Arabidopsis (a model organism for comparison), wheat, oats and several others. Some of the tools and databases included are a browser, an advanced search tool, and databases for markers, proteins, literature and more. The credit for Gramene goes to the Gramene team at both Cornell University and Cold Spring Harbor. Gramene was initially supported by the USDAs CSREES program and since 2004 is supported by a grant from the National Science Foundation.

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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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