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RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response.

Arjun Krishnan1, Chirag Gupta2, Madana M R Ambavaram1

  • 1Virginia Bioinformatics Institute, Virginia Tech, BlacksburgVA, United States.

Frontiers in Plant Science
|October 6, 2017
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Summary

RECoN is a new web resource that uses a network-based approach to interpret gene expression changes in rice plants responding to environmental stresses. It helps identify functional gene modules and regulatory mechanisms, aiding in engineering crop stress tolerance.

Keywords:
abiotic stresscoexpression networkdatabasedroughtricewebserver

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Area of Science:

  • Plant Biology
  • Genomics
  • Bioinformatics

Background:

  • Transcriptional profiling captures crop plant responses to environmental stresses like drought.
  • Interpreting genome-wide gene expression changes is challenging due to incomplete knowledge of rice gene pathways.
  • Existing annotations limit the functional interpretation of new transcriptome datasets.

Purpose of the Study:

  • To present RECoN, a novel web resource for functional and regulatory analysis of rice transcriptome data.
  • To overcome limitations in current genomic knowledge for interpreting gene expression.
  • To enable large-scale functional exploration of abiotic stress responses in rice.

Main Methods:

  • Developed RECoN, a web resource utilizing a network-based approach.
  • Enumerated 1,744 abiotic stress-specific gene modules comprising 28,421 rice genes.
  • Applied RECoN to analyze drought transcriptomes across three rice developmental stages.

Main Results:

  • RECoN identifies significantly perturbed gene modules in new transcriptome datasets.
  • The resource suggests deregulated functional and regulatory mechanisms based on module enrichment.
  • Analysis of drought transcriptomes revealed insights into common and stage-specific stress responses.

Conclusions:

  • RECoN facilitates functional exploration of abiotic stress data in rice on a genome scale.
  • The resource aids in uncovering gene candidates for enhancing crop stress tolerance.
  • RECoN supports the identification of both characterized and uncharacterized genes involved in stress response.