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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #411383
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: Sorghum eFP browser to view gene expression anatomograms in gramene

Author
item O'MEARA, ABIGAIL - Smith College Botanic Garden
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item PASHA, ASHER - University Of Toronto
item PROVART, NICK - University Of Toronto
item Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/12/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Sorghum bicolor, a drought tolerant crop, has gained popularity in the US in recent years and has been a global food staple for millennia. To investigate the impacts of climate change at the molecular level researchers employ RNA sequencing data to scrutinize changes in gene expression patterns in response to various environmental conditions. It provides critical insights into how organisms acclimate to shifting climates and mitigate ecological consequences. Publicly available gene expression datasets deposited in International Sequence Database Collaboration (NCBI, EBI, DDBJ) are a valuable resource, requiring adherence to FAIR principles for reuse. The eFP-seq browser, developed by the Bio-Analytic Resource for Plant Biology (BAR) at the University of Toronto (http://bar.utoronto.ca), enables researchers to explore gene expression across different plant species. It offers an interactive interface and ensures data integration following FAIR principles. Gramene provides baseline gene expression data for 23 plant genomes that have been curated and processed with EMBL-EBI expression atlas (https://www.ebi.ac.uk/gxa/plant/experiments) and is available via Gramene’s search, Gramene’s genome browser and Gramene’s pathway interface, the Plant Reactome. This talk highlights the leverage of baseline gene expression data and visualization of expression data through eFP browser in Gramene using Sorghum as a use case. The eFP browser using developmental and stress expression studies data of Sorghum provides color-coded expression levels across different plant parts for any gene of interest in Sorghum, thus providing a novel resource to study gene expression and function in Gramene.