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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 #417530
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: Gramene Plants And Pan Genome Resources for Plant Communities

Author
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item BRAYNEN, JANEEN - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item Ware, Doreen
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item Gladman, Nicholas

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/22/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Gramene database (https://www.gramene.org), established in 2003, is an integrated resource for comparative genome and functional analysis in plants. More recently, Gramene has expanded to offer pan genome sites dedicated to the study of individual crop groups: maize, rice, sorghum, and grapevine. We work to enhance gene annotations through computational and community-driven efforts – to manually validate gene structures and curate gene functions by scientific literature mining, applying standard identifiers, and controlled vocabularies and thus comply with FAIR principles. The database provides agricultural researchers and plant breeders with valuable biological information on genomes and plant pathways of numerous crops and model species for over 150 plant genomes, thus enabling powerful comparisons across species and within clades. It provides a centralized and user-friendly gene search interface with integrated views of gene structure, expression, homology and pathways, in addition to specialized resources. Gramene allows users to interpret and explore gene annotations, comparative analyses and genomic variation data in the Ensembl genome browser, newly curated rice pathways and orthologous pathway projections to other species in the Plant Reactome, and plant gene expression data from EMBL-EBI Expression Atlas and Bio-Analytic Resources (BAR). Recently Gramene has added eFP Browsers from BAR for visualizing gene expression data from maize, Arabidopsis, soybean and working with the BAR team, generating eFP Browser Maps for Sorghum. Users can also leverage the power of Gramene's resources for exploring genotype by environment (GxE) associations in rice and Arabidopsis using the CLIMTools suite. An array of over 400 climate descriptors were obtained from satellite data for each variety’s geolocation for genome wide association analyses. The resulting datasets, now accessible at gramene.org/climtools, showcase a wealth of valuable information. The Gramene project is supported by USDA ARS (USDA-ARS 8062-21000-041-00D).