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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 #424330
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: empowering agricultural research from genomic diversity through pan-genome analysis

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

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 3/6/2025
Publication Date: 3/6/2025
Citation: Lu, Z., Chougule, K., Kumar, V., Kumari, S., Olson, A., Tello-Ruiz, M., Wei, S., Van Buren, P., Gladman, N.P., Ware, D. 2025. Gramene plants: empowering agricultural research from genomic diversity through pan-genome analysis. Maize Genetics Conference Abstracts. Maize Genetics Conference.

Interpretive Summary:

Technical Abstract: Enhancing crop research and improvement hinges on providing agricultural scientists and plant breeders with comprehensive data and advanced tools to develop robust, high-yielding crop varieties. Comparative genomics and integrated datasets from diverse plant genomes enable the discovery of critical genetic insights. The Gramene Plants database (https://www.gramene.org) supports these efforts by offering access to biological data from 150 plant genomes, spanning major crops and model species, and facilitating cross-species genomic applications. Gramene fosters collaboration within the scientific community by promoting data sharing, maintaining high-quality gene annotations, and adhering to FAIR principles through computational innovations and community-driven curation. Recent updates to Gramene include pan-genome resources for key crops such as maize (maize-pangenome.gramene.org/), rice (oryza.gramene.org/), sorghum (sorghumbase.org/), and grapevine (vitis.gramene.org/). These platforms enable researchers to explore core and accessory genomes, investigate structural variants, and identify presence-absence variations (PAVs) and other genome-specific traits essential for breeding and evolutionary studies. The integration of Reference SNP cluster IDs (rsIDs) facilitates linking genetic traits to variants mapped across multiple genomes, enhancing the utility of pan-genome resources. Gramene also offers advanced tools through the Ensembl genome browser, enabling analyses of gene structure, expression, homology, and metabolic pathways. Collaborations with platforms such as EMBL-EBI Expression Atlas, Bio-Analytic Resources (BAR), and the CLIMTools suite further augment its capabilities. For example, BAR’s eFP Browsers visualize gene expression in crops like maize, Arabidopsis, soybean, and sorghum, while the CLIMTools suite supports genotype-environment (GxE) association studies. By incorporating over 400 climate descriptors from satellite data, CLIMTools enables genome-wide association analyses that inform breeding strategies. These innovations reaffirm Gramene’s role as a vital resource for agricultural genomics, driving collaborative breakthroughs and empowering sustainable crop improvement. The project is supported by USDA ARS (USDA-ARS 8062-21000-051-00D). Funding acknowledgement: United States Department of Agriculture (USDA)