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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 #424594
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: Unlocking genomic diversity through comparative and pan-genome analysis for crop research communities

Author
item KUMARI, SUNITA - COLD SPRING HARBOR LABORATORY
item BRAYNEN, JANEEN - 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 TELLO-RUIZ, MARCELA - COLD SPRING HARBOR LABORATORY
item WEI, SHARON - COLD SPRING HARBOR LABORATORY
item VAN BUREN, PETER - COLD SPRING HARBOR LABORATORY
item WARE, DOREEN
item GLADMAN, NICHOLAS

Submitted to: Advances in Genome Biology and Technology
Publication Type: Abstract Only
Publication Acceptance Date: 3/31/2025
Publication Date: 3/31/2025
Citation: Kumari, S., Braynen, J., Chougule, K., Kumar, V., Lu, Z., Olson, A., Tello-Ruiz, M., Wei, S., Van Buren, P., Ware, D., Gladman, N.P. 2025. Unlocking genomic diversity through comparative and pan-genome analysis for crop research communities. Advances in Genome Biology and Technology. Advances in Genomie Biology and Technology Agriculutral meeting.

Interpretive Summary:

Technical Abstract: Advancing crop research and improvement depends on equipping agricultural scientists and plant breeders with the tools and data needed to develop resilient, high-yielding crop varieties. Integrated genomic datasets and functional annotations from diverse plant genomes, analyzed through comparative genomics, enable researchers to uncover genetic insights. To support these efforts, the Gramene Plants database (https://www.gramene.org) provides access to biological information from over 150 plant genomes, including major crops and model species, empowering breeders to leverage genomic discoveries across the plant kingdom. Gramene further strengthens the research community by fostering collaboration, ensuring robust gene annotations and functional curation, and adhering to FAIR principles through computational innovations and community-driven data stewardship. Recent expansions to Gramene include pan-genome resources for maize(maize-pangenome.gramene.org/), rice (oryza.gramene.org/), sorghum(sorghumbase.org/), and grapevine (vitis.gramene.org/). These crop-focused platforms enable researchers to explore core and accessory genomes; uncovering structural variants, presence-absence variations (PAVs), and genome-specific features critical for breeding programs and evolutionary studies. Integrating Reference SNP cluster IDs (rsIDs), unique identifiers for genetic variation, into the pan-genome sites allows us to link traits to rsIDs mapped to multiple genomes. Gramene also offers advanced tools for analyzing gene structure, expression, homology, and pathways within the Ensembl genome browser. Collaborations with platforms such as the EMBL-EBI Expression Atlas, Bio-Analytic Resources (BAR), and the CLIMTools suite further expand Gramene’s capabilities for agricultural research. The addition of eFP Browsers from BAR enables visualization of gene expression in crops like maize, Arabidopsis, soybean, and sorghum, while the CLIMTools suite supports genotype-environment (GxE) association studies. By integrating over 400 climate descriptors from satellite data, CLIMTools facilitates genome-wide association analyses, providing actionable insights for breeding programs. These advancements underscore Gramene’s commitment to agricultural innovation and solidify its role as a cornerstone for agricultural genomics and collaborative breakthroughs.