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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 #412073
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: Catalyzing Genomic Discoveries: Leveraging rsIDs for Enhanced Trait-Driven Interoperability and Genomic Function Transfer

Author
item WEI, SHARON - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item CESARD, THIMOTHEE - Embl-Ebi
item Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/22/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Reference SNP cluster ID (rsID) serves as a unique identifier for a group of genetic variations (GVs) co-located at a specific position in the genome, facilitating standardized referencing across databases, studies, and publications. While extensively utilized in human research for mutation identification and data integration, its application in plant research has been limited, in part due to insufficient support. However, the maturation of the European Variation Archive (EVA), dedicated to non-human genetic variation data, has led to the assignment of millions of rsIDs to plant genomes, including agriculturally significant ones hosted in Gramene and SorghumBase.This shift allows GVs to be identified by rsIDs rather than being tied to specific assemblies, streamlining information aggregation and marker-based breeding. Gramene capitalized on this opportunity to adopt rsIDs, consolidate scattered GVs knowledge, enhance phenotype prediction and boost trait-based genetic marker discovery. Consequently, Gramene is integrating rsIDs into its databases, linking them to QTL, phenotype, and germplasm data. Currently, four crop genomes have integrated rsIDs: Sorghum (41M), Rice (32M), Maize (78M) and Grape (0.3M). As the number of sequenced pan-genomes increases, computationally calling GVs on each accession's genome becomes impractical. Instead, mapping rsIDs from the reference genome to pan-genomes proves more feasible and efficient. Gramene tested this idea by implementing the variation mapping pipeline from EVA, allowing accurate mapping across different assemblies of the same genome and genomes of different accessions from the same and closely related species. The successful implementation of this method holds unprecedented potential for breeding initiatives. Gramene's efforts are supported by funding from USDA ARS (8062-21000-041-00D).