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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 #417521
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: Genetic variation standardization (rsIDs) enhances 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 Ware, Doreen

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/20/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The Reference SNP cluster ID (rsID) is a unique identifier for groups of genetic variations (GVs) co-located at specific positions in the genome. It facilitates standardized referencing across databases, studies, and publications, primarily in human research for mutation identification and data integration. However, its use in plant research has been limited due to inadequate support. With the maturation of the European Variation Archive (EVA), hundreds of millions of rsIDs have been assigned to plant genomes, including agriculturally significant ones hosted in Gramene (https://www.gramene.org/) and SorghumBase (https://sorghumbase.org/). This development made GV data aggregation and marker-based breeding more feasible. The plant-centered genomic database and browser Gramene has embraced this by ingesting rsIDs from EVA release 5, linking them to QTL, phenotype, and germplasm data. Currently, four crop genomes have integrated rsIDs: Sorghum (41M), Rice (27M), Maize (47M), and Grape (0.3M). For SorghumBase, we also imported GWAS study results from the Sorghum Association Panel population and associated the phenotypes/traits with rsIDs. 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 approach 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 or closely related species. This method's successful implementation holds significant potential for breeding initiatives. Gramene's efforts are supported by funding from USDA ARS (8062-21000-041-00D).