Skip to main content
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 #433505
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: Standardized rsID Propagation and Community-Driven SNP Genotyping: An Integrated, FAIR Framework for Crop Pan-Genomics and Molecular Breeding

Author
item WEI, SHARON - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KIM, SUYUN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: CONFERENCE ON THE BIOLOGY OF GENOMES
Publication Type: Abstract Only
Publication Acceptance Date: 5/5/2026
Publication Date: 5/5/2026
Citation: Wei, S., Chougule, K., Kim, S., Olson, A., Lu, Z., Ware, D. 2026. Standardized rsID Propagation and Community-Driven SNP Genotyping: An Integrated, FAIR Framework for Crop Pan-Genomics and Molecular Breeding. CONFERENCE ON THE BIOLOGY OF GENOMES. Conference on the Biology of Genomes.

Interpretive Summary:

Technical Abstract: The establishment of stable and interoperable variant identifiers is critical for advancing crop genomics and accelerating molecular breeding. Inspired by the success of reference SNP cluster IDs (rsIDs) in human genetics, we integrated over 193 million standardized rsIDs from the European Variation Archive (EVA) into Gramene’s crop pan-genome databases, including sorghum, rice, maize, and grape. Because rsIDs are initially assigned only to single reference assemblies, we pioneered a strategy to propagate these identifiers across multiple assemblies and pan-genomes using EVA’s Ensembl Variant Remapping pipeline. Validation in sorghum demonstrated high remapping accuracy (~98% between reference versions and ~87% across pan-genomes), enabling scalable implementation in rice and maize. These stable identifiers are accessible through Gramene’s genome browser as searchable variant tracks and gene-level annotations, supporting cross-assembly comparisons, trait association studies, and translational research. Complementing this informatics framework, we developed and validated a community-driven, mid-density sorghum SNP genotyping array using the PlexSeq™ NGS platform. The array comprises 2,421 SNPs distributed across all ten Sorghum bicolor chromosomes, including trait-associated and quality-control markers prioritized by stakeholders. Genotyping 2,726 diverse accessions achieved high call rates, low missing data, and population structure resolution consistent with whole-genome datasets. Importantly, genomic prediction accuracy for key agronomic traits matched high-density genotyping-by-sequencing platforms. Together, standardized rsID propagation and an accessible, targeted genotyping platform provide a stable, FAIR, and cost-effective infrastructure to support germplasm management, genomic prediction, and breeding applications in sorghum and other crops.