Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse

Area of Science:

• Agricultural genomics
• Bioinformatics
• Data science

Background:

• Agricultural research faces data sharing challenges, hindering collaboration and data reuse.
• Findable, Accessible, Interoperable, and Reusable (FAIR) principles are underutilized in agricultural genomics compared to biomedical research.

Purpose of the Study:

• To address the lag in FAIR data practices within agricultural genomics.
• To promote the adoption of standards for managing agricultural genetic variation data.

Main Methods:

• Surveyed current standards for agricultural genetic variation data management.
• Recommended the adoption of reference SNP identifiers (rsIDs).
• Presented case studies from crop research communities with diverse data maturity.

Main Results:

• Introduced approximately 220 million rsIDs to Gramene and pangenome databases.
• Developed methods to project rsIDs from reference to pangenome varieties in sorghum and maize.
• Created an agricultural FAIR guide for rsID adoption.

Conclusions:

• Adopting rsIDs is a crucial step towards FAIR agricultural genetic variation data.
• Enhanced coordination among data stakeholders is vital for interoperability and accelerating genetic variant discovery.
• Improved data practices will accelerate crop trait improvement.